WorldWideScience

Sample records for underlying evolutionary history

  1. Evolutionary biology and life histories

    Directory of Open Access Journals (Sweden)

    Brown, C. R.

    2004-06-01

    Full Text Available The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demographic rates, such as survival, fecundity, and age of first breeding, and biologists from both fields have a vested interest in good analytical machinery for the estimation and analysis of these demographic rates. In the EURING conferences, we have been striving since the mid 1980s to promote a quantitative understanding of demographic rates through interdisciplinary collaboration between ecologists and statisticians. From the ecological side, the principal impetus has come from population biology, and in particular from wildlife biology, but the importance of good quantitative insights into demographic processes has long been recognized by a number of evolutionary biologists (e.g., Nichols & Kendall, 1995; Clobert, 1995; Cooch et al., 2002. In organizing this session, we have aimed to create a forum for those committed to gaining the best possible understanding of evolutionary processes through the application of modern quantitative methods for the collection and interpretation of data on marked animal populations. Here we present a short overview of the material presented in the session on evolutionary biology and life histories. In a plenary talk, Brown & Brown (2004 explored how mark–recapture methods have allowed a better understanding of the evolution of group–living and alternative reproductive tactics in colonial cliff swallows (Petrochelidon pyrrhonota. By estimating the number of transient birds passing through colonies of different sizes, they

  2. Evolutionary games under incompetence.

    Science.gov (United States)

    Kleshnina, Maria; Filar, Jerzy A; Ejov, Vladimir; McKerral, Jody C

    2018-02-26

    The adaptation process of a species to a new environment is a significant area of study in biology. As part of natural selection, adaptation is a mutation process which improves survival skills and reproductive functions of species. Here, we investigate this process by combining the idea of incompetence with evolutionary game theory. In the sense of evolution, incompetence and training can be interpreted as a special learning process. With focus on the social side of the problem, we analyze the influence of incompetence on behavior of species. We introduce an incompetence parameter into a learning function in a single-population game and analyze its effect on the outcome of the replicator dynamics. Incompetence can change the outcome of the game and its dynamics, indicating its significance within what are inherently imperfect natural systems.

  3. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

    KAUST Repository

    Jackson, Andrew P.

    2014-05-05

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

  4. The Ancient Evolutionary History of Polyomaviruses.

    Directory of Open Access Journals (Sweden)

    Christopher B Buck

    2016-04-01

    Full Text Available Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

  5. An evolutionary approach to financial history.

    Science.gov (United States)

    Ferguson, N

    2009-01-01

    Financial history is not conventionally thought of in evolutionary terms, but it should be. Traditional ways of thinking about finance, dating back to Hilferding, emphasize the importance of concentration and economies of scale. But these approaches overlook the rich "biodiversity" that characterizes the financial world. They also overlook the role of natural selection. To be sure, natural selection in the financial world is not exactly analogous to the processes first described by Darwin and elaborated on by modern biologists. There is conscious adaptation as well as random mutation. Moreover, there is something resembling "intelligent design" in finance, whereby regulators and legislators act in a quasidivine capacity, putting dinosaurs on life support. The danger is that such interventions in the natural processes of the market may ultimately distort the evolutionary process, by getting in the way of Schumpeter's "creative destruction."

  6. Evolutionary dynamics under interactive diversity

    Science.gov (United States)

    Su, Qi; Li, Aming; Wang, Long

    2017-10-01

    As evidenced by many cases in human societies, individuals often make different behavior decisions in different interactions, and adaptively adjust their behavior in changeable interactive scenarios. However, up to now, how such diverse interactive behavior affects cooperation dynamics has still remained unknown. Here we develop a general framework of interactive diversity, which models individuals’ separated behavior against distinct opponents and their adaptive adjustment in response to opponents’ strategies, to explore the evolution of cooperation. We find that interactive diversity enables individuals to reciprocate every single opponent, and thus sustains large-scale reciprocal interactions. Our work witnesses an impressive boost of cooperation for a notably extensive range of parameters and for all pairwise games. These results are robust against well-mixed and various networked populations, and against degree-normalized and cumulative payoff patterns. From the perspective of network dynamics, distinguished from individuals competing for nodes in most previous work, in this paper, the system evolves in the form of behavior disseminating along edges. We propose a theoretical method based on evolution of edges, which predicts well both the frequency of cooperation and the compact cooperation clusters. Our thorough investigation clarifies the positive role of interactive diversity in resolving social dilemmas and highlights the significance of understanding evolutionary dynamics from the viewpoint of edge dynamics.

  7. Deciphering the evolutionary history of open and closed mitosis.

    Science.gov (United States)

    Sazer, Shelley; Lynch, Michael; Needleman, Daniel

    2014-11-17

    The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Teaching about Adaptation: Why Evolutionary History Matters

    Science.gov (United States)

    Kampourakis, Kostas

    2013-01-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

  9. Predicting loss of evolutionary history: Where are we?

    Science.gov (United States)

    Veron, Simon; Davies, T Jonathan; Cadotte, Marc W; Clergeau, Philippe; Pavoine, Sandrine

    2017-02-01

    The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic

  10. Evolutionary assembly rules for fish life histories

    DEFF Research Database (Denmark)

    Charnov, E.L.; Gislason, Henrik; Pope, J.G.

    2012-01-01

    length along the growth trajectory within the species. We then interpret K in terms of the VBGE in mass , and show that the previous equation is itself equivalent to a -1/3 power function rule between M and the mass at first reproduction (W α); this new -1/3 power function emerges directly from the life...... history that maximizes Darwinian fitness in non-growing populations. We merge this M, W α power function with other power functions to produce general across-species scaling rules for yearly reproductive allocation, reproductive effort and age at first reproduction in fish. We then suggest a new way...

  11. Book Review: Evolutionary Ecology of Birds: Life Histories, Mating ...

    African Journals Online (AJOL)

    Abstract. Book Title: Evolutionary Ecology of Birds: Life Histories, Mating Systems and Extinction. Book Authors: P.M. Bennett & I.P.F. Owens. Oxford University. Press. 2002. Pp. 272. Price £24.95 (paperback). ISBN 0 19 851089 6.

  12. Evolutionary history of the somatostatin and somatostatin receptors

    Indian Academy of Sciences (India)

    Somatostatin and its receptors have a critical role in mammalian growth through their control pattern of secretion of growth hormone, but the evolutionary history of somatostatin and somatostatin receptors are ill defined. We used comparative whole genome analysis of Danio rerio, Carassius auratus, Xenopus tropicalis, ...

  13. The surprising evolutionary history of South American deer.

    Science.gov (United States)

    Duarte, José Maurício Barbanti; González, Susana; Maldonado, Jesus E

    2008-10-01

    To clarify the systematic relationships and evolutionary history of South American deer, we conducted a comprehensive phylogenetic analysis using representative species of all of the genera of Neotropical deer. Our results revealed high levels of molecular and cytogenetic divergence between groups of morphologically similar species of brockets (Mazama), and suggest a polyphyletic origin. At least eight ancestral forms of deer invaded South America during the late Pliocene (2.5-3 MYA), and members of the red brockets had an independent early explosive diversification soon after their ancestor arrived there, giving rise to a number of morphologically cryptic species.

  14. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).

    Science.gov (United States)

    Poliseno, Angelo; Feregrino, Christian; Sartoretto, Stéphane; Aurelle, Didier; Wörheide, Gert; McFadden, Catherine S; Vargas, Sergio

    2017-10-01

    Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Cyclostome embryology and early evolutionary history of vertebrates.

    Science.gov (United States)

    Ota, Kinya G; Kuratani, Shigeru

    2007-09-01

    Modern agnathans include only two groups, the lampreys and the hagfish, that collectively comprise the group Cyclostomata. Although accumulating molecular data support the cyclostomes as a monophyletic group, there remain some unsettled questions regarding the evolutionary relationships of these animals in that they differ greatly in anatomical and developmental patterns and in their life histories. In this review, we summarize recent developmental data on the lamprey and discuss some questions related to vertebrate evolutionary development raised by the limited information available on hagfish embryos. Comparison of the lamprey and gnathostome developmental patterns suggests some plesiomorphic traits of vertebrates that would have already been established in the most recent common ancestor of the vertebrates. Understanding hagfish development will further clarify the, as yet, unrecognized ancestral characters that either the lampreys or hagfishes may have lost. We stress the immediate importance of hagfish embryology in the determination of the most plausible scenario for the early history of vertebrate evolution, by addressing questions about the origins of the neural crest, thyroid, and adenohypophysis as examples.

  16. Evolutionary history of lagomorphs in response to global environmental change.

    Directory of Open Access Journals (Sweden)

    Deyan Ge

    Full Text Available Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C(3 plants, while for the diet of leporids, more than 16% of plant species are identified as C(4 (31% species are from Poaceae. The ability of several leporid species to consume C(4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C(4 plants in the late Miocene, the so-called 'nature's green revolution', induced by global environmental change, is suggested to be one of the major 'ecological opportunities', which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of

  17. Climate constrains the evolutionary history and biodiversity of crocodylians.

    Science.gov (United States)

    Mannion, Philip D; Benson, Roger B J; Carrano, Matthew T; Tennant, Jonathan P; Judd, Jack; Butler, Richard J

    2015-09-24

    The fossil record of crocodylians and their relatives (pseudosuchians) reveals a rich evolutionary history, prompting questions about causes of long-term decline to their present-day low biodiversity. We analyse climatic drivers of subsampled pseudosuchian biodiversity over their 250 million year history, using a comprehensive new data set. Biodiversity and environmental changes correlate strongly, with long-term decline of terrestrial taxa driven by decreasing temperatures in northern temperate regions, and biodiversity decreases at lower latitudes matching patterns of increasing aridification. However, there is no relationship between temperature and biodiversity for marine pseudosuchians, with sea-level change and post-extinction opportunism demonstrated to be more important drivers. A 'modern-type' latitudinal biodiversity gradient might have existed throughout pseudosuchian history, and range expansion towards the poles occurred during warm intervals. Although their fossil record suggests that current global warming might promote long-term increases in crocodylian biodiversity and geographic range, the 'balancing forces' of anthropogenic environmental degradation complicate future predictions.

  18. Revising the recent evolutionary history of equids using ancient DNA.

    Science.gov (United States)

    Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

    2009-12-22

    The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

  19. The antiquity and evolutionary history of social behavior in bees.

    Directory of Open Access Journals (Sweden)

    Sophie Cardinal

    Full Text Available A long-standing controversy in bee social evolution concerns whether highly eusocial behavior has evolved once or twice within the corbiculate Apidae. Corbiculate bees include the highly eusocial honey bees and stingless bees, the primitively eusocial bumble bees, and the predominantly solitary or communal orchid bees. Here we use a model-based approach to reconstruct the evolutionary history of eusociality and date the antiquity of eusocial behavior in apid bees, using a recent molecular phylogeny of the Apidae. We conclude that eusociality evolved once in the common ancestor of the corbiculate Apidae, advanced eusociality evolved independently in the honey and stingless bees, and that eusociality was lost in the orchid bees. Fossil-calibrated divergence time estimates reveal that eusociality first evolved at least 87 Mya (78 to 95 Mya in the corbiculates, much earlier than in other groups of bees with less complex social behavior. These results provide a robust new evolutionary framework for studies of the organization and genetic basis of social behavior in honey bees and their relatives.

  20. The Antiquity and Evolutionary History of Social Behavior in Bees

    Science.gov (United States)

    Cardinal, Sophie; Danforth, Bryan N.

    2011-01-01

    A long-standing controversy in bee social evolution concerns whether highly eusocial behavior has evolved once or twice within the corbiculate Apidae. Corbiculate bees include the highly eusocial honey bees and stingless bees, the primitively eusocial bumble bees, and the predominantly solitary or communal orchid bees. Here we use a model-based approach to reconstruct the evolutionary history of eusociality and date the antiquity of eusocial behavior in apid bees, using a recent molecular phylogeny of the Apidae. We conclude that eusociality evolved once in the common ancestor of the corbiculate Apidae, advanced eusociality evolved independently in the honey and stingless bees, and that eusociality was lost in the orchid bees. Fossil-calibrated divergence time estimates reveal that eusociality first evolved at least 87 Mya (78 to 95 Mya) in the corbiculates, much earlier than in other groups of bees with less complex social behavior. These results provide a robust new evolutionary framework for studies of the organization and genetic basis of social behavior in honey bees and their relatives. PMID:21695157

  1. Evolutionary history of hunter-gatherer marriage practices.

    Directory of Open Access Journals (Sweden)

    Robert S Walker

    Full Text Available BACKGROUND: The universality of marriage in human societies around the world suggests a deep evolutionary history of institutionalized pair-bonding that stems back at least to early modern humans. However, marriage practices vary considerably from culture to culture, ranging from strict prescriptions and arranged marriages in some societies to mostly unregulated courtship in others, presence to absence of brideservice and brideprice, and polyandrous to polygynous unions. The ancestral state of early human marriage is not well known given the lack of conclusive archaeological evidence. METHODOLOGY: Comparative phylogenetic analyses using data from contemporary hunter-gatherers around the world may allow for the reconstruction of ancestral human cultural traits. We attempt to reconstruct ancestral marriage practices using hunter-gatherer phylogenies based on mitochondrial DNA sequences. RESULTS: Arranged marriages are inferred to go back at least to first modern human migrations out of Africa. Reconstructions are equivocal on whether or not earlier human marriages were arranged because several African hunter-gatherers have courtship marriages. Phylogenetic reconstructions suggest that marriages in early ancestral human societies probably had low levels of polygyny (low reproductive skew and reciprocal exchanges between the families of marital partners (i.e., brideservice or brideprice. DISCUSSION: Phylogenetic results suggest a deep history of regulated exchange of mates and resources among lineages that enhanced the complexity of human meta-group social structure with coalitions and alliances spanning across multiple residential communities.

  2. An intertwined evolutionary history of methanogenic archaea and sulfate reduction.

    Directory of Open Access Journals (Sweden)

    Dwi Susanti

    Full Text Available Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420-dependent sulfite reductase (Fsr where N- and C-terminal halves (Fsr-N and Fsr-C are homologs of F(420H(2 dehydrogenase and dissimilatory sulfite reductase (Dsr, respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP, both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest, carrying a coupled siroheme-[Fe(4-S(4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex, with group I features, a Dsr-type peripheral [Fe(4-S(4] cluster and an additional [Fe(4-S(4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4-S(4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420H(2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago biologically produced sulfide deposit.

  3. Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis.

    Directory of Open Access Journals (Sweden)

    Nadia Mhedbi-Hajri

    Full Text Available Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes--geographical and ecological speciation--that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25,000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar.

  4. Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms.

    Directory of Open Access Journals (Sweden)

    Ryan D Groussman

    Full Text Available Ferroproteins arose early in Earth's history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world's oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III permease; iron storage (ferritin; iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6 and defense against reactive oxygen species (superoxide dismutases. Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of

  5. Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms.

    Science.gov (United States)

    Groussman, Ryan D; Parker, Micaela S; Armbrust, E Virginia

    2015-01-01

    Ferroproteins arose early in Earth's history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world's oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III) permease); iron storage (ferritin); iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6) and defense against reactive oxygen species (superoxide dismutases). Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of paralogs. This

  6. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    Science.gov (United States)

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-02-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

  7. Evolutionary history of the ABCB2 genomic region in teleosts

    Science.gov (United States)

    Palti, Y.; Rodriguez, M.F.; Gahr, S.A.; Hansen, J.D.

    2007-01-01

    Gene duplication, silencing and translocation have all been implicated in shaping the unique genomic architecture of the teleost MH regions. Previously, we demonstrated that trout possess five unlinked regions encoding MH genes. One of these regions harbors ABCB2 which in all other vertebrate classes is found in the MHC class II region. In this study, we sequenced a BAC contig for the trout ABCB2 region. Analysis of this region revealed the presence of genes homologous to those located in the human class II (ABCB2, BRD2, ??DAA), extended class II (RGL2, PHF1, SYGP1) and class III (PBX2, Notch-L) regions. The organization and syntenic relationships of this region were then compared to similar regions in humans, Tetraodon and zebrafish to learn more about the evolutionary history of this region. Our analysis indicates that this region was generated during the teleost-specific duplication event while also providing insight about potential MH paralogous regions in teleosts. ?? 2006 Elsevier Ltd. All rights reserved.

  8. The Natural Science Underlying Big History

    Directory of Open Access Journals (Sweden)

    Eric J. Chaisson

    2014-01-01

    Full Text Available Nature’s many varied complex systems—including galaxies, stars, planets, life, and society—are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics is needed to describe cosmic evolution’s major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density—contrasting with information content or entropy production—is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated.

  9. The Natural Science Underlying Big History

    Science.gov (United States)

    Chaisson, Eric J.

    2014-01-01

    Nature's many varied complex systems—including galaxies, stars, planets, life, and society—are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density—contrasting with information content or entropy production—is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated. PMID:25032228

  10. Fixation times in evolutionary games under weak selection

    International Nuclear Information System (INIS)

    Altrock, Philipp M; Traulsen, Arne

    2009-01-01

    In evolutionary game dynamics, reproductive success increases with the performance in an evolutionary game. If strategy A performs better than strategy B, strategy A will spread in the population. Under stochastic dynamics, a single mutant will sooner or later take over the entire population or go extinct. We analyze the mean exit times (or average fixation times) associated with this process. We show analytically that these times depend on the payoff matrix of the game in an amazingly simple way under weak selection, i.e. strong stochasticity: the payoff difference Δπ is a linear function of the number of A individuals i, Δπ=u i+v. The unconditional mean exit time depends only on the constant term v. Given that a single A mutant takes over the population, the corresponding conditional mean exit time depends only on the density dependent term u. We demonstrate this finding for two commonly applied microscopic evolutionary processes.

  11. New insights into the evolutionary history of biological nitrogen fixation

    Directory of Open Access Journals (Sweden)

    Eric eBoyd

    2013-08-01

    Full Text Available Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2 to ammonia (NH3, accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of this fundamental biological process. One key question is whether the limited availability of fixed nitrogen was a factor in life’s origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth’s biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained by deep phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex and life sustaining process.

  12. Life history determines genetic structure and evolutionary potential of host-parasite interactions.

    Science.gov (United States)

    Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

    2008-12-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

  13. The Evolutionary History of Tariff System of China's Railway

    OpenAIRE

    Ou, Guoli

    2004-01-01

    This thesis discusses the history change of the China's railway tariff analyzes different period of development and change of the China's railway tariff and the internal characters of each period. It also analyzes the Internal mechanism of the history change.

  14. Evolutionary stability for matrix games under time constraints.

    Science.gov (United States)

    Garay, József; Csiszár, Villő; Móri, Tamás F

    2017-02-21

    Game theory focuses on payoffs and typically ignores time constraints that play an important role in evolutionary processes where the repetition of games can depend on the strategies, too. We introduce a matrix game under time constraints, where each pairwise interaction has two consequences: both players receive a payoff and they cannot play the next game for a specified time duration. Thus our model is defined by two matrices: a payoff matrix and an average time duration matrix. Maynard Smith's concept of evolutionary stability is extended to this class of games. We illustrate the effect of time constraints by the well-known prisoner's dilemma game, where additional time constraints can ensure the existence of unique evolutionary stable strategies (ESS), both pure and mixed, or the coexistence of two pure ESS. Our general results may be useful in several fields of biology where evolutionary game theory is applied, principally in ecological games, where time constraints play an inevitable role. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

    Science.gov (United States)

    von der Heyden, Sophie

    2017-03-01

    Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning for protection and conservation in marine systems is complex, but usually focuses on maintaining levels of biodiversity and protecting special and unique landscape features while avoiding negative impacts to socio-economic benefits. Conversely, the integration of evolutionary processes that have shaped extant species assemblages is rarely taken into account. However, it is as important to protect processes as it is to protect patterns for maintaining the evolutionary trajectories of populations and species. This review focuses on different approaches for integrating genetic analyses, such as phylogenetic diversity, phylogeography and the delineation of management units, temporal and spatial monitoring of genetic diversity and quantification of adaptive variation for protecting evolutionary resilience, into marine spatial planning, specifically for coral reef fishes. Many of these concepts are not yet readily applied to coral reef fish studies, but this synthesis highlights their potential and the importance of including historical processes into systematic biodiversity planning for conserving not only extant, but also future, biodiversity and its evolutionary potential.

  16. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

  17. Evolutionary history of genus Macrobrachium inferred from mitochondrial markers: a molecular clock approach.

    Science.gov (United States)

    Jose, Deepak; Harikrishnan, Mahadevan

    2018-04-17

    Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers. Previous studies on Macrobrachium relied on the highly variable morphological characters which were insufficient for accurate diagnosis of natural species groups. Present study focuses on the utility of molecular markers (viz. COI and 16S rRNA) for resolving the evolutionary history of genus Macrobrachium using a combination of phylogeny and timescale components. It is for the first time a molecular clock approach had been carried out towards genus Macrobrachium in a broad aspect with the incorporation of congeners inhabiting diverse geographical realms including endemic species M. striatum from South West coast of India. Molecular results obtained revealed the phylogenetic relationships between congeners of genus Macrobrachium at intra/inter-continental level along with the corresponding evolutionary time estimates.

  18. Using single cell sequencing data to model the evolutionary history of a tumor.

    Science.gov (United States)

    Kim, Kyung In; Simon, Richard

    2014-01-24

    The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic content of mixtures of cells. Recently developed single cell sequencing technology can identify variation within a single cell. Characterization of multiple samples from a tumor using single cell sequencing can potentially provide information on the evolutionary history of that tumor. This may facilitate understanding how key mutations accumulate and evolve in lineages to form a heterogeneous tumor. We provide a computational method to infer an evolutionary mutation tree based on single cell sequencing data. Our approach differs from traditional phylogenetic tree approaches in that our mutation tree directly describes temporal order relationships among mutation sites. Our method also accommodates sequencing errors. Furthermore, we provide a method for estimating the proportion of time from the earliest mutation event of the sample to the most recent common ancestor of the sample of cells. Finally, we discuss current limitations on modeling with single cell sequencing data and possible improvements under those limitations. Inferring the temporal ordering of mutational sites using current single cell sequencing data is a challenge. Our proposed method may help elucidate relationships among key mutations and their role in tumor progression.

  19. Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma

    Directory of Open Access Journals (Sweden)

    Whittle Carrie A

    2010-07-01

    Full Text Available Abstract Background The self-fertile filamentous ascomycete Neurospora tetrasperma contains a large (~7 Mbp and young (mat chromosomes. The objective of the present study is to reveal the evolutionary history, including key genomic events, associated with the various regions of the mat chromosomes among ten strains representing all the nine known species (lineages contained within the N. tetrasperma species complex. Results Comparative analysis of sequence divergence among alleles of 24 mat-linked genes (mat A and mat a indicates that a large region of suppressed recombination exists within the mat chromosome for each of nine lineages of N. tetrasperma sensu latu. The recombinationally suppressed region varies in size and gene composition among lineages, and is flanked on both ends by normally recombining regions. Genealogical analyses among lineages reveals that eight gene conversion events have occurred between homologous mat A and mat a-linked alleles of genes located within the region of restricted recombination during the evolutionary history of N. tetrasperma. Conclusions We conclude that the region of suppressed recombination in the mat chromosomes has likely been subjected to independent contraction and/or expansion during the evolutionary history of the N. tetrasperma species complex. Furthermore, we infer that gene conversion events are likely a common phenomenon within this recombinationally suppressed genomic region. We argue that gene conversions might provide an efficient mechanism of adaptive editing of functional genes, including the removal of deleterious mutations, within the young recombinationally suppressed region of the mat chromosomes.

  20. The evolutionary history of testicular externalization and the origin of ...

    Indian Academy of Sciences (India)

    Author Affiliations. Karel Kleisner1 Richard Ivell2 Jaroslav Flegr1. Department of Philosophy and History of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA5005, Australia ...

  1. Timing of the evolutionary history of Corallinaceae (Corallinales, Rhodophyta).

    Science.gov (United States)

    Rösler, Anja; Perfectti, Francisco; Peña, Viviana; Aguirre, Julio; Braga, Juan Carlos

    2017-06-01

    The temporal dimension of the most recent Corallinaceae (order Corallinales) phylogeny was presented here, based on first occurrence time estimates from the fossil record. Calibration of the molecular clock of the genetic marker SSU entailed a separation of Corallinales from Hapalidiales in the Albian (Early Cretaceous ~105 mya). Neither the calibration nor the fossil record resolved the succession of appearance of the first three emerging subfamilies: Mastophoroideae, Corallinoideae, and Neogoniolithoideae. The development of the tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials was an evolutionary novelty emerging at the Cretaceous-Paleogene boundary (~66 mya). This novelty was shared by the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae, which diverged in the early Paleogene. Subclades within the Metagoniolithoideae and Lithophylloideae diversified in the late Oligocene-middle Miocene (~28-12 mya). The most common reef corallinaceans (Hydrolithon, Porolithon, Harveylithon, "Pneophyllum" conicum, and subclades within Lithophylloideae) appeared in this interval in the Indo-Australian Archipelago. © 2017 Phycological Society of America.

  2. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.

    Science.gov (United States)

    Zhaxybayeva, Olga; Doolittle, W Ford; Papke, R Thane; Gogarten, J Peter

    2009-09-02

    Prochlorococcus is a genus of marine cyanobacteria characterized by small cell and genome size, an evolutionary trend toward low GC content, the possession of chlorophyll b, and the absence of phycobilisomes. Whereas many shared derived characters define Prochlorococcus as a clade, many genome-based analyses recover them as paraphyletic, with some low-light adapted Prochlorococcus spp. grouping with marine Synechococcus. Here, we use 18 Prochlorococcus and marine Synechococcus genomes to analyze gene flow within and between these taxa. We introduce embedded quartet scatter plots as a tool to screen for genes whose phylogeny agrees or conflicts with the plurality phylogenetic signal, with accepted taxonomy and naming, with GC content, and with the ecological adaptation to high and low light intensities. We find that most gene families support high-light adapted Prochlorococcus spp. as a monophyletic clade and low-light adapted Prochlorococcus sp. as a paraphyletic group. But we also detect 16 gene families that were transferred between high-light adapted and low-light adapted Prochlorococcus sp. and 495 gene families, including 19 ribosomal proteins, that do not cluster designated Prochlorococcus and Synechococcus strains in the expected manner. To explain the observed data, we propose that frequent gene transfer between marine Synechococcus spp. and low-light adapted Prochlorococcus spp. has created a "highway of gene sharing" (Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA. 102:14332-14337) that tends to erode genus boundaries without erasing the Prochlorococcus-specific ecological adaptations.

  3. Evolutionary history of the angiosperm flora of China

    Science.gov (United States)

    Lu, Li-Min; Mao, Ling-Feng; Yang, Tuo; Ye, Jian-Fei; Liu, Bing; Li, Hong-Lei; Sun, Miao; Miller, Joseph T.; Mathews, Sarah; Hu, Hai-Hua; Niu, Yan-Ting; Peng, Dan-Xiao; Chen, You-Hua; Smith, Stephen A.; Chen, Min; Xiang, Kun-Li; Le, Chi-Toan; Dang, Viet-Cuong; Lu, An-Ming; Soltis, Pamela S.; Soltis, Douglas E.; Li, Jian-Hua; Chen, Zhi-Duan

    2018-02-01

    High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai-Tibetan Plateau and the development of the monsoon—provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04-25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29-18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and

  4. Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses

    Directory of Open Access Journals (Sweden)

    Nawaz-ul-Rehman Muhammad

    2010-04-01

    Full Text Available Abstract Background Viruses of the genus Begomovirus (family Geminiviridae have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component. Results Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component. Conclusions The analysis has highlighted the greater genetic variation of DNA-B components, in

  5. Life history determines genetic structure and evolutionary potential of host–parasite interactions

    OpenAIRE

    Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

    2008-01-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the f...

  6. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history.

    Science.gov (United States)

    Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

    2008-03-05

    Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Based on a long-term (1972-2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependent on recent ecological processes.

  7. Evolutionary history of the porpoise family (Phocoenidae) : A perspective from mitogenomes

    NARCIS (Netherlands)

    Ben Chehida, Yacine; Aguilar, A. A.; Borrell, A.; Ferreira, M.; Taylor, B.L.; Rojas-Bracho, L.; Robertson, K.; Thumloup, Julie; Schumacher, C.; Vikingsson, G.A.; Morin, Phillip A.; Fontaine, Michael Christophe

    2017-01-01

    The six species of porpoises inhabit the cold waters of the globe, displaying a textbook example of anti-tropical distribution in marine mammals. Nevertheless, the evolutionary history of the porpoises still remained poorly understood, but this knowledge is crucial to illuminate the conservation

  8. Host use does not clarify the evolutionary history of African ticks ...

    African Journals Online (AJOL)

    Where host-parasite associations are rigid and unique, the host preference(s) of parasites and the evolutionary relationships between their hosts may offer insights into the parasites' evolu–tionary history. Where such associations are less rigid, however, the assumption that current host preferences are useful in formulating ...

  9. Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

    Science.gov (United States)

    Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

    2016-01-01

    The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary

  10. Ecological and evolutionary consequences of linked life-history stages in the sea.

    Science.gov (United States)

    Marshall, Dustin J; Morgan, Steven G

    2011-09-27

    Naturalists and scientists have been captivated by the diversity of marine larval forms since they were discovered following the advent of the microscope. Because they often bear little resemblance to adults, larvae were identified initially as new life forms, classified into different groups based on the similarity of their body plans and given new names that are still with us today. The radically different body plans and lifestyles of marine larvae and adults have led most investigators historically to study the two phases of complex life cycles in isolation. More recently, important ecological insights have sprung from taking a holistic view of marine life cycles. Meanwhile, the evolutionary (phenotypic and genetic) links among life-history phases remain less appreciated. In this review, our objective is to evaluate the evolutionary links within marine life cycles, and explore their ecological and evolutionary consequences. We provide a brief overview of marine life histories, discuss the phenotypic and genetic links between the two phases of the life cycle and pose challenges to advance our understanding of the evolutionary constraints acting on marine life histories. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

    Science.gov (United States)

    Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

    2013-05-01

    The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

  12. Building evolutionary resilience for conserving biodiversity under climate change.

    Science.gov (United States)

    Sgrò, Carla M; Lowe, Andrew J; Hoffmann, Ary A

    2011-03-01

    Evolution occurs rapidly and is an ongoing process in our environments. Evolutionary principles need to be built into conservation efforts, particularly given the stressful conditions organisms are increasingly likely to experience because of climate change and ongoing habitat fragmentation. The concept of evolutionary resilience is a way of emphasizing evolutionary processes in conservation and landscape planning. From an evolutionary perspective, landscapes need to allow in situ selection and capture high levels of genetic variation essential for responding to the direct and indirect effects of climate change. We summarize ideas that need to be considered in planning for evolutionary resilience and suggest how they might be incorporated into policy and management to ensure that resilience is maintained in the face of environmental degradation.

  13. Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction

    Science.gov (United States)

    Hwang, Wei Song; Weirauch, Christiane

    2012-01-01

    Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11–14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears

  14. Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

    Science.gov (United States)

    MacLeod, Amy; Rodríguez, Ariel; Vences, Miguel; Orozco-terWengel, Pablo; García, Carolina; Trillmich, Fritz; Gentile, Gabriele; Caccone, Adalgisa; Quezada, Galo; Steinfartz, Sebastian

    2015-01-01

    The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island—ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole. PMID:26041359

  15. Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana.

    Science.gov (United States)

    MacLeod, Amy; Rodríguez, Ariel; Vences, Miguel; Orozco-terWengel, Pablo; García, Carolina; Trillmich, Fritz; Gentile, Gabriele; Caccone, Adalgisa; Quezada, Galo; Steinfartz, Sebastian

    2015-06-22

    The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50,000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island--ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  16. Transdisciplinary Perspectives in Bioethics: A Co-evolutionary Introduction from the Big History

    Directory of Open Access Journals (Sweden)

    Javier Collado-Ruano

    2016-10-01

    Full Text Available The main objective of this work is to expand the bioethics notion expressed in the Article 17th of the Universal Declaration on Bioethics and Human Rights, concerning the interconnections between human beings and other life forms. For this purpose, it is combined the transdisciplinary methodology with the theoretical framework of the “Big History” to approach the co-evolutionary phenomena that life is developing on Earth for some 3.8 billion years. As a result, the study introduces us to the unification, integration and inclusion of the history of the universe, the solar system, Earth, and life with the history of human beings. In conclusion, I consider to safeguard the cosmic miracle that represents the emergence of life we must adopt new transdisciplinary perspectives into bioethics to address the ecosystem complexity of co-evolutionary processes of life on Gaia as a whole.

  17. Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait

    Directory of Open Access Journals (Sweden)

    Shirai Leila T

    2012-02-01

    Full Text Available Abstract Background The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eyespot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions The evolutionary history of gene

  18. A rapid loss of stripes: the evolutionary history of the extinct quagga

    OpenAIRE

    Leonard, Jennifer A; Rohland, Nadin; Glaberman, Scott; Fleischer, Robert C; Caccone, Adalgisa; Hofreiter, Michael

    2005-01-01

    Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature 312, 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated...

  19. Using single cell sequencing data to model the evolutionary history of a tumor

    OpenAIRE

    Kim, Kyung In; Simon, Richard

    2014-01-01

    Background The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic content of mixtures of cells. Recently developed single cell sequencing technology can identify variation within a single cell. Characterization of multiple samples from a tumor using single cell sequencing can potentially provide information on the evolutionary history of that tumo...

  20. Bifurcation routes to volatility clustering under evolutionary learning

    NARCIS (Netherlands)

    Gaunersdorfer, A.; Hommes, C.H.; Wagener, F.O.O.

    2008-01-01

    A simple asset pricing model with two types of boundedly rational traders, fundamentalists and chartists, is studied. Fractions of trader types change over time according to evolutionary learning, with chartists conditioning their forecasting rule upon deviations from a benchmark fundamental.

  1. Reconstructing the Evolutionary History of Powdery Mildew Lineages (Blumeria graminis) at Different Evolutionary Time Scales with NGS Data.

    Science.gov (United States)

    Menardo, Fabrizio; Wicker, Thomas; Keller, Beat

    2017-02-01

    Blumeria graminis (Ascomycota) includes fungal pathogens that infect numerous grasses and cereals. Despite its economic impact on agriculture and its scientific importance in plant-pathogen interaction studies, the evolution of different lineages with different host ranges is poorly understood. Moreover, the taxonomy of grass powdery mildew is rather exceptional: there is only one described species (B. graminis) subdivided in different formae speciales (ff.spp.), which are defined by their host range. In this study we applied phylogenomic and population genomic methods to whole genome sequence data of 31 isolates of B. graminis belonging to different ff.spp. and reconstructed the evolutionary relationships between different lineages. The results of the phylogenomic analysis support a pattern of co-evolution between some of the ff.spp. and their host plant. In addition, we identified exceptions to this pattern, namely host jump events and the recent radiation of a clade less than 280,000 years ago. Furthermore, we found a high level of gene tree incongruence localized in the youngest clade. To distinguish between incomplete lineage sorting and lateral gene flow, we applied a coalescent-based method of demographic inference and found evidence of horizontal gene flow between recently diverged lineages. Overall we found that different processes shaped the diversification of B. graminis, co-evolution with the host species, host jump and fast radiation. Our study is an example of how genomic data can resolve complex evolutionary histories of cryptic lineages at different time scales, dealing with incomplete lineage sorting and lateral gene flow. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme.

    Science.gov (United States)

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    -associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme.

  3. Reasoning about Evolutionary History: Post-Secondary Students' Knowledge of Most Recent Common Ancestry and Homoplasy

    Science.gov (United States)

    Morabito, Nancy P.; Catley, Kefyn M.; Novick, Laura R.

    2010-01-01

    Evolution curricula are replete with information about Darwin's theory of evolution as well as microevolutionary mechanisms underlying this process of change. However, other fundamental facets of evolutionary theory, particularly those related to macroevolution are often missing. One crucial idea typically overlooked is that of most recent common…

  4. Cultural and climatic changes shape the evolutionary history of the Uralic languages.

    Science.gov (United States)

    Honkola, T; Vesakoski, O; Korhonen, K; Lehtinen, J; Syrjänen, K; Wahlberg, N

    2013-06-01

    Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both 'biotic' interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both 'biotic' and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  5. Variations in morphological and life-history traits under extreme ...

    Indian Academy of Sciences (India)

    Madhsudhan

    increases in ecologically extreme environments, thus promoting more rapid evolutionary change. An alternative hypothesis (Johnson and Frey 1967; Blum 1988) assumes that heritability decreases under stress, which may lead to deceleration of the evolutionary process. At present, it seems that neither of these hypotheses ...

  6. Evolutionary History of the Enzymes Involved in the Calvin-Benson Cycle in Euglenids.

    Science.gov (United States)

    Markunas, Chelsea M; Triemer, Richard E

    2016-05-01

    Euglenids are an ancient lineage that may have existed as early as 2 billion years ago. A mere 65 years ago, Melvin Calvin and Andrew A. Benson performed experiments on Euglena gracilis and elucidated the series of reactions by which carbon was fixed and reduced during photosynthesis. However, the evolutionary history of this pathway (Calvin-Benson cycle) in euglenids was more complex than Calvin and Benson could have imagined. The chloroplast present today in euglenophytes arose from a secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga. A long period of evolutionary time existed before this secondary endosymbiotic event took place, which allowed for other endosymbiotic events or gene transfers to occur prior to the establishment of the green chloroplast. This research revealed the evolutionary history of the major enzymes of the Calvin-Benson cycle throughout the euglenid lineage and showed that the majority of genes for Calvin-Benson cycle enzymes shared an ancestry with red algae and/or chromophytes suggesting they may have been transferred to the nucleus prior to the acquisition of the green chloroplast. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

  7. Effect of Recombination in the Evolutionary Dynamics of HIV under the Surveillance of Immune System

    Science.gov (United States)

    Peng, Weiqun; Yang, Wenjing; Wang, Guanyu

    2009-03-01

    Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS), which has become one of the most destructive pandemics in history. The fact that HIV virus evolves very fast plays a central role in AIDS immunopathogenesis and the difficulty we face in finding a cure or a vaccine for AIDS. A distinguishing feature of HIV is its high frequency of recombination. The effect of recombination in the HIV evolution is not clear. We establish a mathematical model of the evolutionary dynamics. This model incorporates both point mutation and recombination for genetic diversity, and employs a fitness function developed by Wang and Deem (PRL 97, 188106, 2006) that accounts for the effect of immune system. Using this model, we explore the role of recombination in the battle between the virus population and the immune system, with a special focus on the condition under which recombination helps the virus population to escape from the immune system.

  8. Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions

    Science.gov (United States)

    Olsson, Lennart; Levit, Georgy S.; Hoßfeld, Uwe

    2010-11-01

    Evolutionary theory has been likened to a “universal acid” (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research—evolutionary developmental biology—has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin’s Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the “Jena school” of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about “biometabolic modi” are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research—heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the

  9. Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions.

    Science.gov (United States)

    Olsson, Lennart; Levit, Georgy S; Hossfeld, Uwe

    2010-11-01

    Evolutionary theory has been likened to a "universal acid" (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research--evolutionary developmental biology--has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin's Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the "Jena school" of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about "biometabolic modi" are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research--heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of

  10. The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography

    DEFF Research Database (Denmark)

    Bunce, M; Worthy, T H; Phillips, M J

    2009-01-01

    The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction approximately 600 years ago. The phylogeny and evolutionary history of this morphologically diverse order has remained...... controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all...... of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20-30 Ma. The data reveal that the patterns of genetic diversity within...

  11. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms

    Directory of Open Access Journals (Sweden)

    Achal Rastogi

    2015-07-01

    Full Text Available Recent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.

  12. The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons

    Science.gov (United States)

    Rowe-Magnus, Dean A.; Guerout, Anne-Marie; Ploncard, Pascaline; Dychinco, Broderick; Davies, Julian; Mazel, Didier

    2001-01-01

    Integrons are genetic elements that acquire and exchange exogenous DNA, known as gene cassettes, by a site-specific recombination mechanism. Characterized gene cassettes consist of a target recombination sequence (attC site) usually associated with a single open reading frame coding for an antibiotic resistance determinant. The affiliation of multiresistant integrons (MRIs), which contain various combinations of antibiotic resistance gene cassettes, with transferable elements underlies the rapid evolution of multidrug resistance among diverse Gram-negative bacteria. Yet the origin of MRIs remains unknown. Recently, a chromosomal super-integron (SI) harboring hundreds of cassettes was identified in the Vibrio cholerae genome. Here, we demonstrate that the activity of its associated integrase is identical to that of the MRI integrase, IntI1. We have also identified equivalent integron superstructures in nine distinct genera throughout the γ-proteobacterial radiation. Phylogenetic analysis revealed that the evolutionary history of the system paralleled that of the radiation, indicating that integrons are ancient structures. The attC sites of the 63 antibiotic-resistance gene cassettes identified thus far in MRIs are highly variable. Strikingly, one-fifth of these were virtually identical to the highly related yet species-specific attC sites of the SIs described here. Furthermore, antimicrobial resistance homologues were identified among the thousands of genes entrapped by these SIs. Because the gene cassettes of SIs are substrates for MRIs, these data identify SIs as the source of contemporary MRIs and their cassettes. However, our demonstration of the metabolic functions, beyond antibiotic resistance and virulence, of three distinct SI gene cassettes indicates that integrons function as a general gene-capture system for bacterial innovation. PMID:11209061

  13. Sixty-Five Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders.

    Science.gov (United States)

    Barnes, Richard; Clark, Adam Thomas

    2017-07-01

    For many taxa and systems, species richness peaks at midelevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary midelevation regions. To test this hypothesis, we use records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to midelevation bands by using the model to predict plethodontid evolutionary history and contemporary geographic distributions. Our results show that models that incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.

  14. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

    Science.gov (United States)

    Ornelas, Juan Francisco; Sosa, Victoria; Soltis, Douglas E; Daza, Juan M; González, Clementina; Soltis, Pamela S; Gutiérrez-Rodríguez, Carla; de los Monteros, Alejandro Espinosa; Castoe, Todd A; Bell, Charles; Ruiz-Sanchez, Eduardo

    2013-01-01

    Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage

  15. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

    Directory of Open Access Journals (Sweden)

    Juan Francisco Ornelas

    Full Text Available Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents, and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex

  16. Investigating the evolutionary history of irrigated agricultural technology in the Heihe River Basin, China

    Science.gov (United States)

    Wu, S.; Wei, Y.; Zhao, Y.; Zheng, H.

    2017-12-01

    Human's innovative abilities do not only enable rapid expansion of civilization, but also lead to enormous modifications on the natural environment. Technology, while a key factor embedded in socioeconomic developments, its impacts have been rarely appropriately considered in river basin management. This research aims to examine the evolutionary history of irrigated agricultural technology in the Heihe River Basin, China, and how its characteristics interacted with the river basin environment. It adopts a content analysis approach to collect and summarize quantitative technological information in the Heihe River Basin across a time span of more than 2000 years from the Han Dynasty (206 BC) to 2015. Two Chinese academic research databases: Wan Fang Data and China National Knowledge Infrastructure (CNKI) were chosen as data sources. The results show that irrigated agricultural technologies in Heihe River Basin have shifted from focusing on developing new farming tools and cultivation methods to adapting modernized, water-saving irrigation methods and water diversion infrastructures. In additions, the center of irrigated agricultural technology in the Heihe river basin has moved from downstream to middle stream since the Ming Dynasty (1368AD) as a result of degraded natural environment. The developing trend of technology in the Heihe River Basin thus coincides with the change of societal focus from agricultural production efficiency to the human-water balance and environmental remediation. This research demonstrates that irrigated agricultural technologies had a twisted evolutionary history in the Heihe River Basin, influenced by a diverse range of environmental and socioeconomic factors. It provides insights into the fact that technology exhibits a co-evolutionary characteristic with the social development history in the region, pointing towards the urgent need to maintain the balance between human and environment.

  17. Bichordites from the early Eocene of Cuba: significance in the evolutionary history of the spatangoids

    Science.gov (United States)

    Villegas-Martín, Jorge; Netto, Renata Guimarães

    2017-12-01

    The trace fossil Bichordites monastiriensis is found in early Eocene turbiditic sandstones of the upper-slope deposits from the Capdevila Formation in Los Palacios Basin, Pinar del Río region, western Cuba. The potential tracemakers of B. monastiriensis include fossil spatangoids from the family Eupatagidae. The record of Bichordites in the deposits from Cuba allows to suppose that Eupatagidae echinoids were the oldest potential tracemakers of Bichordites isp. and reinforce the hypothesis that the ichnological record are relevant in envisaging the evolutionary history of the spatangoids.

  18. Variations in morphological and life-history traits under extreme ...

    Indian Academy of Sciences (India)

    Madhsudhan

    The genetic variations for all the quantitative and life-history traits were higher at ... variation in quantitative traits has important evolutionary ..... Mean ± SE and phenotypic variance (s2) of morphometric and life-history traits in D. ananassae reared at different temperatures. 18°C. 25°C. 32°C. Trait. Sex. Mean ± SE s2. Mean ± ...

  19. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands

    OpenAIRE

    Sun, Ye; Vargas-Mendoza, Carlos F.

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genet...

  20. Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates.

    Science.gov (United States)

    Ghersi, Bruno M; Jia, Hongwei; Aiewsakun, Pakorn; Katzourakis, Aris; Mendoza, Patricia; Bausch, Daniel G; Kasper, Matthew R; Montgomery, Joel M; Switzer, William M

    2015-10-29

    Although simian foamy viruses (SFV) are the only exogenous retroviruses to infect New World monkeys (NWMs), little is known about their evolutionary history and epidemiology. Previous reports show distinct SFVs among NWMs but were limited to small numbers of captive or wild monkeys from five (Cebus, Saimiri, Ateles, Alouatta, and Callithrix) of the 15 NWM genera. Other studies also used only PCR testing or serological assays with limited validation and may have missed infection in some species. We developed and validated new serological and PCR assays to determine the prevalence of SFV in blood specimens from a large number of captive NWMs in the US (n = 274) and in captive and wild-caught NWMs (n = 236) in Peruvian zoos, rescue centers, and illegal trade markets. Phylogenetic and co-speciation reconciliation analyses of new SFV polymerase (pol) and host mitochondrial cytochrome B sequences, were performed to infer SFV and host co-evolutionary histories. 124/274 (45.2 %) of NWMs captive in the US and 59/157 (37.5 %) of captive and wild-caught NWMs in Peru were SFV WB-positive representing 11 different genera (Alouatta, Aotus, Ateles, Cacajao, Callithrix, Cebus, Lagothrix, Leontopithecus, Pithecia, Saguinus and Saimiri). Seroprevalences were lower at rescue centers (10/53, 18.9 %) compared to zoos (46/97, 47.4 %) and illegal trade markets (3/7, 8/19, 42.9 %) in Peru. Analyses showed that the trees of NWM hosts and SFVs have remarkably similar topologies at the level of species and sub-populations suggestive of co-speciation. Phylogenetic reconciliation confirmed 12 co-speciation events (p history of SFV in NWMs at the species level. Additional studies are necessary to further explore the epidemiology and natural history of SFV infection of NWMs and to determine the zoonotic potential for persons exposed to infected monkeys in captivity and in the wild.

  1. Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness

    Directory of Open Access Journals (Sweden)

    Mark A. Genung

    2014-03-01

    Full Text Available The relationship between biodiversity and ecosystem function has received a great deal of attention in ecological research and recent results, from re-analyses, suggest that ecosystem function improves with increases in phylogenetic diversity. However, many of these results have been generalized across a range of different species and clades, and plants with different evolutionary histories could display different relationships between biodiversity and ecosystem function. To experimentally test this hypothesis, we manipulated species richness and phylogenetic diversity using 26 species from two subgenera of the genus Eucalyptus (subgenus Eucalyptus and subgenus Symphyomyrtus. We found that plant biomass (a measurement of ecosystem function sometimes, but not always, responded to increases in species richness and phylogenetic diversity. Specifically, Symphyomyrtus plants showed a positive response while no comparable effect was observed for Eucalyptus plants, showing that responses to biodiversity can vary across different phylogenetic groups. Our results show that the impacts of evolutionary history may complicate the relationship between the diversity of plant communities and plant biomass.

  2. Is evolutionary history repeatedly rewritten in light of new fossil discoveries?

    Science.gov (United States)

    Tarver, J E; Donoghue, P C J; Benton, M J

    2011-02-22

    Mass media and popular science journals commonly report that new fossil discoveries have 'rewritten evolutionary history'. Is this merely journalistic hyperbole or is our sampling of systematic diversity so limited that attempts to derive evolutionary history from these datasets are premature? We use two exemplars-catarrhine primates (Old World monkeys and apes) and non-avian dinosaurs-to investigate how the maturity of datasets can be assessed. Both groups have been intensively studied over the past 200 years and so should represent pinnacles in our knowledge of vertebrate systematic diversity. We test the maturity of these datasets by assessing the completeness of their fossil records, their susceptibility to changes in macroevolutionary hypotheses and the balance of their phylogenies through study time. Catarrhines have shown prolonged stability, with discoveries of new species being evenly distributed across the phylogeny, and thus have had little impact on our understanding of their fossil record, diversification and evolution. The reverse is true for dinosaurs, where the addition of new species has been non-random and, consequentially, their fossil record, tree shape and our understanding of their diversification is rapidly changing. The conclusions derived from these analyses are relevant more generally: the maturity of systematic datasets can and should be assessed before they are exploited to derive grand macroevolutionary hypotheses.

  3. Diversification events and the effects of mass extinctions on Crocodyliformes evolutionary history.

    Science.gov (United States)

    Bronzati, Mario; Montefeltro, Felipe C; Langer, Max C

    2015-05-01

    The rich fossil record of Crocodyliformes shows a much greater diversity in the past than today in terms of morphological disparity and occupation of niches. We conducted topology-based analyses seeking diversification shifts along the evolutionary history of the group. Our results support previous studies, indicating an initial radiation of the group following the Triassic/Jurassic mass extinction, here assumed to be related to the diversification of terrestrial protosuchians, marine thalattosuchians and semi-aquatic lineages within Neosuchia. During the Cretaceous, notosuchians embodied a second diversification event in terrestrial habitats and eusuchian lineages started diversifying before the end of the Mesozoic. Our results also support previous arguments for a minor impact of the Cretaceous/Palaeogene mass extinction on the evolutionary history of the group. This argument is not only based on the information from the fossil record, which shows basal groups surviving the mass extinction and the decline of other Mesozoic lineages before the event, but also by the diversification event encompassing only the alligatoroids in the earliest period after the extinction. Our results also indicate that, instead of a continuous process through time, Crocodyliformes diversification was patchy, with events restricted to specific subgroups in particular environments and time intervals.

  4. New clues to the evolutionary history of the main European paternal lineage M269

    DEFF Research Database (Denmark)

    Valverde, Laura; Illescas, Maria José; Villaescusa, Patricia

    2016-01-01

    The dissection of S116 in more than 1500 individuals from Atlantic Europe and the Iberian Peninsula has provided important clues about the controversial evolutionary history of M269. First, the results do not point to an origin of M269 in the Franco-Cantabrian refuge, owing to the lack of subline......The dissection of S116 in more than 1500 individuals from Atlantic Europe and the Iberian Peninsula has provided important clues about the controversial evolutionary history of M269. First, the results do not point to an origin of M269 in the Franco-Cantabrian refuge, owing to the lack...... of sublineage diversity within M269, which supports the new theories proposing its origin in Eastern Europe. Second, S116 shows frequency peaks and spatial distribution that differ from those previously proposed, indicating an origin farther west, and it also shows a high frequency in the Atlantic coastline...... generated at least two episodes of expansion in the Franco-Cantabrian area. This study demonstrates the importance of continuing the dissection of the M269 lineage in different European populations because the discovery and study of new sublineages can adjust or even completely revise the theories about...

  5. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony.

    Science.gov (United States)

    Shi, Tao

    2016-03-01

    Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. However, phylogenomic approaches, such as gene tree parsimony (GTP), show advantage over some other approaches in its ability to use gene families with duplications. GTP searches the 'optimal' species tree by minimizing the total cost of biological events such as duplications, but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of different gene families can impact on species tree inference, 3900 gene families from seven angiosperms encompassing a wide range of gene content, lineage-specific expansions and contractions were analyzed. It was found that the gene content and total duplication number in a gene family strongly influence species tree inference accuracy, with the highest accuracy achieved at either very low or very high gene content (or duplication number) and lowest accuracy centered in intermediate gene content (or duplication number), as the relationship can fit a binomial regression. Besides, for gene families of similar level of average gene content, those with relatively higher lineage-specific expansion or duplication rates tend to show lower accuracy. Additional correlation tests support that high accuracy for those gene families with large gene content may rely on abundant ancestral copies to provide many subtrees to resolve conflicts, whereas high accuracy for single or low copy gene families are just subject to sequence substitution per se. Very low accuracy reached by gene families of intermediate gene content or duplication number can be due to insufficient subtrees to resolve the conflicts from loss of alternative copies. As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by

  6. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

    Directory of Open Access Journals (Sweden)

    Nicole Stoesser

    2016-03-01

    Full Text Available Escherichia coli sequence type 131 (ST131 has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n = 215 of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of a blaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of blaCTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the blaCTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli. These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages.

  7. Molecular phylogeography and evolutionary history of Poropuntius huangchuchieni (Cyprinidae in Southwest China.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Wu

    Full Text Available The evolution of the Yunnan Plateau's drainages network during the Pleistocene was dominated by the intense uplifts of the Qinghai-Tibetan Plateau. In the present study, we investigated the association between the evolutionary histories of three main drainage systems and the geographic patterns of genetic differentiation of Poropuntius huangchuchieni.We sequenced the complete sequences of mitochondrial control region for 304 specimens and the sequences of Cytochrome b gene for 15 specimens of the species P. huangchuchieni and 5 specimens of Poropuntius opisthoptera. Phylogenetic analysis identified five major lineages, of which lineages MK-A and MK-B constrained to the Mekong River System, lineages RL and LX to the Red River System, and lineage SW to the Salween River System. The genetic distance and network analysis detected significant divergences among these lineages. Mismatch distribution analysis implied that the population of P. huangchuchieni underwent demographic stability and the lineage MK-B, sublineages MK-A1 and LX-1 underwent a recent population expansion. The divergence of the 5 major lineages was dated back to 0.73-1.57 MYA.Our results suggest that P. opisthoptera was a paraphyletic group of P. huangchuchieni. The phylogenetic pattern of P. huangchuchieni was mostly associated with the drainage's structures and the geomorphological history of the Southwest Yunnan Plateau. Also the differentiation of the major lineages among the three drainages systems coincides with the Kunlun-Yellow River Movement (1.10-0.60 MYA. The genetic differentiation within river basins and recent demographical expansions that occurred in some lineages and sublineages are consistent with the palaeoclimatic oscillations during the Pleistocene. Additionally, our results also suggest that the populations of P. huangchuchieni had keep long term large effective population sizes and demographic stability in the recent evolutionary history, which may be

  8. Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family

    Directory of Open Access Journals (Sweden)

    Aronson Nathan N

    2007-06-01

    Full Text Available Abstract Background Chitinases (EC.3.2.1.14 hydrolyze the β-1,4-linkages in chitin, an abundant N-acetyl-β-D-glucosamine polysaccharide that is a structural component of protective biological matrices such as insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 (GH18 family of chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Mammals are not known to synthesize chitin or metabolize it as a nutrient, yet the human genome encodes eight GH18 family members. Some GH18 proteins lack an essential catalytic glutamic acid and are likely to act as lectins rather than as enzymes. This study used comparative genomic analysis to address the evolutionary history of the GH18 multiprotein family, from early eukaryotes to mammals, in an effort to understand the forces that shaped the human genome content of chitinase related proteins. Results Gene duplication and loss according to a birth-and-death model of evolution is a feature of the evolutionary history of the GH18 family. The current human family likely originated from ancient genes present at the time of the bilaterian expansion (approx. 550 mya. The family expanded in the chitinous protostomes C. elegans and D. melanogaster, declined in early deuterostomes as chitin synthesis disappeared, and expanded again in late deuterostomes with a significant increase in gene number after the avian/mammalian split. Conclusion This comprehensive genomic study of animal GH18 proteins reveals three major phylogenetic groups in the family: chitobiases, chitinases/chitolectins, and stabilin-1 interacting chitolectins. Only the chitinase/chitolectin group is associated with expansion in late deuterostomes. Finding that the human GH18 gene family is closely linked to the human major histocompatibility complex paralogon on chromosome 1, together with the recent association of GH18 chitinase activity with Th2 cell inflammation, suggests that its late expansion

  9. Assessing variation in life-history tactics within a population using mixture regression models: a practical guide for evolutionary ecologists.

    Science.gov (United States)

    Hamel, Sandra; Yoccoz, Nigel G; Gaillard, Jean-Michel

    2017-05-01

    Mixed models are now well-established methods in ecology and evolution because they allow accounting for and quantifying within- and between-individual variation. However, the required normal distribution of the random effects can often be violated by the presence of clusters among subjects, which leads to multi-modal distributions. In such cases, using what is known as mixture regression models might offer a more appropriate approach. These models are widely used in psychology, sociology, and medicine to describe the diversity of trajectories occurring within a population over time (e.g. psychological development, growth). In ecology and evolution, however, these models are seldom used even though understanding changes in individual trajectories is an active area of research in life-history studies. Our aim is to demonstrate the value of using mixture models to describe variation in individual life-history tactics within a population, and hence to promote the use of these models by ecologists and evolutionary ecologists. We first ran a set of simulations to determine whether and when a mixture model allows teasing apart latent clustering, and to contrast the precision and accuracy of estimates obtained from mixture models versus mixed models under a wide range of ecological contexts. We then used empirical data from long-term studies of large mammals to illustrate the potential of using mixture models for assessing within-population variation in life-history tactics. Mixture models performed well in most cases, except for variables following a Bernoulli distribution and when sample size was small. The four selection criteria we evaluated [Akaike information criterion (AIC), Bayesian information criterion (BIC), and two bootstrap methods] performed similarly well, selecting the right number of clusters in most ecological situations. We then showed that the normality of random effects implicitly assumed by evolutionary ecologists when using mixed models was often

  10. Reconstruction of the evolutionary history of the LexA-binding sequence.

    Science.gov (United States)

    Mazón, Gerard; Erill, Ivan; Campoy, Susana; Cortés, Pilar; Forano, Evelyne; Barbé, Jordi

    2004-11-01

    In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the 'Alphaproteobacteria', 'Deltaproteobacteria' and 'Gammaproteobacteria' classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with the F. succinogenes one, reported here, directed mutagenesis of the F. succinogenes LexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and 'Alphaproteobacteria' LexA-binding sequences, and the other giving rise to the F. succinogenes and Myxococcus xanthus ones, in a transitional step towards the current 'Gammaproteobacteria' LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the 'Alphaproteobacteria' lost its vertically received lexA gene, but received later through lateral gene transfer a new lexA gene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the

  11. A Tale of Two Drug Targets: The Evolutionary History of BACE1 and BACE2

    Directory of Open Access Journals (Sweden)

    Christopher eSouthan

    2013-12-01

    Full Text Available The beta amyloid (APP cleaving enzyme (BACE1 has been a drug target for Alzheimer's Disease (AD since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralogue, BACE2, became a new target for type II diabetes (T2DM having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologues (UrBACEs in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans. UrBACEs are predominantly single copy, show 35% to 45% protein sequence identity with mammalian BACE1, are approximately 100 residues longer than cathepsin paralogues with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogues in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5’ exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.

  12. The evolutionary history of bears is characterized by gene flow across species.

    Science.gov (United States)

    Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A; Janke, Axel

    2017-04-19

    Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

  13. Consensus between genes and stones in the biogeographic and evolutionary history of Central America

    Science.gov (United States)

    Gutiérrez-García, Tania Anaid; Vázquez-Domínguez, Ella

    2013-05-01

    Results from genetic and geologic studies can be combined to elucidate some general patterns of the biogeographic and evolutionary history of Central America (CA) and of its biota. Based on an ample review of geologic, biogeographic and genetic studies, our aim was to examine how common genetic patterns can be linked with geologic processes. Considering information about geologic and tectonic evolution of CA, we subdivided the region into four tectonic blocks: Maya, Chortis, Chorotega and Chocó. Species exchange between North/South America and CA encompasses three events: a first migration during the Late Cretaceous-Early Paleocene, a second through a terrestrial corridor preceding the formation of the Isthmus of Panama (IP), and the third involving a major dispersion through the IP. Such events caused similar genetic differentiation patterns and left a signature on the diversification of extant taxa, which we propose as three evolutionary groups: 1) Mayan, characterized by marked genetic structure and divergence, multiple refugia and formation of cryptic species; 2) Mid-CA, defined by high differentiation at the population level and between highland and lowlands, associated with intense volcanic activity; 3) Panamian, distinguished by migration from north to south and vice versa via de IP, with markedly high species divergence and speciation.

  14. The evolutionary history of bears is characterized by gene flow across species

    Science.gov (United States)

    Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A.; Janke, Axel

    2017-01-01

    Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow. PMID:28422140

  15. Phylogenetic relationships and evolutionary history of the greater horseshoe bat, Rhinolophus ferrumequinum, in Northeast Asia

    Directory of Open Access Journals (Sweden)

    Tong Liu

    2016-10-01

    Full Text Available The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations.

  16. Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama.

    Science.gov (United States)

    Crawford, Andrew J; Lips, Karen R; Bermingham, Eldredge

    2010-08-03

    Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

  17. The evolutionary history of mariner-like elements in Neotropical drosophilids.

    Science.gov (United States)

    Wallau, Gabriel Luz; Hua-Van, Aurelie; Capy, Pierre; Loreto, Elgion L S

    2011-03-01

    The evolutionary history of mariner-like elements (MLEs) in 49 mainly Neotropical drosophilid species is described. So far, the investigations about the distribution of MLEs were performed mainly using hybridization assays with the Mos1 element (the first mariner active element described) in a widely range of drosophilid species and these sequences were found principally in species that arose in Afrotropical and Sino-Indian regions. Our analysis in mainly Neotropical drosophilid species shows that twenty-three species presented MLEs from three different subfamilies in their genomes: eighteen species had MLEs from subfamily mellifera, fifteen from subfamily mauritiana and three from subfamily irritans. Eleven of these species exhibited elements from more than one subfamily in their genome. In two subfamilies, the analyzed coding region was uninterrupted and contained conserved catalytic motifs. This suggests that these sequences were probably derived from active elements. The species with these putative active elements are Drosophila mediopunctata and D. busckii for the mauritiana subfamily, and D. paramediostriata for the mellifera subfamily. The phylogenetic analysis of MLE, shows a complex evolutionary pattern, exhibiting vertical transfer, stochastic loss and putative events of horizontal transmission occurring between different Drosophilidae species, and even those belonging to more distantly related taxa such as Bactrocera tryoni (Tephritidae family), Sphyracephala europaea (Diopsoidea superfamily) and Buenoa sp. (Hemiptera order). Moreover, our data show that the distribution of MLEs is not restricted to Afrotropical and Sino-Indian species. Conversely, these TEs are also widely distributed in drosophilid species arisen in the Neotropical region.

  18. Olfactory receptors on the maxillary palps of small ermine moth larvae: evolutionary history of benzaldehyde sensitivity

    Science.gov (United States)

    Xu, Sen; Menken, Steph B. J.

    2007-01-01

    In lepidopterous larvae the maxillary palps contain a large portion of the sensory equipment of the insect. Yet, knowledge about the sensitivity of these cells is limited. In this paper a morphological, behavioral, and electrophysiological investigation of the maxillary palps of Yponomeuta cagnagellus (Lepidoptera: Yponomeutidae) is presented. In addition to thermoreceptors, CO2 receptors, and gustatory receptors, evidence is reported for the existence of two groups of receptor cells sensitive to plant volatiles. Cells that are mainly sensitive to (E)-2-hexenal and hexanal or to (Z)-3-hexen-1-ol and 1-hexanol were found. Interestingly, a high sensitivity for benzaldehyde was also found. This compound is not known to be present in Euonymus europaeus, the host plant of the monophagous Yponomeuta cagnagellus, but it is a prominent compound in Rosaceae, the presumed hosts of the ancestors of Y. cagnagellus. To elucidate the evolutionary history of this sensitivity, and its possible role in host shifts, feeding responses of three Yponomeuta species to benzaldehyde were investigated. The results confirm the hypothesis that the sensitivity to benzaldehyde evolved during the ancestral shift from Celastraceae to Rosaceae and can be considered an evolutionary relict, retained in the recently backshifted Celastraceae-specialist Y. cagnagellus. PMID:17372741

  19. A rapid loss of stripes: the evolutionary history of the extinct quagga.

    Science.gov (United States)

    Leonard, Jennifer A; Rohland, Nadin; Glaberman, Scott; Fleischer, Robert C; Caccone, Adalgisa; Hofreiter, Michael

    2005-09-22

    Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature312, 282-284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

  20. The Evolutionary History and Spatiotemporal Dynamics of the NC Lineage of Citrus Tristeza Virus

    Directory of Open Access Journals (Sweden)

    María José Benítez-Galeano

    2017-10-01

    Full Text Available Citrus tristeza virus (CTV is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV’s evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the aim to delve deeper into the CTV-NC (New Clade genotype evolution, we estimated an evolution rate of 1.19 × 10−3 subs/site/year and the most common recent ancestor in 1977. Furthermore, the place of origin of the genotype was in the United States, and a great expansion of the population was observed in Uruguay. This expansion phase could be a consequence of the increment in the number of naïve citrus trees in Uruguayan orchards encompassing citrus industry growth in the past years.

  1. Attachment within life history theory: an evolutionary perspective on individual differences in attachment.

    Science.gov (United States)

    Szepsenwol, Ohad; Simpson, Jeffry A

    2018-03-15

    In this article, we discuss theory and research on how individual differences in adult attachment mediate the adaptive calibration of reproductive strategies, cognitive schemas, and emotional expression and regulation. We first present an integration of attachment theory and life history theory. Then, we discuss how early harsh and/or unpredictable environments may promote insecure attachment by hampering parents' ability to provide sensitive and reliable care to their children. Finally, we discuss how, in the context of harsh and/or unpredictable environments, different types of insecure attachment (i.e. anxiety and avoidance) may promote evolutionary adaptive reproductive strategies, cognitive schemas, and emotional expression and regulation profiles. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Evolutionary history of the HAP2/GCS1 gene and sexual reproduction in metazoans.

    Directory of Open Access Journals (Sweden)

    Robert E Steele

    2009-11-01

    Full Text Available The HAP2/GCS1 gene first appeared in the common ancestor of plants, animals, and protists, and is required in the male gamete for fusion to the female gamete in the unicellular organisms Chlamydomonas and Plasmodium. We have identified a HAP2/GCS1 gene in the genome sequence of the sponge Amphimedon queenslandica. This finding provides a continuous evolutionary history of HAP2/GCS1 from unicellular organisms into the metazoan lineage. Divergent versions of the HAP2/GCS1 gene are also present in the genomes of some but not all arthropods. By examining the expression of the HAP2/GCS1 gene in the cnidarian Hydra, we have found the first evidence supporting the hypothesis that HAP2/GCS1 was used for male gamete fusion in the ancestor of extant metazoans and that it retains that function in modern cnidarians.

  3. Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

    Directory of Open Access Journals (Sweden)

    Christidis Les

    2008-07-01

    Full Text Available Abstract Background Little is known about the role ecological shifts play in the evolution of Neotropical radiations that have colonized a variety of environments. We here examine habitat shifts in the evolutionary history of Elaenia flycatchers, a Neotropical bird lineage that lives in a range of forest and open habitats. We evaluate phylogenetic relationships within the genus based on mitochondrial and nuclear DNA sequence data, and then employ parsimony-based and Bayesian methods to reconstruct preferences for a number of habitat types and migratory behaviour throughout the evolutionary history of the genus. Using a molecular clock approach, we date the most important habitat shifts. Results Our analyses resolve phylogenetic relationships among Elaenia species and confirm several species associations predicted by morphology while furnishing support for other taxon placements that are in conflict with traditional classification, such as the elevation of various Elaenia taxa to species level. While savannah specialism is restricted to one basal clade within the genus, montane forest was invaded from open habitat only on a limited number of occasions. Riparian growth may have been favoured early on in the evolution of the main Elaenia clade and subsequently been deserted on several occasions. Austral long-distance migratory behaviour evolved on several occasions. Conclusion Ancestral reconstructions of habitat preferences reveal pronounced differences not only in the timing of the emergence of certain habitat preferences, but also in the frequency of habitat shifts. The early origin of savannah specialism in Elaenia highlights the importance of this habitat in Neotropical Pliocene and late Miocene biogeography. While forest in old mountain ranges such as the Tepuis and the Brazilian Shield was colonized early on, the most important colonization event of montane forest was in conjunction with Pliocene Andean uplift. Riparian habitats may have

  4. Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda.

    Science.gov (United States)

    Eyun, Seong-Il; Soh, Ho Young; Posavi, Marijan; Munro, James B; Hughes, Daniel S T; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, HarshaVardhan; Worley, Kim C; Muzny, Donna M; Park, Eun-Ok; Silva, Joana C; Gibbs, Richard A; Richards, Stephen; Lee, Carol Eunmi

    2017-08-01

    Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also examine hypotheses on which arthropod CRG family is most ancient. Thus, we reconstructed phylogenies of CRGs, including those from new arthropod genomes and transcriptomes, and mapped CRG gains and losses across arthropod lineages. Our analysis was strengthened by including crustaceans, especially copepods, which reside outside the hexapod/branchiopod clade within the subphylum Pancrustacea. We generated the first high-resolution genome sequence of the copepod Eurytemora affinis and annotated its CRGs. We found odorant receptors and odorant binding proteins present only in hexapods (insects) and absent from all other arthropod lineages, indicating that they are not universal adaptations to land. Gustatory receptors likely represent the oldest chemosensory receptors among CRGs, dating back to the Placozoa. We also clarified and confirmed the evolutionary history of antennal ionotropic receptors across the Arthropoda. All antennal ionotropic receptors in E. affinis were expressed more highly in males than in females, suggestive of an association with male mate-recognition behavior. This study is the most comprehensive comparative analysis to date of CRG family evolution across the largest and most speciose metazoan phylum Arthropoda. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Emotional labour underlying caring: an evolutionary concept analysis.

    Science.gov (United States)

    Huynh, Truc; Alderson, Marie; Thompson, Mary

    2008-10-01

    This paper is a report of a concept analysis of emotional labour. Caring is considered as the essence of nursing. Underpinning caring, the internal regulation of emotions or the emotional labour of nurses is invisible. The concept of emotional labour is relatively underdeveloped in nursing. A literature search using keywords 'emotional labour', 'emotional work' and 'emotions' was performed in CINAHL, PsycINFO and REPERE from 1990 to January 2008. We analysed 72 papers whose main focus of inquiry was on emotional labour. We followed Rodgers' evolutionary method of concept analysis. Emotional labour is a process whereby nurses adopt a 'work persona' to express their autonomous, surface or deep emotions during patient encounters. Antecedents to this adoption of a work persona are events occurring during patient-nurse encounters, and which consist of three elements: organization (i.e. social norms, social support), nurse (i.e. role identification, professional commitment, work experience and interpersonal skills) and job (i.e. autonomy, task routine, degree of emotional demand, interaction frequency and work complexity). The attributes of emotional labour have two dimensions: nurses' autonomous response and their work persona strategies (i.e. surface or deep acts). The consequences of emotional labour include organizational (i.e. productivity, 'cheerful environment') and nurse aspects (i.e. negative or positive). The concept of emotional labour should be introduced into preregistration programmes. Nurses also need to have time and a supportive environment to reflect, understand and discuss their emotional labour in caring for 'difficult' patients to deflate the dominant discourse about 'problem' patients.

  6. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Core collapse supernovae from blue supergiant progenitors : The evolutionary history of SN 1987A

    Science.gov (United States)

    Menon, Athira

    2015-08-01

    SN 1987A is historically one of the most remarkable supernova explosions to be seen from Earth. Due to the proximity of its location in the LMC, it remains the most well-studied object outside the solar system. It was also the only supernova whose progenitor was observed prior to its explosion.SN 1987A however, was a unique and enigmatic core collapse supernova. It was the first Type II supernova to have been observed to have exploded while its progenitor was a blue supergiant (BSG). Until then Type II supernovae were expected to originate from explosions of red supergiants (RSGs). A spectacular triple-ring nebula structure, rich in helium and nitrogen, was observed around the remnant, indicating a recent RSG phase before becoming a BSG. Even today it is not entirely understood what the evolutionary history may have been to cause a BSG to explode. The most commonly accepted hypothesis for its origin is the merger of a massive binary star system.An evolutionary scenario for such a binary system, was proposed by Podsiadlowski (1992) (P92). Through SPH simulations of the merger and the stellar evolution of the post-merger remnant, Ivanova & Podsiadlowski (2002) and (2003) (I&M) could successfully obtain the RSG to BSG transition of the progenitor.The aim of the present work is to produce the evolutionary history of the progenitor of SN 1987A and its explosion. We construct our models based on the results of P92 and I&M. Here, the secondary (less massive) star is accreted on the primary, while being simultaneously mixed in its envelope over a period of 100 years. The merged star is evolved until the onset of core collapse. For this work we use the 1-dimensional, implicit, hydrodynamical stellar evolution code, KEPLER. A large parameter space is explored, consisting of primary (16-20 Ms) and secondary masses (5-8 Ms), mixing boundaries, and accreting timescales. Those models whose end states match the observed properties of the progenitor of SN 1987A are exploded. The

  8. Tools for opening new chapters in the book of Treponema pallidum evolutionary history.

    Science.gov (United States)

    Gogarten, J F; Düx, A; Schuenemann, V J; Nowak, K; Boesch, C; Wittig, R M; Krause, J; Calvignac-Spencer, S; Leendertz, F H

    2016-11-01

    Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  9. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

    Science.gov (United States)

    vonHoldt, Bridgett M.; Pollinger, John P.; Earl, Dent A.; Knowles, James C.; Boyko, Adam R.; Parker, Heidi; Geffen, Eli; Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Jedrzejewska, Bogumila; Sidorovich, Vadim; Greco, Claudia; Randi, Ettore; Musiani, Marco; Kays, Roland; Bustamante, Carlos D.; Ostrander, Elaine A.; Novembre, John; Wayne, Robert K.

    2011-01-01

    High-throughput genotyping technologies developed for model species can potentially increase the resolution of demographic history and ancestry in wild relatives. We use a SNP genotyping microarray developed for the domestic dog to assay variation in over 48K loci in wolf-like species worldwide. Despite the high mobility of these large carnivores, we find distinct hierarchical population units within gray wolves and coyotes that correspond with geographic and ecologic differences among populations. Further, we test controversial theories about the ancestry of the Great Lakes wolf and red wolf using an analysis of haplotype blocks across all 38 canid autosomes. We find that these enigmatic canids are highly admixed varieties derived from gray wolves and coyotes, respectively. This divergent genomic history suggests that they do not have a shared recent ancestry as proposed by previous researchers. Interspecific hybridization, as well as the process of evolutionary divergence, may be responsible for the observed phenotypic distinction of both forms. Such admixture complicates decisions regarding endangered species restoration and protection. PMID:21566151

  10. Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions.

    Science.gov (United States)

    Huang, Danwei; Goldberg, Emma E; Roy, Kaustuv

    2015-04-21

    Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.

  11. Inside the Melanoplinae: new molecular evidence for the evolutionary history of the Eurasian Podismini (Orthoptera: Acrididae).

    Science.gov (United States)

    Chintauan-Marquier, Ioana C; Amédégnato, Christiane; Nichols, Richard A; Pompanon, François; Grandcolas, Philippe; Desutter-Grandcolas, Laure

    2014-02-01

    The Podismini are melanopline grasshoppers with a Holarctic distribution and well represented in the Eurasian fauna. To investigate their controversial taxonomy and evolutionary history, we studied 86%, 78% and 33% respectively of the Eurasian, European and Asian Palaearctic genera (Otte, 1995; Eades et al., 2013). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of four genes (ITS1, 16S, 12S, CO2). We applied a Bayesian molecular clock to estimate the times of species divergence, and the event-based parsimony method to depict the biogeographic framework of the diversification. Our results suggest that the selected Eurasian Podismini constitute a monophyletic group inside the Melanoplinae, provided it includes the North American genus Phaulotettix. The clades proposed by the present study inside the Podismini do not fit the older morphological or cytological classifications, but are in agreement with more recent proposals. Furthermore, our results can be explained by a plausible biogeographic history in which the present geographical distribution of the Eurasian Podismini resulted from known changes, to the Cenozoic climate and vegetation, induced by major geological events including the genesis of high mountain chains (e.g., Himalayas, Altay, Alps) and large deserts (e.g., Gobi, Karakoum, Taklamakan), and the opening of marginal seas (e.g., Bering, Japanese and Yellow Seas). Copyright © 2014. Published by Elsevier Inc.

  12. Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

    Science.gov (United States)

    Huang, Danwei; Goldberg, Emma E.; Roy, Kaustuv

    2015-04-01

    Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.

  13. The genetic diversity and evolutionary history of hepatitis C virus in Vietnam.

    Science.gov (United States)

    Li, Chunhua; Yuan, Manqiong; Lu, Ling; Lu, Teng; Xia, Wenjie; Pham, Van H; Vo, An X D; Nguyen, Mindie H; Abe, Kenji

    2014-11-01

    Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (pinaceae): range-wide evolutionary history and implications for conservation

    Science.gov (United States)

    Kevin M. Potter; Valerie D. Hipkins; Mary F. Mahalovich; Robert E. Means

    2013-01-01

    Premise of the study: Ponderosa pine ( Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic...

  15. A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants

    Czech Academy of Sciences Publication Activity Database

    Nicolas, M.; Marais, G.; Hykelová, Vladimíra; Janoušek, Bohuslav; Laporte, V.; Vyskot, Boris; Mouchiroud, D.; Negrutiu, I.; Charlesworth, D.; Moneger, F.

    2005-01-01

    Roč. 3, - (2005), s. 47-56 ISSN 1544-9173 Institutional research plan: CEZ:AV0Z50040507 Keywords : sex chromosomes * evolutionary history * X and Y chromosomes Subject RIV: BO - Biophysics Impact factor: 14.672, year: 2005

  16. The Origin and Evolutionary History of HIV-1 Subtype C in Senegal

    Science.gov (United States)

    Jung, Matthieu; Leye, Nafissatou; Vidal, Nicole; Fargette, Denis; Diop, Halimatou; Toure Kane, Coumba; Gascuel, Olivier; Peeters, Martine

    2012-01-01

    Background The classification of HIV-1 strains in subtypes and Circulating Recombinant Forms (CRFs) has helped in tracking the course of the HIV pandemic. In Senegal, which is located at the tip of West Africa, CRF02_AG predominates in the general population and Female Sex Workers (FSWs). In contrast, 40% of Men having Sex with Men (MSM) in Senegal are infected with subtype C. In this study we analyzed the geographical origins and introduction dates of HIV-1 C in Senegal in order to better understand the evolutionary history of this subtype, which predominates today in the MSM population Methodology/Principal Findings We used a combination of phylogenetic analyses and a Bayesian coalescent-based approach, to study the phylogenetic relationships in pol of 56 subtype C isolates from Senegal with 3,025 subtype C strains that were sampled worldwide. Our analysis shows a significantly well supported cluster which contains all subtype C strains that circulate among MSM in Senegal. The MSM cluster and other strains from Senegal are widely dispersed among the different subclusters of African HIV-1 C strains, suggesting multiple introductions of subtype C in Senegal from many different southern and east African countries. More detailed analyses show that HIV-1 C strains from MSM are more closely related to those from southern Africa. The estimated date of the MRCA of subtype C in the MSM population in Senegal is estimated to be in the early 80's. Conclusions/Significance Our evolutionary reconstructions suggest that multiple subtype C viruses with a common ancestor originating in the early 1970s entered Senegal. There was only one efficient spread in the MSM population, which most likely resulted from a single introduction, underlining the importance of high-risk behavior in spread of viruses. PMID:22470456

  17. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

    Directory of Open Access Journals (Sweden)

    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  18. The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies.

    Directory of Open Access Journals (Sweden)

    Daniel R O'Donnell

    Full Text Available Standing genetic variation and the historical environment in which that variation arises (evolutionary history are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.

  19. Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles.

    Science.gov (United States)

    Lischer, Heidi E L; Excoffier, Laurent; Heckel, Gerald

    2014-04-01

    Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

  20. Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography.

    Science.gov (United States)

    Hao, Zhen-Zhen; Liu, Yan-Yan; Nazaire, Mare; Wei, Xiao-Xin; Wang, Xiao-Quan

    2015-06-01

    Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and

  1. Evolutionary history influences the salinity preference of bacterial taxa in wetland soils

    Directory of Open Access Journals (Sweden)

    Ember M Morrissey

    2015-10-01

    Full Text Available Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetlands soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences and activity (e.g., extracellular enzyme activity, CO2, and CH4 production. These changes in community composition and activity rates were strongly correlated, which suggests the effect of environment on function could be mediated, at least in part, by microbial community composition. Based on their distribution across treatments, each phylotype was categorized as having a salinity preference (freshwater, saltwater, or none and phylogenetic analyses revealed a significant influence of evolutionary history on these groupings. This finding was corroborated by examining the salinity preferences of high-level taxonomic groups. For instance, we found that the majority of alpha- and gamma-proteobacteria preferred saltwater, while many beta-proteobacteria prefer freshwater. Overall, our results indicate the effect of salinity on bacterial community composition results from phylogenetically-clustered salinity preferences.

  2. Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence.

    Science.gov (United States)

    Nan, Fangru; Feng, Jia; Lv, Junping; Liu, Qi; Fang, Kunpeng; Gong, Chaoyan; Xie, Shulian

    2017-06-07

    Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415-484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.

  3. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes

    Science.gov (United States)

    Lee, JunMo; Kim, Kyeong Mi; Yang, Eun Chan; Miller, Kathy Ann; Boo, Sung Min; Bhattacharya, Debashish; Yoon, Hwan Su

    2016-01-01

    The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta. PMID:27030297

  4. Evolutionary history of Indian Ocean nycteribiid bat flies mirroring the ecology of their hosts.

    Directory of Open Access Journals (Sweden)

    Pablo Tortosa

    Full Text Available Bats and their parasites are increasingly investigated for their role in maintenance and transmission of potentially emerging pathogens. The islands of the western Indian Ocean hold nearly 50 bat species, mostly endemic and taxonomically well studied. However, investigation of associated viral, bacterial, and external parasites has lagged behind. In the case of their ectoparasites, more detailed information should provide insights into the evolutionary history of their hosts, as well as pathogen cycles in these wild animals. Here we investigate species of Nycteribiidae, a family of obligate hematophagous wingless flies parasitizing bats. Using morphological and molecular approaches, we describe fly species diversity sampled on Madagascar and the Comoros for two cave-roosting bat genera with contrasting ecologies: Miniopterus and Rousettus. Within the sampling area, 11 endemic species of insect-feeding Miniopterus occur, two of which are common to Madagascar and Comoros, while fruit-consuming Rousettus are represented by one species endemic to each of these zones. Morphological and molecular characterization of flies reveals that nycteribiids associated with Miniopterus bats comprise three species largely shared by most host species. Flies of M. griveaudi, one of the two bats found on Madagascar and certain islands in the Comoros, belong to the same taxon, which accords with continued over-water population exchange of this bat species and the lack of inter-island genetic structuring. Flies parasitizing Rousettus belong to two distinct species, each associated with a single host species, again in accordance with the distribution of each endemic bat species.

  5. Evolutionary history of LINE-1 in the major clades of placental mammals.

    Directory of Open Access Journals (Sweden)

    Paul D Waters

    2007-01-01

    Full Text Available LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria hypothesis.LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

  6. Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures.

    Science.gov (United States)

    Barriuso, Jorge; Martínez, María Jesús

    2017-01-03

    Fungal "Versatile carboxylic ester hydrolases" are enzymes with great biotechnological interest. Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling. Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. The properties of the ancestral candidates are discussed on the basis of their three-dimensional structural models, the hydrophobicity of the lid, and the substrate binding intramolecular tunnel, revealing all of them featured properties of these enzymes. The evolutionary history of the putative lipases revealed an increase on the length and hydrophobicity of the lid region, as well as in the size of the substrate binding pocket, during evolution time. These facts suggest the enzymes' specialization towards certain substrates and their subsequent loss of promiscuity. These results bring to light the presence of different pools of lipases in fungi with different habitats and life styles. Despite the consistency of the data gathered from reconstruction of ancestral sequences, the heterologous expression of some of these candidates would be essential to corroborate enzymes' activities.

  7. Evolutionary history of PEPC genes in green plants: Implications for the evolution of CAM in orchids.

    Science.gov (United States)

    Deng, Hua; Zhang, Liang-Sheng; Zhang, Guo-Qiang; Zheng, Bao-Qiang; Liu, Zhong-Jian; Wang, Yan

    2016-01-01

    The phosphoenolpyruvate carboxylase (PEPC) gene is the key enzyme in CAM and C4 photosynthesis. A detailed phylogenetic analysis of the PEPC family was performed using sequences from 60 available published plant genomes, the Phalaenopsis equestris genome and RNA-Seq of 15 additional orchid species. The PEPC family consists of three distinct subfamilies, PPC-1, PPC-2, and PPC-3, all of which share a recent common ancestor in chlorophyte algae. The eudicot PPC-1 lineage separated into two clades due to whole genome duplication (WGD). Similarly, the monocot PPC-1 lineage also divided into PPC-1M1 and PPC-1M2 through an ancient duplication event. The monocot CAM- or C4-related PEPC originated from the clade PPC-1M1. WGD may not be the major driver for the performance of CAM function by PEPC, although it increased the number of copies of the PEPC gene. CAM may have evolved early in monocots, as the CAM-related PEPC of orchids originated from the monocot ancient duplication, and the earliest CAM-related PEPC may have evolved immediately after the diversification of monocots, with CAM developing prior to C4. Our results represent the most complete evolutionary history of PEPC genes in green plants to date and particularly elucidate the origin of PEPC in orchids. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Evolutionary history and taxonomy of a short-horned grasshopper subfamily: the Melanoplinae (Orthoptera: Acrididae).

    Science.gov (United States)

    Chintauan-Marquier, Ioana C; Jordan, Steve; Berthier, Pierre; Amédégnato, Christiane; Pompanon, François

    2011-01-01

    The Melanoplinae is one of the largest subfamilies of the Acrididae grasshoppers, with a Holarctic-Neotropical distribution. To investigate its controversial taxonomy and evolutionary history, we studied 19 species representative of its main tribes, and 7 Acridoidea outgroup species. More than 1650 base pairs of three regions of nuclear rDNA (18S, ITS1, 28S) and one mitochondrial rDNA (12S) were combined and used to construct parsimony, maximum likelihood and Bayesian phylogenies. Our results correspond with the present geographical distribution of the taxa rather than the existing taxonomy based on morphological characters. The morphologically unclassified and atypical taxa group with the Neotropical Melanoplinae. The currently recognized Melanoplinae appear to be polyphyletic due to inclusion of the Mexican genus Netrosoma. The distribution of the American and Eurasiatic Melanoplinae fauna can be explained by climatic and geological events, such as the Andean uplift, that would have affected the diversification and migration of Neotropical taxa. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. Unraveling the evolutionary history of the Chilostoma Fitzinger, 1833 (Mollusca, Gastropoda, Pulmonata) lineages in Greece.

    Science.gov (United States)

    Psonis, Nikolaos; Vardinoyannis, Katerina; Mylonas, Moisis; Poulakakis, Nikos

    2015-10-01

    The land snails of the genus Chilostoma Fitzinger, 1833 that includes, in Greece, the (sub)genera Cattania, Josephinella and Thiessea, are highly diversified and present high levels of endemism. However, their evolutionary history is unknown and their taxonomy is complex and continuously revised. The aim of this study is to investigate the phylogenetic relationships of the lineages of the genus Chilostoma distributed in Greece based on partial DNA sequences of two mitochondrial DNA (16S rRNA and COI) genes. Complete sequences of one nuclear gene (ITS1) representing the major mitochondrial lineages were also analyzed. The phylogenetic trees revealed three distinct major clades that correspond to the three (sub)genera. Several taxonomical incongruencies were made obvious, thus, raising questions about the "true" number of species in each clade, while rendering a taxonomic re-evaluation necessary. From a phylogeographic point of view, it seems that the three major phylogenetic clades were separated in the late Miocene. They started differentiating into distinct species during the Pliocene and Pleistocene through several vicariance and dispersal events. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Conservatism of lizard thermal tolerances and body temperatures across evolutionary history and geography.

    Science.gov (United States)

    Grigg, Joseph W; Buckley, Lauren B

    2013-04-23

    Species may exhibit similar thermal tolerances via either common ancestry or environmental filtering and local adaptation, if the species inhabit similar environments. We ask whether upper and lower thermal limits (critical thermal maxima and minima) and body temperatures are more strongly conserved across evolutionary history or geography for lizard populations distributed globally. We find that critical thermal maxima are highly conserved with location accounting for a higher proportion of the variation than phylogeny. Notably, thermal tolerance breadth is conserved across the phylogeny despite critical thermal minima showing little niche conservatism. Body temperatures observed during activity in the field show the greatest degree of conservatism, with phylogeny accounting for most of the variation. This suggests that propensities for thermoregulatory behaviour, which can buffer body temperatures from environmental variation, are similar within lineages. Phylogeny and geography constrain thermal tolerances similarly within continents, but variably within clades. Conservatism of thermal tolerances across lineages suggests that the potential for local adaptation to alleviate the impacts of climate change on lizards may be limited.

  11. Vertebral development of modern salamanders provides insights into a unique event of their evolutionary history.

    Science.gov (United States)

    Boisvert, Catherine Anne

    2009-01-15

    The origin of salamanders and their interrelationships to the two other modern amphibian orders (frogs and caecilians) are problematic owing to an 80-100 million year gap in the fossil record between the Carboniferous to the Lower Jurassic. This is compounded by a scarcity of adult skeletal characters linking the early representatives of the modern orders to their stem-group in the Paleozoic. The use of ontogenetic characters can be of great use in the resolution of these questions. Growth series of all ten modern salamander families (a 120 cleared and stained larvae) were examined for pattern and timing of vertebral elements chondrification and ossification. The primitive pattern is that of the neural arches developing before the centra, while the reverse represents the derived condition. Both the primitive and derived conditions are observed within the family Hynobiidae, whereas only the derived condition is observed in all other salamanders. This provides support to the claims that Hynobiidae is both the most basal of modern families and potentially polyphyletic (with Ranodon and Hybobius forming the most basal clade and Salamandrella being a part of the most derived clade). This provides insight into a unique event in salamander evolutionary history and suggests that the developmental pattern switch occurred between the Triassic and the mid-Jurassic before the last major radiation. (c) 2008 Wiley-Liss, Inc.

  12. Evolutionary history influences the salinity preference of bacterial taxa in wetland soils.

    Science.gov (United States)

    Morrissey, Ember M; Franklin, Rima B

    2015-01-01

    Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetland soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences) and activity (CO2 and CH4 production, and extracellular enzyme activity). These changes in community composition and activity rates were strongly correlated, which suggests the effect of environment on function could be mediated, at least in part, by microbial community composition. Based on their distribution across treatments, each phylotype was categorized as having a salinity preference (freshwater, saltwater, or none) and phylogenetic analyses revealed a significant influence of evolutionary history on these groupings. This finding was corroborated by examining the salinity preferences of high-level taxonomic groups. For instance, we found that the majority of α- and γ-proteobacteria in these wetland soils preferred saltwater, while many β-proteobacteria prefer freshwater. Overall, our results indicate the effect of salinity on bacterial community composition results from phylogenetically-clustered salinity preferences.

  13. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

    Science.gov (United States)

    Chang, Dan; Knapp, Michael; Enk, Jacob; Lippold, Sebastian; Kircher, Martin; Lister, Adrian; MacPhee, Ross D. E.; Widga, Christopher; Czechowski, Paul; Sommer, Robert; Hodges, Emily; Stümpel, Nikolaus; Barnes, Ian; Dalén, Love; Derevianko, Anatoly; Germonpré, Mietje; Hillebrand-Voiculescu, Alexandra; Constantin, Silviu; Kuznetsova, Tatyana; Mol, Dick; Rathgeber, Thomas; Rosendahl, Wilfried; Tikhonov, Alexey N.; Willerslev, Eske; Hannon, Greg; Lalueza-Fox, Carles; Joger, Ulrich; Poinar, Hendrik; Hofreiter, Michael; Shapiro, Beth

    2017-01-01

    Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths. PMID:28327635

  14. Reconstruction of the Evolutionary History and Dispersal of Usutu Virus, a Neglected Emerging Arbovirus in Europe and Africa.

    Science.gov (United States)

    Engel, Dimitri; Jöst, Hanna; Wink, Michael; Börstler, Jessica; Bosch, Stefan; Garigliany, Mutien-Marie; Jöst, Artur; Czajka, Christina; Lühken, Renke; Ziegler, Ute; Groschup, Martin H; Pfeffer, Martin; Becker, Norbert; Cadar, Daniel; Schmidt-Chanasit, Jonas

    2016-02-02

    Usutu virus (USUV), one of the most neglected Old World encephalitic flaviviruses, causes epizootics among wild and captive birds and sporadic infection in humans. The dynamics of USUV spread and evolution in its natural hosts are unknown. Here, we present the phylogeny and evolutionary history of all available USUV strains, including 77 newly sequenced complete genomes from a variety of host species at a temporal and spatial scaled resolution. The results showed that USUV can be classified into six distinct lineages and that the most recent common ancestor of the recent European epizootics emerged in Africa at least 500 years ago. We demonstrated that USUV was introduced regularly from Africa into Europe in the last 50 years, and the genetic diversity of European lineages is shaped primarily by in situ evolution, while the African lineages have been driven by extensive gene flow. Most of the amino acid changes are deleterious polymorphisms removed by purifying selection, with adaptive evolution restricted to the NS5 gene and several others evolving under episodic directional selection, indicating that the ecological or immunological factors were mostly the key determinants of USUV dispersal and outbreaks. Host-specific mutations have been detected, while the host transition analysis identified mosquitoes as the most likely origin of the common ancestor and birds as the source of the recent European USUV lineages. Our results suggest that the major migratory bird flyways could predict the continental and intercontinental dispersal patterns of USUV and that migratory birds might act as potential long-distance dispersal vehicles. Usutu virus (USUV), a mosquito-borne flavivirus of the Japanese encephalitis virus antigenic group, caused massive bird die-offs, mostly in Europe. There is increasing evidence that USUV appears to be pathogenic for humans, becoming a potential public health problem. The emergence of USUV in Europe allows us to understand how an arbovirus

  15. Effects of tectonics and large scale climatic changes on the evolutionary history of Hyalomma ticks.

    Science.gov (United States)

    Sands, Arthur F; Apanaskevich, Dmitry A; Matthee, Sonja; Horak, Ivan G; Harrison, Alan; Karim, Shahid; Mohammad, Mohammad K; Mumcuoglu, Kosta Y; Rajakaruna, Rupika S; Santos-Silva, Maria M; Matthee, Conrad A

    2017-09-01

    Hyalomma Koch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also some of the mechanisms involved in the diversification of the genus, we sequenced and analysed data derived from two mtDNA fragments, three nuclear DNA genes and 47 morphological characters. Bayesian and Parsimony analyses based on the combined data (2242 characters for 84 taxa) provided maximum resolution and strongly supported the monophyly of Hyalomma and the subgenus Euhyalomma Filippova, 1984 (including H. punt Hoogstraal, Kaiser and Pedersen, 1969). A predicted close evolutionary association was found between morphologically similar H. dromedarii Koch, 1844, H. somalicum Tonelli Rondelli, 1935, H. impeltatum Schulze and Schlottke, 1929 and H. punt, and together they form a sister lineage to H. asiaticum Schulze and Schlottke, 1929, H. schulzei Olenev, 1931 and H. scupense Schulze, 1919. Congruent with morphological suggestions, H. anatolicum Koch, 1844, H. excavatum Koch, 1844 and H. lusitanicum Koch, 1844 form a clade and so also H. glabrum Delpy, 1949, H. marginatum Koch, 1844, H. turanicum Pomerantzev, 1946 and H. rufipes Koch, 1844. Wide scale continental sampling revealed cryptic divergences within African H. truncatum Koch, 1844 and H. rufipes and suggested that the taxonomy of these lineages is in need of a revision. The most basal lineages in Hyalomma represent taxa currently confined to Eurasia and molecular clock estimates suggest that members of the genus started to diverge approximately 36.25 million years ago (Mya). The early diversification event coincides well with the collision of the Indian and Eurasian Plates, an event that was also characterized by large scale faunal turnover in the region. Using S

  16. A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda).

    Science.gov (United States)

    Bracken-Grissom, Heather D; Cannon, Maren E; Cabezas, Patricia; Feldmann, Rodney M; Schweitzer, Carrie E; Ahyong, Shane T; Felder, Darryl L; Lemaitre, Rafael; Crandall, Keith A

    2013-06-20

    The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history-phylogeny, divergence times, character evolution and diversification-of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224-296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights

  17. Evolutionary history of enigmatic bears in the Tibetan Plateau–Himalaya region and the identity of the yeti

    Science.gov (United States)

    Lan, Tianying; Gill, Stephanie; Bellemain, Eva; Bischof, Richard; Nawaz, Muhammad Ali

    2017-01-01

    Although anecdotally associated with local bears (Ursus arctos and U. thibetanus), the exact identity of ‘hominid’-like creatures important to folklore and mythology in the Tibetan Plateau–Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region. Phylogenetic analyses of mitochondrial DNA sequences determined clade affinities of the purported yeti samples in this study, strongly supporting the biological basis of the yeti legend to be local, extant bears. Complete mitochondrial genomes were assembled for Himalayan brown bear (U. a. isabellinus) and black bear (U. t. laniger) for the first time. Our results demonstrate that the Himalayan brown bear is one of the first-branching clades within the brown bear lineage, while Tibetan brown bears diverged much later. The estimated times of divergence of the Tibetan Plateau and Himalayan bear lineages overlap with Middle to Late Pleistocene glaciation events, suggesting that extant bears in the region are likely descendants of populations that survived in local refugia during the Pleistocene glaciations. PMID:29187630

  18. Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti.

    Science.gov (United States)

    Lan, Tianying; Gill, Stephanie; Bellemain, Eva; Bischof, Richard; Nawaz, Muhammad Ali; Lindqvist, Charlotte

    2017-12-13

    Although anecdotally associated with local bears ( Ursus arctos and U. thibetanus ), the exact identity of 'hominid'-like creatures important to folklore and mythology in the Tibetan Plateau-Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region. Phylogenetic analyses of mitochondrial DNA sequences determined clade affinities of the purported yeti samples in this study, strongly supporting the biological basis of the yeti legend to be local, extant bears. Complete mitochondrial genomes were assembled for Himalayan brown bear ( U. a. isabellinus ) and black bear ( U. t. laniger ) for the first time. Our results demonstrate that the Himalayan brown bear is one of the first-branching clades within the brown bear lineage, while Tibetan brown bears diverged much later. The estimated times of divergence of the Tibetan Plateau and Himalayan bear lineages overlap with Middle to Late Pleistocene glaciation events, suggesting that extant bears in the region are likely descendants of populations that survived in local refugia during the Pleistocene glaciations. © 2017 The Authors.

  19. A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

    Science.gov (United States)

    Lin, XuXun; Yuan, PengCheng

    2018-01-01

    In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

  20. Evolutionary history of human disease genes reveals phenotypic connections and comorbidity among genetic diseases.

    Science.gov (United States)

    Park, Solip; Yang, Jae-Seong; Kim, Jinho; Shin, Young-Eun; Hwang, Jihye; Park, Juyong; Jang, Sung Key; Kim, Sanguk

    2012-01-01

    The extent to which evolutionary changes have impacted the phenotypic relationships among human diseases remains unclear. In this work, we report that phenotypically similar diseases are connected by the evolutionary constraints on human disease genes. Human disease groups can be classified into slowly or rapidly evolving classes, where the diseases in the slowly evolving class are enriched with morphological phenotypes and those in the rapidly evolving class are enriched with physiological phenotypes. Our findings establish a clear evolutionary connection between disease classes and disease phenotypes for the first time. Furthermore, the high comorbidity found between diseases connected by similar evolutionary constraints enables us to improve the predictability of the relative risk of human diseases. We find the evolutionary constraints on disease genes are a new layer of molecular connection in the network-based exploration of human diseases.

  1. Taxonomic affinities and evolutionary history of the Early Pleistocene hominids of Java: dentognathic evidence.

    Science.gov (United States)

    Kaifu, Yousuke; Baba, Hisao; Aziz, Fachroel; Indriati, Etty; Schrenk, Friedemann; Jacob, Teuku

    2005-12-01

    Temporal changes, within-group variation, and phylogenetic positions of the Early Pleistocene Javanese hominids remain unclear. Recent debate focused on the age of the oldest Javanese hominids, but the argument so far includes little morphological basis for the fossils. To approach these questions, we analyzed a comprehensive dentognathic sample from Sangiran, which includes most of the existing hominid mandibles and teeth from the Early Pleistocene of Java. The sample was divided into chronologically younger and older groups. We examined morphological differences between these chronological groups, and investigated their affinities with other hominid groups from Africa and Eurasia. The results indicated that 1) there are remarkable morphological differences between the chronologically younger and older groups of Java, 2) the chronologically younger group is morphologically advanced, showing a similar degree of dentognathic reduction to that of Middle Pleistocene Chinese H. erectus, and 3) the chronologically older group exhibits some features that are equally primitive as or more primitive than early H. erectus of Africa. These findings suggest that the evolutionary history of early Javanese H. erectus was more dynamic than previously thought. Coupled with recent discoveries of the earliest form of H. erectus from Dmanisi, Georgia, the primitive aspects of the oldest Javanese hominid remains suggest that hominid groups prior to the grade of ca. 1.8-1.5 Ma African early H. erectus dispersed into eastern Eurasia during the earlier Early Pleistocene, although the age of the Javanese hominids themselves is yet to be resolved. Subsequent periods of the Early Pleistocene witnessed remarkable changes in the Javanese hominid record, which are ascribed either to significant in situ evolution or replacement of populations. 2005 Wiley-Liss, Inc.

  2. Evolutionary history and novel biotic interactions determine plant responses to elevated CO2 and nitrogen fertilization.

    Directory of Open Access Journals (Sweden)

    Rachel Wooliver

    plant evolutionary history and introduced species will shape community productivity in a changing world.

  3. Different Evolutionary History for Basque Diaspora Populations in USA and Argentina Unveiled by Mitochondrial DNA Analysis.

    Science.gov (United States)

    Baeta, Miriam; Núñez, Carolina; Cardoso, Sergio; Palencia-Madrid, Leire; Piñeiro-Hermida, Sergio; Arriba-Barredo, Miren; Villanueva-Millán, María Jesús; M de Pancorbo, Marian

    2015-01-01

    The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.

  4. The effects of ecology and evolutionary history on robust capuchin morphological diversity.

    Science.gov (United States)

    Wright, Kristin A; Wright, Barth W; Ford, Susan M; Fragaszy, Dorothy; Izar, Patricia; Norconk, Marilyn; Masterson, Thomas; Hobbs, David G; Alfaro, Michael E; Lynch Alfaro, Jessica W

    2015-01-01

    Recent molecular work has confirmed the long-standing morphological hypothesis that capuchins are comprised of two distinct clades, the gracile (untufted) capuchins (genus Cebus, Erxleben, 1777) and the robust (tufted) capuchins (genus Sapajus Kerr, 1792). In the past, the robust group was treated as a single, undifferentiated and cosmopolitan species, with data from all populations lumped together in morphological and ecological studies, obscuring morphological differences that might exist across this radiation. Genetic evidence suggests that the modern radiation of robust capuchins began diversifying ∼2.5 Ma, with significant subsequent geographic expansion into new habitat types. In this study we use a morphological sample of gracile and robust capuchin craniofacial and postcranial characters to examine how ecology and evolutionary history have contributed to morphological diversity within the robust capuchins. We predicted that if ecology is driving robust capuchin variation, three distinct robust morphotypes would be identified: (1) the Atlantic Forest species (Sapajus xanthosternos, S. robustus, and S. nigritus), (2) the Amazonian rainforest species (S. apella, S. cay and S. macrocephalus), and (3) the Cerrado-Caatinga species (S. libidinosus). Alternatively, if diversification time between species pairs predicts degree of morphological difference, we predicted that the recently diverged S. apella, S. macrocephalus, S. libidinosus, and S. cay would be morphologically comparable, with greater variation among the more ancient lineages of S. nigritus, S. xanthosternos, and S. robustus. Our analyses suggest that S. libidinosus has the most derived craniofacial and postcranial features, indicative of inhabiting a more terrestrial niche that includes a dependence on tool use for the extraction of imbedded foods. We also suggest that the cranial robusticity of S. macrocephalus and S. apella are indicative of recent competition with sympatric gracile capuchin

  5. Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling.

    Science.gov (United States)

    Betancur-R, Ricardo

    2009-07-23

    Ariids or sea catfishes are one of the two otophysan fish families (out of about 67 families in four orders) that inhabit mainly marine and brackish waters (although some species occur strictly in fresh waters). The group includes over 150 species placed in approximately 29 genera and two subfamilies (Galeichthyinae and Ariinae). Despite their global distribution, ariids are largely restricted to the continental shelves due in part to their specialized reproductive behavior (i.e., oral incubation). Thus, among marine fishes, ariids offer an excellent opportunity for inferring historical biogeographic scenarios. Phylogenetic hypotheses available for ariids have focused on restricted geographic areas and comprehensive phylogenies are still missing. This study inferred phylogenetic hypotheses for 123 ariid species in 28 genera from different biogeographic provinces using both mitochondrial and nuclear sequences (up to approximately 4 kb). While the topologies obtained support the monophyly of basal groups, up to ten genera validated in previous morphological studies were incongruent with the molecular topologies. New World ariines were recovered as paraphyletic and Old World ariines were grouped into a well-supported clade that was further divided into subclades mainly restricted to major Gondwanan landmasses. A general area cladogram derived from the area cladograms of ariines and three other fish groups was largely congruent with the geological area cladogram of Gondwana. Nonetheless, molecular clock estimations provided variable results on the timing of ariine diversification (approximately 105-41 mya). This study provides the most comprehensive phylogeny of sea catfishes to date and highlights the need for re-assessment of their classification. While from a topological standpoint the evolutionary history of ariines is mostly congruent with vicariance associated with the sequence of events during Gondwanan fragmentation, ambiguous divergence time estimations

  6. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Directory of Open Access Journals (Sweden)

    Damian Labuda

    Full Text Available The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  7. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Science.gov (United States)

    Labuda, Damian; Yotova, Vania; Lefebvre, Jean-François; Moreau, Claudia; Utermann, Gerd; Williams, Scott M

    2013-01-01

    The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  8. Underexplored biodiversity of Eastern Mediterranean biota: systematics and evolutionary history of the genus Aubrieta (Brassicaceae).

    Science.gov (United States)

    Koch, Marcus A; Karl, Robert; German, Dmitry A

    2017-01-01

    Aubrieta is a taxonomically difficult genus from the Brassicaceae family with approximately 20 species centred in Turkey and Greece. Species boundaries and their evolutionary history are poorly understood. Therefore, we analysed bio- and phylogeographic relationships and evaluated morphological variation to study the evolution of this genus. Phylogenetic analyses of DNA sequence variation of nuclear-encoded loci and plastid DNA were used to unravel phylogeographic patterns. Morphometric analyses were conducted to study species delimitation. DNA sequence-based mismatch distribution and climate-niche analyses were performed to explain various radiations in space and time during the last 2·5 million years. Species groups largely show non-overlapping distribution patterns in the eastern Mediterranean and Asia Minor. We recognized 20 species and provide evidence for overlooked species, thereby highlighting taxonomical difficulties but also demonstrating underexplored species diversity. The centre of origin of Aubrieta is probably Turkey, from which various clades expanded independently towards Asia Minor, south to Lebanon and west to Greece and the Balkans during the Pleistocene. Pleistocene climatic fluctuations had a pronounced effect on Aubrieta speciation and radiation during the last 1·1 million years in the Eastern Mediterranean and Asia Minor. In contrast to many other Brassicaceae, speciation processes did not involve excessive formation of polyploids, but displayed formation of diploids with non-overlapping present-day distribution areas. Expansions from the Aubrieta centre of origin and primary centre of species diversity showed adaptation trends towards higher temperature and drier conditions. However, later expansion and diversification of taxa from within the second centre of species diversity in Greece started ∼0·19 Mya and were associated with a general transition of species adaptation towards milder temperatures and less dry conditions. © The

  9. Lineage-specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

    Directory of Open Access Journals (Sweden)

    Cyril Jourda

    2016-12-01

    Full Text Available Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases, starch synthases (SS, starch branching enzymes (SBE, debranching enzymes (DBE, -amylases (AMY and -amylases (BAM. Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPases, SS, SBE and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPases, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage

  10. A comparative phylogeographic study reveals discordant evolutionary histories of alpine ground beetles (Coleoptera, Carabidae).

    Science.gov (United States)

    Weng, Yi-Ming; Yang, Man-Miao; Yeh, Wen-Bin

    2016-04-01

    Taiwan, an island with three major mountain ranges, provides an ideal topography to study mountain-island effect on organisms that would be diversified in the isolation areas. Glaciations, however, might drive these organisms to lower elevations, causing gene flow among previously isolated populations. Two hypotheses have been proposed to depict the possible refugia for alpine organisms during glaciations. Nunatak hypothesis suggests that alpine species might have stayed in situ in high mountain areas during glaciations. Massif de refuge, on the other hand, proposes that alpine species might have migrated to lower ice-free areas. By sampling five sympatric carabid species of Nebria and Leistus, and using two mitochondrial genes and two nuclear genes, we evaluated the mountain-island effect on alpine carabids and tested the two proposed hypotheses with comparative phylogeographic method. Results from the phylogenetic relationships, network analysis, lineage calibration, and genetic structure indicate that the deep divergence among populations in all L. smetanai, N. formosana, and N. niitakana was subjected to long-term isolation, a phenomenon in agreement with the nunatak hypothesis. However, genetic admixture among populations of N. uenoiana and some populations of L. nokoensis complex suggests that gene flow occurred during glaciations, as a massif de refuge depicts. The speciation event in N. niitakana is estimated to have occurred before 1.89 million years ago (Mya), while differentiation among isolated populations in N. niitakana, N. formosana, L. smetanai, and L. nokoensis complex might have taken place during 0.65-1.65 Mya. While each of the alpine carabids arriving in Taiwan during different glaciation events acquired its evolutionary history, all of them had confronted the existing mountain ranges.

  11. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.

    Science.gov (United States)

    Paijmans, Johanna L A; Barnett, Ross; Gilbert, M Thomas P; Zepeda-Mendoza, M Lisandra; Reumer, Jelle W F; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F; Leonard, Jennifer A; Rohland, Nadin; Westbury, Michael V; Barlow, Axel; Hofreiter, Michael

    2017-11-06

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera.

    Science.gov (United States)

    Cridland, Julie M; Tsutsui, Neil D; Ramírez, Santiago R

    2017-02-01

    The western honey bee, Apis mellifera, provides critical pollination services to agricultural crops worldwide. However, despite substantial interest and prior investigation, the early evolution and subsequent diversification of this important pollinator remain uncertain. The primary hypotheses place the origin of A. mellifera in either Asia or Africa, with subsequent radiations proceeding from one of these regions. Here, we use two publicly available whole-genome data sets plus newly sequenced genomes and apply multiple population genetic analysis methods to investigate the patterns of ancestry and admixture in native honey bee populations from Europe, Africa, and the Middle East. The combination of these data sets is critical to the analyses, as each contributes samples from geographic locations lacking in the other, thereby producing the most complete set of honey bee populations available to date. We find evidence supporting an origin of A. mellifera in the Middle East or North Eastern Africa, with the A and Y lineages representing the earliest branching lineages. This finding has similarities with multiple contradictory hypotheses and represents a disentangling of genetic relationships, geographic proximity, and secondary contact to produce a more accurate picture of the origins of A. mellifera. We also investigate how previous studies came to their various conclusions based on incomplete sampling of populations, and illustrate the importance of complete sampling in understanding evolutionary processes. These results provide fundamental knowledge about genetic diversity within Old World honey bee populations and offer insight into the complex history of an important pollinator. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Evolutionary history of larval skeletal morphology in sea urchin Echinometridae (Echinoidea: Echinodermata) as deduced from mitochondrial DNA molecular phylogeny.

    Science.gov (United States)

    Kinjo, Sonoko; Shirayama, Yoshihisa; Wada, Hiroshi

    2008-01-01

    The larval skeletons of sea urchins show considerable morphological diversity, even between closely related species, although the evolutionary history and functional significance of this diversity are poorly understood. To infer the evolutionary history of the skeletal morphology, we focused on echinometrid species for which the morphological variation in larval skeletons had been investigated qualitatively and quantitatively. We reconstructed the phylogenetic relationships among 14 echinometrid species based on mitochondrial ND1 and ND2 genes and mapped the morphological characters onto the resultant trees. The monophyly of each genus in the Echinometridae was well supported by our results, as was the close affinity between Colobocentrotus, Heterocentrotus, and Echinometra. The mapping of the morphological characters of the larval skeletons indicated that the length, direction, and density of spines on the postoral rods was well conserved in each group of Echinometridae and that the abundance of spines and the size and shape of the body skeleton changed relatively frequently and hence were less conserved. In Echinometrid species, morphological variation in relatively unconserved features tends to be associated with latitudinal distributions, rather than phylogenetic relationships, indicating that the morphological diversity of larval skeletons could have been caused by adaptation to the habitat environment. Some morphological differences, however, seem to be nonfunctional and generated by the constraints on larval skeletogenesis. Thus, echinometrid species can be a good model with which to study the evolutionary history from both ecological and developmental standpoints.

  14. Land plants acquired active stomatal control early in their evolutionary history.

    Science.gov (United States)

    Ruszala, Elizabeth M; Beerling, David J; Franks, Peter J; Chater, Caspar; Casson, Stuart A; Gray, Julie E; Hetherington, Alistair M

    2011-06-21

    Stomata are pores that regulate plant gas exchange [1]. They evolved more than 400 million years ago [2, 3], but the origin of their active physiological responses to endogenous and environmental cues is unclear [2-6]. Recent research suggests that the stomata of lycophytes and ferns lack pore closure responses to abscisic acid (ABA) and CO(2). This evidence led to the hypothesis that a fundamental transition from passive to active control of plant water balance occurred after the divergence of ferns 360 million years ago [7, 8]. Here we show that stomatal responses of the lycophyte Selaginella [9] to ABA and CO(2) are directly comparable to those of the flowering plant Arabidopsis [10]. Furthermore, we show that the underlying intracellular signaling pathways responsible for stomatal aperture control are similar in both basal and modern vascular plant lineages. Our evidence challenges the hypothesis that acquisition of active stomatal control of plant carbon and water balance represents a critical turning point in land plant evolution [7, 8]. Instead, we suggest that the critical evolutionary development is represented by the innovation of stomata themselves and that physiologically active stomatal control originated at least as far back as the emergence of the lycophytes (circa 420 million years ago) [11]. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.

    Science.gov (United States)

    Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

    2015-07-01

    Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen

  16. Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks

    Science.gov (United States)

    Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

    2015-01-01

    Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen

  17. Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

    Science.gov (United States)

    Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

    2017-10-01

    In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a

  18. The joint evolutionary histories of Wolbachia and mitochondria in Hypolimnas bolina

    Directory of Open Access Journals (Sweden)

    Roderick George K

    2009-03-01

    Full Text Available Abstract Background The interaction between the Blue Moon butterfly, Hypolimnas bolina, and Wolbachia has attracted interest because of the high prevalence of male-killing achieved within the species, the ecological consequences of this high prevalence, the intensity of selection on the host to suppress the infection, and the presence of multiple Wolbachia infections inducing different phenotypes. We examined diversity in the co-inherited marker, mtDNA, and the partitioning of this between individuals of different infection status, as a means to investigate the population biology and evolutionary history of the Wolbachia infections. Results Part of the mitochondrial COI gene was sequenced from 298 individuals of known infection status revealing ten different haplotypes. Despite very strong biological evidence that the sample represents a single species, the ten haplotypes did not fall within a monophyletic clade within the Hypolimnas genus, with one haplotype differing by 5% from the other nine. There were strong associations between infection status and mtDNA haplotype. The presence of wBol1 infection in association with strongly divergent haplotypes prompted closer examination of wBol1 genetic variation. This revealed the existence of two cryptic subtypes, wBol1a and wBol1b. The wBol1a infection, by far the most common, was in strict association with the single divergent mtDNA haplotype. The wBol1b infection was found with two haplotypes that were also observed in uninfected specimens. Finally, the wBol2 infection was associated with a large diversity of mtDNA haplotypes, most often shared with uninfected sympatric butterflies. Conclusion This data overall supports the hypothesis that high prevalence of male-killing Wolbachia (wBol1 in H. bolina is associated with very high transmission efficiency rather than regular horizontal transmission. It also suggests this infection has undergone a recent selective sweep and was introduced in this

  19. A clarified position for solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae

    Directory of Open Access Journals (Sweden)

    Causse Mathilde

    2008-12-01

    Full Text Available Abstract Background The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme. We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals. Results Molecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection. Conclusion The extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and

  20. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes.

    Science.gov (United States)

    Thinh, Van Ngoc; Mootnick, Alan R; Geissmann, Thomas; Li, Ming; Ziegler, Thomas; Agil, Muhammad; Moisson, Pierre; Nadler, Tilo; Walter, Lutz; Roos, Christian

    2010-03-12

    Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies. Based on phylogenetic tree reconstructions, several monophyletic clades were detected, corresponding to genera, species and subspecies. A significantly supported branching pattern was obtained for members of the genus Nomascus but not for the genus Hylobates. The phylogenetic relationships among the four genera were also not well resolved. Nevertheless, the new data permitted the estimation of divergence ages for all taxa for the first time and showed that most lineages emerged during four short time periods. In the first, between approximately 6.7 and approximately 8.3 mya, the four gibbon genera diverged from each other. In the second (approximately 3.0 - approximately 3.9 mya) and in the third period (approximately 1.3 - approximately 1.8 mya), Hylobates and Hoolock differentiated. Finally, between approximately 0.5 and approximately 1.1 mya, Hylobates lar diverged into subspecies. In contrast, differentiation of Nomascus into species and subspecies was a continuous and prolonged process lasting from approximately 4.2 until approximately 0.4 mya. Although relationships among gibbon taxa on various levels remain unresolved, the present study provides a more complete view of the evolutionary and biogeographic history of the hylobatid family, and a more solid genetic basis for the taxonomic classification of the surviving taxa. We also show that mtDNA constitutes a useful marker for the accurate identification of individual gibbons, a tool which is

  1. Similarity in Evolutionary Histories of Eocene Sediments from Subathu and Cambay Basins: Geochemical and Palaeontological Studies

    Science.gov (United States)

    Chaudhuri, S.; Halder, K.; Sarkar, S.

    2017-12-01

    elements may support increased erosional power, manifested as a quantitative increase in detrital flux for both the basins. So the geochemical and paleontological studies of Subathu and Cambay Shale Formations reveal similar evolutionary history in spite of their different tectonic scenario.

  2. Genetic structure and evolutionary history of three alpine sclerophyllous oaks in East Himalaya-Hengduan Mountains and adjacent regions

    Directory of Open Access Journals (Sweden)

    Li Feng

    2016-11-01

    Full Text Available The East Himalaya-Hengduan Mountains (EH-HM region has a high biodiversity and harbours numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Q. spinosa, Q. aquifolioides and Q. rehderiana using both cytoplasmic-nuclear markers and ecological niche models (ENMs, and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG to the last glacial maximum (LGM, which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

  3. Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions.

    Science.gov (United States)

    Feng, Li; Zheng, Qi-Jian; Qian, Zeng-Qiang; Yang, Jia; Zhang, Yan-Ping; Li, Zhong-Hu; Zhao, Gui-Fang

    2016-01-01

    The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides , and Quercus rehderiana ) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.

  4. A New Model of the Early Paleozoic Tectonics and Evolutionary History in the Northern Qinling, China

    Science.gov (United States)

    Dong, Yunpeng; Zhang, Guowei; Yang, Zhao; Qu, Hongjun; Liu, Xiaoming

    2010-05-01

    The Qinling Orogenic Belt extends from the Qinling Mountains in the west to the Dabie Mountains in the east. It lies between the North China and South China Blocks, and is bounded on the north by the Lushan fault and on the south by the Mianlue-Bashan-Xiangguang fault (Zhang et al., 2000). The Qinling Orogenic Belt itself is divided into the North and South Qinling Terranes by the Shangdan suture zone. Although the Shangdan zone is thought to represent the major suture separating the two blocks, there still exists debate about the timing and mechanism of convergence between these two blocks. For instance, some authors suggested an Early Paleozoic collision between the North China Block and South China Block (Ren et al., 1991; Kroner et al., 1993; Zhai et al., 1998). Others postulated left-lateral strike-slip faulting along the Shangdan suture at ca. 315 Ma and inferred a pre-Devonian collision between the two blocks (Mattauer et al., 1985; Xu et al., 1988). Geochemistry of fine-grained sediments in the Qinling Mountains was used to argue for a Silurian-Devonian collision (Gao et al., 1995). A Late Triassic collision has also been proposed (Sengor, 1985; Hsu et al., 1987; Wang et al., 1989), based on the formation of ultrahigh-pressure metamorphic rocks in the easternmost part of the Qinling Orogenic Belt at ~230 Ma (e.g., Li et al., 1993; Ames et al., 1996). Paleomagnetic data favor a Late Triassic-Middle Jurassic amalgamation of the North China and South China Blocks (Zhao and Coe, 1987; Enkin et al., 1992). It is clear that most authors thought that the Qinling Mountains are a collisional orogen, even they have different methods about the timing of the orogeny. Based on new detailed investigations, we propose a new model of the Early Paleozoic Tectonics and Evolutionary History between the North China and South China Blocks along the Shangdan Suture. The Shangdan suture is marked by a great number of ophiolites, island-arc volcanic rocks and other related rock

  5. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  6. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (hypericaceae).

    Science.gov (United States)

    Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel

    2015-03-01

    In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that "the present is the key to the past." Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account "ecological connectivity" through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an

  7. Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

    DEFF Research Database (Denmark)

    Palomo, Alejandro; Pedersen, Anders Gorm; Fowler, Jane

    2018-01-01

    The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary hi...

  8. GR 290 (ROMANO’S STAR). II. LIGHT HISTORY AND EVOLUTIONARY STATE

    Energy Technology Data Exchange (ETDEWEB)

    Polcaro, V. F.; Nesci, R.; Chieffi, A.; Viotti, R. F. [INAF-IAPS, Via del Fosso del Cavaliere, 100, I-00133 Roma (Italy); Maryeva, O. [Special Astrophysical Observatory of the Russian Academy of Science, Nizhnii Arkhyz, 369167 (Russian Federation); Calabresi, M.; Haver, R. [ARA, Via Carlo Emanuele I, 12A, I-00185 Roma (Italy); Galleti, S.; Gualandi, R. [INAF—Osservatorio Astronomico di Bologna, Via Ranzani 1, I-40127 Bologna (Italy); Mills, O. F.; Osborn, W. H. [Yerkes Observatory, 373 W. Geneva Street, Williams Bay, WI 53115 (United States); Pasquali, A. [Astronomisches Rechen-Institut, Zentrum für Astronomie, Universität Heidelberg, Mönchhofstrasse 12-14, D-69120 Heidelberg (Germany); Rossi, C. [Università La Sapienza, Pza A.Moro 5, I-00185 Roma (Italy); Vasilyeva, T., E-mail: vitofrancesco.polcaro@iaps.inaf.it [Pulkovo Astronomical Observatory, 196140, Saint-Petersburg, Pulkovskoye chaussee 65/1 (Russian Federation)

    2016-06-01

    We have investigated the past light history of the luminous variable star GR 290 (M33/V532, Romano’s Star) in the M33 galaxy, and collected new spectrophotometric observations in order to analyze links between this object, the LBV category, and the Wolf–Rayet stars of the nitrogen sequence. We have built the historical light curve of GR 290 back to 1901, from old observations of the star found in several archival plates of M33. These old recordings together with published and new data on the star allowed us to infer that for at least half a century the star was in a low luminosity state, with B ≃ 18–19, most likely without brighter luminosity phases. After 1960, five large variability cycles of visual luminosity were recorded. The amplitude of the oscillations was seen increasing toward the 1992–1994 maximum, then decreasing during the last maxima. The recent light curve indicates that the photometric variations have been quite similar in all the bands and that the B – V color index has been constant within ±0.1{sup m} despite the 1.5{sup m} change of the visual luminosity. The spectrum of GR 290 at the large maximum of 1992–94 was equivalent to late-B-type, while, during 2002–2014, it varied between WN10h-11h near the visual maxima to WN8h-9h at the luminosity minima. We have detected, during this same period, a clear anti-correlation between the visual luminosity, the strength of the He ii 4686 Å emission line, the strength of the 4600–4700 Å lines’ blend, and the spectral type. From a model analysis of the spectra collected during the whole 2002–2014 period, we find that the Rosseland radius R {sub 2/3}, changed between the minimum and maximum luminosity phases by a factor of three while T {sub eff} varied between about 33,000 and 23,000 K. We confirm that the bolometric luminosity of the star has not been constant, but has increased by a factor of ∼1.5 between minimum and maximum luminosity, in phase with the apparent luminosity

  9. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

    DEFF Research Database (Denmark)

    Jacobsen, Magnus W.; Hansen, Michael Møller; Orlando, Ludovic

    2012-01-01

    the evolutionary history of the endangered Danish North Sea houting (NSH) and other closely related Danish and Baltic European lake whitefish (ELW). Two well-supported clades were found within both ELW and NSH, probably reflecting historical introgression via Baltic migrants. Although ELW and NSH...... colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long-term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence...

  10. Novel stable structure of Li3PS4 predicted by evolutionary algorithm under high-pressure

    Directory of Open Access Journals (Sweden)

    S. Iikubo

    2018-01-01

    Full Text Available By combining theoretical predictions and in-situ X-ray diffraction under high pressure, we found a novel stable crystal structure of Li3PS4 under high pressures. At ambient pressure, Li3PS4 shows successive structural transitions from γ-type to β-type and from β-type to α type with increasing temperature, as is well established. In this study, an evolutionary algorithm successfully predicted the γ-type crystal structure at ambient pressure and further predicted a possible stable δ-type crystal structures under high pressure. The stability of the obtained structures is examined in terms of both static and dynamic stability by first-principles calculations. In situ X-ray diffraction using a synchrotron radiation revealed that the high-pressure phase is the predicted δ-Li3PS4 phase.

  11. Beyond mental health: an evolutionary analysis of development under risky and supportive environmental conditions: an introduction to the special section.

    Science.gov (United States)

    Ellis, Bruce J; Bjorklund, David F

    2012-05-01

    Evolutionary approaches to behavior have increasingly captured the attention and imagination of academics and laypeople alike. One part of this trend has been the increasing influence of evolutionary theory in developmental science. The articles in this special section of Developmental Psychology attempt to demonstrate why an evolutionary analysis is needed to more fully understand the contexts and contingencies of development. The 3 theoretical articles articulate the core evolutionary logic underlying conditional adaptation (and maladaptation) to both stressful and supportive environmental conditions over development. These theoretical articles are then followed by 9 empirical articles that test these evolutionary-developmental theories and hypotheses. Finally, 6 commentaries evaluate the prospects, pitfalls, and implications of this body of work.

  12. Revisiting the age, evolutionary history and species level diversity of the genus Hydra (Cnidaria: Hydrozoa).

    Science.gov (United States)

    Schwentner, Martin; Bosch, Thomas C G

    2015-10-01

    The genus Hydra has long served as a model system in comparative immunology, developmental and evolutionary biology. Despite its relevance for fundamental research, Hydra's evolutionary origins and species level diversity are not well understood. Detailed previous studies using molecular techniques identified several clades within Hydra, but how these are related to described species remained largely an open question. In the present study, we compiled all published sequence data for three mitochondrial and nuclear genes (COI, 16S and ITS), complemented these with some new sequence data and delimited main genetic lineages (=hypothetical species) objectively by employing two DNA barcoding approaches. Conclusions on the species status of these main lineages were based on inferences of reproductive isolation. Relevant divergence times within Hydra were estimated based on relaxed molecular clock analyses with four genes (COI, 16S, EF1α and 28S) and four cnidarians fossil calibration points All in all, 28 main lineages could be delimited, many more than anticipated from earlier studies. Because allopatric distributions were common, inferences of reproductive isolation often remained ambiguous but reproductive isolation was rarely refuted. Our results support three major conclusions which are central for Hydra research: (1) species level diversity was underestimated by molecular studies; (2) species affiliations of several crucial 'workhorses' of Hydra evolutionary research were wrong and (3) crown group Hydra originated ∼200mya. Our results demonstrate that the taxonomy of Hydra requires a thorough revision and that evolutionary studies need to take this into account when interspecific comparisons are made. Hydra originated on Pangea. Three of four extant groups evolved ∼70mya ago, possibly on the northern landmass of Laurasia. Consequently, Hydra's cosmopolitan distribution is the result of transcontinental and transoceanic dispersal. Copyright © 2015 Elsevier Inc

  13. Graphing evolutionary pattern and process: a history of techniques in archaeology and paleobiology.

    Science.gov (United States)

    Lyman, R Lee

    2009-02-01

    Graphs displaying evolutionary patterns are common in paleontology and in United States archaeology. Both disciplines subscribed to a transformational theory of evolution and graphed evolution as a sequence of archetypes in the late nineteenth and early twentieth centuries. U.S. archaeologists in the second decade of the twentieth century, and paleontologists shortly thereafter, developed distinct graphic styles that reflected the Darwinian variational model of evolution. Paleobiologists adopted the view of a species as a set of phenotypically variant individuals and graphed those variations either as central tendencies or as histograms of frequencies of variants. Archaeologists presumed their artifact types reflected cultural norms of prehistoric artisans and the frequency of specimens in each type reflected human choice and type popularity. They graphed cultural evolution as shifts in frequencies of specimens representing each of several artifact types. Confusion of pattern and process is exemplified by a paleobiologist misinterpreting the process illustrated by an archaeological graph, and an archaeologist misinterpreting the process illustrated by a paleobiological graph. Each style of graph displays particular evolutionary patterns and implies particular evolutionary processes. Graphs of a multistratum collection of prehistoric mammal remains and a multistratum collection of artifacts demonstrate that many graph styles can be used for both kinds of collections.

  14. Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

    KAUST Repository

    Ishikawa, Masakazu

    2016-06-19

    Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

  15. Evolutionary history and phylodynamics of influenza A and B neuraminidase (NA genes inferred from large-scale sequence analyses.

    Directory of Open Access Journals (Sweden)

    Jianpeng Xu

    Full Text Available Influenza neuraminidase (NA is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking.Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The d(N/d(S ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding.The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance.

  16. Ancient connections among the European rivers and watersheds revealed from the evolutionary history of the genus Telestes (Actinopterygii; Cypriniformes)

    Science.gov (United States)

    Buj, Ivana; Ćaleta, Marko; Šanda, Radek; Geiger, Matthias F.; Freyhof, Jörg; Machordom, Annie; Vukić, Jasna

    2017-01-01

    In order to better understand the complex geologic history of the Mediterranean area, we have analysed evolutionary history, phylogeographic structure and molecular diversity of freshwater fishes belonging to the genus Telestes. As primary freshwater fishes distributed largely in the Mediterranean basin, this genus represents a suitable model system for investigating the historical biogeography of freshwater drainage systems in southern Europe. In this investigation we have included samples representing all Telestes species and based our analyses on one mitochondrial and one nuclear gene. We have investigated phylogenetic structure inside the genus Telestes, estimated divergence times, reconstructed ancestral distribution ranges and described intraspecific molecular diversity. Diversification of Telestes started in the Early Miocene, when the ancestors of T. souffia, lineage comprising T. croaticus and T. fontinalis, and the one comprising T. pleurobipunctatus and T. beoticus got isolated. The remaining species are genetically more closely related and form a common cluster in the recovered phylogenetic trees. Complex geological history of southern Europe, including formation of continental bridges, fragmentation of landmass, closing of the sea corridor, local tectonic activities, led to complicated biogeographical pattern of this genus, caused by multiple colonization events and passovers between ancient rivers and water basins. Especially pronounced diversity of Telestes found in the Adriatic watershed in Croatia and Bosnia and Herzegovina is a consequence of a triple colonization of this area by different lineages, which led to an existence of genetically distinct species in neighboring areas. Significant intraspecific structuring is present in T. souffia, T. muticellus, T. croaticus and T. pleurobipunctatus. Besides in well-structured species, elevated levels of genetic polymorphism were found inside T. turskyi and T. ukliva, as a consequence of their old origin

  17. Contrasting population-level responses to Pleistocene climatic oscillations in an alpine bat revealed by complete mitochondrial genomes and evolutionary history inference

    DEFF Research Database (Denmark)

    Alberdi, Antton; Gilbert, M. Thomas P; Razgour, Orly

    2015-01-01

    Aim: We used an integrative approach to reconstruct the evolutionary history of the alpine long-eared bat, Plecotus macrobullaris, to test whether the variable effects of Pleistocene climatic oscillations across geographical regions led to contrasting population-level demographic histories within...

  18. Paleotemperature proxies from leaf fossils reinterpreted in light of evolutionary history.

    Science.gov (United States)

    Little, Stefan A; Kembel, Steven W; Wilf, Peter

    2010-12-22

    Present-day correlations between leaf physiognomic traits (shape and size) and climate are widely used to estimate paleoclimate using fossil floras. For example, leaf-margin analysis estimates paleotemperature using the modern relation of mean annual temperature (MAT) and the site-proportion of untoothed-leaf species (NT). This uniformitarian approach should provide accurate paleoclimate reconstructions under the core assumption that leaf-trait variation principally results from adaptive environmental convergence, and because variation is thus largely independent of phylogeny it should be constant through geologic time. Although much research acknowledges and investigates possible pitfalls in paleoclimate estimation based on leaf physiognomy, the core assumption has never been explicitly tested in a phylogenetic comparative framework. Combining an extant dataset of 21 leaf traits and temperature with a phylogenetic hypothesis for 569 species-site pairs at 17 sites, we found varying amounts of non-random phylogenetic signal in all traits. Phylogenetic vs. standard regressions generally support prevailing ideas that leaf-traits are adaptively responding to temperature, but wider confidence intervals, and shifts in slope and intercept, indicate an overall reduced ability to predict climate precisely due to the non-random phylogenetic signal. Notably, the modern-day relation of proportion of untoothed taxa with mean annual temperature (NT-MAT), central in paleotemperature inference, was greatly modified and reduced, indicating that the modern correlation primarily results from biogeographic history. Importantly, some tooth traits, such as number of teeth, had similar or steeper slopes after taking phylogeny into account, suggesting that leaf teeth display a pattern of exaptive evolution in higher latitudes. This study shows that the assumption of convergence required for precise, quantitative temperature estimates using present-day leaf traits is not supported by

  19. On the evolutionary and biogeographic history of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.).

    Science.gov (United States)

    DeChaine, Eric G; Anderson, Stacy A; McNew, Jennifer M; Wendling, Barry M

    2013-01-01

    Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting

  20. On the evolutionary and biogeographic history of Saxifraga sect. Trachyphyllum (Gaud. Koch (Saxifragaceae Juss..

    Directory of Open Access Journals (Sweden)

    Eric G DeChaine

    Full Text Available Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss. provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud. Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and

  1. Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

    Directory of Open Access Journals (Sweden)

    Jones Huw

    2011-11-01

    Full Text Available Abstract Background Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm. Results The evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture. Conclusions The discovery of population structure, combined with knowledge of associated phenotypes and

  2. Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis.

    Science.gov (United States)

    Ishikawa, Masakazu; Yuyama, Ikuko; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

    2016-08-03

    Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. L'etat, c'est moi. Fifty years of history and philosophy of evolutionary biology.

    Science.gov (United States)

    Ruse, Michael

    2016-01-01

    I reflect on my fifty-year history as a philosopher of biology, showing how it has taken me from rather narrow analytic studies, through the history of ideas, and now on to issues to do with science and religion. I argue that moral concerns were and still are a major motivation behind what I do and write. Copyright: © 2016 by Fabrizio Serra editore, Pisa · Roma.

  4. Life history lability underlies rapid climate niche evolution in the angiosperm clade Montiaceae.

    Science.gov (United States)

    Matthew Ogburn, R; Edwards, Erika J

    2015-11-01

    Despite the recent focus on phylogenetic niche conservatism in macroevolutionary studies, many clades have diversified widely along multiple niche dimensions. The factors underlying lineage-specific niche lability are still not well understood. We examined morphological and climate niche evolution in Montiaceae (Caryophyllales), an ecologically variable plant lineage distributed primarily along the mountain chains of the western Americas. Montiaceae inhabit a broader range of temperatures than their relatives, with an increase in the evolutionary rate of temperature niche diversification at the node subtending this clade. Within Montiaceae, life history is highly labile and significantly correlated with temperature, with perennials consistently occurring in cooler environments. This elevated evolutionary lability facilitated repeated shifts between habitats as new environments were created by post-Eocene orogenic events and aridification in the western Americas. The shifts between annual and perennial forms are elaborations of an underlying rosette body plan in most cases, and may involve simple alterations in biomass allocation. Montiaceae stand as another clear counterexample to phylogenetic niche conservatism, and demonstrate a mechanism by which pronounced ecological shifts may occur frequently and rapidly among closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree

    Science.gov (United States)

    Jofré, Paula; Das, Payel; Bertranpetit, Jaume; Foley, Robert

    2017-05-01

    Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an evolutionary tree from which three branches emerge. These are interpreted as stellar populations that separate in age and kinematics and can be thus attributed to the thin disc, the thick disc and an intermediate population of probable distinct origin. We further find six lone stars of intermediate age that could not be assigned to any population with enough statistical significance. Combining the ages of the stars with their position on the tree, we are able to quantify the mean rate of chemical enrichment of each of the populations, and thus show in a purely empirical way that the star formation rate in the thick disc is much higher than that in the thin disc. We are also able to estimate the relative contribution of dynamical processes such as radial migration and disc heating to the distribution of chemical elements in the solar neighbourhood. Our method offers an alternative approach to chemical tagging methods with the advantage of visualizing the behaviour of chemical elements in evolutionary trees. This offers a new way to search for 'common ancestors' that can reveal the origin of solar neighbourhood stars.

  6. Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations.

    Science.gov (United States)

    Adebali, Ogun; Reznik, Alexander O; Ory, Daniel S; Zhulin, Igor B

    2016-10-01

    Predicting the phenotypic effects of mutations has become an important application in clinical genetic diagnostics. Computational tools evaluate the behavior of the variant over evolutionary time and assume that variations seen during the course of evolution are probably benign in humans. However, current tools do not take into account orthologous/paralogous relationships. Paralogs have dramatically different roles in Mendelian diseases. For example, whereas inactivating mutations in the NPC1 gene cause the neurodegenerative disorder Niemann-Pick C, inactivating mutations in its paralog NPC1L1 are not disease-causing and, moreover, are implicated in protection from coronary heart disease. We identified major events in NPC1 evolution and revealed and compared orthologs and paralogs of the human NPC1 gene through phylogenetic and protein sequence analyses. We predicted whether an amino acid substitution affects protein function by reducing the organism's fitness. Removing the paralogs and distant homologs improved the overall performance of categorizing disease-causing and benign amino acid substitutions. The results show that a thorough evolutionary analysis followed by identification of orthologs improves the accuracy in predicting disease-causing missense mutations. We anticipate that this approach will be used as a reference in the interpretation of variants in other genetic diseases as well.Genet Med 18 10, 1029-1036.

  7. Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes

    DEFF Research Database (Denmark)

    Ulvskov, Peter; Paiva, Dionisio Soares; Domozych, David

    2013-01-01

    The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved....... In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from the Rhodophyta and Virideplantae and the well-defined CAZy database on glycosyltransferases were included in the analysis. The number...... of glycosyltransferases found in the Rhodophyta and Chlorophyta are generally much lower then in land plants (Embryophyta). Three specific features exhibited by land plants increase the number of glycosyltransferases in their genomes: (1) cell wall biosynthesis, the more complex land plant cell walls require a larger...

  8. Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle.

    Science.gov (United States)

    Bunce, Michael; Szulkin, Marta; Lerner, Heather R L; Barnes, Ian; Shapiro, Beth; Cooper, Alan; Holdaway, Richard N

    2005-01-01

    Prior to human settlement 700 years ago New Zealand had no terrestrial mammals--apart from three species of bats--instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10-15 kg; 2-3 m wingspan) was 30%-40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.

  9. Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle.

    Directory of Open Access Journals (Sweden)

    Michael Bunce

    2005-01-01

    Full Text Available Prior to human settlement 700 years ago New Zealand had no terrestrial mammals--apart from three species of bats--instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10-15 kg; 2-3 m wingspan was 30%-40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja, and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.

  10. Roots of angiosperm formins: The evolutionary history of plant FH2 domain-containing proteins

    Directory of Open Access Journals (Sweden)

    Žárský Viktor

    2008-04-01

    Full Text Available Abstract Background Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. Results The Rho GTPase-binding domain (GBD/FH3 reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm formins that define a specific branch (Class III of the formin family. Conclusion We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms.

  11. Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae).

    Science.gov (United States)

    Qi, Xin-Shuai; Chen, Chen; Comes, Hans Peter; Sakaguchi, Shota; Liu, Yi-Hui; Tanaka, Nobuyuki; Sakio, Hitoshi; Qiu, Ying-Xiong

    2012-10-01

    East Asia's temperate deciduous forests served as sanctuary for Tertiary relict trees, but their ages and response to past climate change remain largely unknown. To address this issue, we elucidated the evolutionary and population demographic history of Cercdiphyllum, comprising species in China/Japan (Cercdiphyllum japonicum) and central Japan (Cercdiphyllum magnificum). Fifty-three populations were genotyped using chloroplast and ribosomal DNA sequences and microsatellite loci to assess molecular structure and diversity in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modelling. Late Tertiary climate cooling was reflected in a relatively recent speciation event, dated at the Mio-/Pliocene boundary. During glacials, the warm-temperate C. japonicum experienced massive habitat losses in some areas (north-central China/north Japan) but increases in others (southwest/-east China, East China Sea landbridge, south Japan). In China, the Sichuan Basin and/or the middle-Yangtze were source areas of postglacial northward recolonization; in Japan, this may have been facilitated through introgressive hybridization with the cool-temperate C. magnificum. Our findings challenge the notion of relative evolutionary and demographic stability of Tertiary relict trees, and may serve as a guideline for assessing the impact of Neogene climate change on the evolution and distribution of East Asian temperate plants. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  12. Evolution of male life histories and age-dependent sexual signals under female choice

    Directory of Open Access Journals (Sweden)

    Joel J. Adamson

    2013-12-01

    Full Text Available Sexual selection theory models evolution of sexual signals and preferences using simple life histories. However, life-history models predict that males benefit from increasing sexual investment approaching old age, producing age-dependent sexual traits. Age-dependent traits require time and energy to grow, and will not fully mature before individuals enter mating competition. Early evolutionary stages pose several problems for these traits. Age-dependent traits suffer from strong viability selection and gain little benefit from mate choice when rare. Few males will grow large traits, and they will rarely encounter choosy females. The evolutionary origins of age-dependent traits therefore remain unclear. I used numerical simulations to analyze evolution of preferences, condition (viability and traits in an age-structured population. Traits in the model depended on age and condition (“good genes” in a population with no genetic drift. I asked (1 if age-dependent indicator traits and their preferences can originate depending on the strength of selection and the size of the trait; (2 which mode of development (age-dependent versus age-independent eventually predominates when both modes occur in the population; and (3 if age-independent traits can invade a population with age-dependent traits. Age-dependent traits evolve under weaker selection and at smaller sizes than age-independent traits. This result held in isolation and when the types co-occur. Evolution of age-independent traits depends only on trait size, whereas evolution of age-dependent traits depends on both strength of selection and growth rate. Invasion of age-independence into populations with established traits followed a similar pattern with age-dependence predominating at small trait sizes. I suggest that reduced adult mortality facilitates sexual selection by favoring the evolution of age-dependent sexual signals under weak selection.

  13. Evolutionary ecology of endocrine-mediated life-history variation in the garter snake Thamnophis elegans.

    Science.gov (United States)

    Sparkman, Amanda M; Vleck, Carol M; Bronikowski, Anne M

    2009-03-01

    The endocrine system plays an integral role in the regulation of key life-history traits. Insulin-like growth factor-1 (IGF-1) is a hormone that promotes growth and reproduction, and it has been implicated in the reduction of lifespan. IGF-1 is also capable of responding plastically to environmental stimuli such as resource availability and temperature. Thus pleiotropic control of life-history traits by IGF-1 could provide a mechanism for the evolution of correlated life-history traits in a new or changing environment. An ideal system in which to investigate the role of IGF-1 in life-history evolution exists in two ecotypes of the garter snake Thamnophis elegans, which derive from a single recent ancestral source but have evolved genetically divergent life-history characteristics. Snakes from meadow populations near Eagle Lake, California (USA) exhibit slower growth rates, lower annual reproductive output, and longer median adult lifespans relative to populations along the lakeshore. We hypothesized that the IGF-1 system has differentiated between these ecotypes and can account for increased growth and reproduction and reduced survival in lakeshore vs. meadow snakes. We tested for a difference in plasma IGF-1 levels in free-ranging snakes from replicate populations of each ecotype over three years. IGF-1 levels were significantly associated with adult body size, reproductive output, and season in a manner that reflects established differences in prey ecology and age/size-specific reproduction between the ecotypes. These findings are discussed in the context of theoretical expectations for a tradeoff between reproduction and lifespan that is mediated by pleiotropic endocrine mechanisms.

  14. Variation in stem anatomical characteristics of Campanuloideae species in relation to evolutionary history and ecological preferences.

    Directory of Open Access Journals (Sweden)

    Fritz Hans Schweingruber

    Full Text Available BACKGROUND: The detailed knowledge of plant anatomical characters and their variation among closely related taxa is key to understanding their evolution and function. We examined anatomical variation in 46 herbaceous taxa from the subfamily Campanuloideae (Campanulaceae to link this information with their phylogeny, ecology and comparative material of 56 woody tropical taxa from the subfamily Lobelioideae. The species studied covered major environmental gradients from Mediterranean to Arctic zones, allowing us to test hypotheses on the evolution of anatomical structure in relation to plant competitive ability and ecological preferences. METHODOLOGY/PRINCIPAL FINDINGS: To understand the evolution of anatomical diversity, we reconstructed the phylogeny of studied species from nucleotide sequences and examined the distribution of anatomical characters on the resulting phylogenetic tree. Redundancy analysis, with phylogenetic corrections, was used to separate the evolutionary inertia from the adaptation to the environment. A large anatomical diversity exists within the Campanuloideae. Traits connected with the quality of fibres were the most congruent with phylogeny, and the Rapunculus 2 ("phyteumoid" clade was especially distinguished by a number of characters (absence of fibres, pervasive parenchyma, type of rays from two other clades (Campanula s. str. and Rapunculus 1 characterized by the dominance of fibres and the absence of parenchyma. Septate fibres are an exclusive trait in the Lobelioideae, separating it clearly from the Campanuloideae where annual rings, pervasive parenchyma and crystals in the phellem are characteristic features. CONCLUSIONS/SIGNIFICANCE: Despite clear phylogenetic inertia in the anatomical features studied, the ecological attributes and plant height had a significant effect on anatomical divergence. From all three evolutionary clades, the taller species converged towards similar anatomical structure, characterized by a

  15. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra).

    Science.gov (United States)

    Rodríguez, Fernando; Pérez, Trinidad; Hammer, Sabine E; Albornoz, Jesús; Domínguez, Ana

    2010-07-22

    The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range. We found discordant microsatellite (musat) and mitochondrial (mt) DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE), at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya), in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (< 0.5 mya). New microsatellite multilocus genotypes added to previously published data revealed differences between every pair of subspecies, forming three well defined groups (musatW, musatC and musatE) also with a strong geographic signature. Grouping does not correspond with the mitochondrial lineages but is closer to morphology and taxonomic classification. Recent drastic reductions in population size can be noted for the subspecies

  16. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra

    Directory of Open Access Journals (Sweden)

    Albornoz Jesús

    2010-07-01

    Full Text Available Abstract Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region and microsatellites (20 loci to include all subspecies and cover its entire distribution range. Results We found discordant microsatellite (μsat and mitochondrial (mt DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE, at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya, in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly

  17. Evolutionary history of the genus Tarentola (Gekkota: Phyllodactylidae from the Mediterranean Basin, estimated using multilocus sequence data

    Directory of Open Access Journals (Sweden)

    Rato Catarina

    2012-01-01

    Full Text Available Abstract Background The pronounced morphological conservatism within Tarentola geckos contrasted with a high genetic variation in North Africa, has led to the hypothesis that this group could represent a cryptic species complex, a challenging system to study especially when trying to define distinct evolutionary entities and address biogeographic hypotheses. In the present work we have re-examined the phylogenetic and phylogeographic relationships between and within all Mediterranean species of Tarentola, placing the genealogies obtained into a temporal framework. In order to do this, we have investigated the sequence variation of two mitochondrial (12S rRNA and 16S rRNA, and four nuclear markers (ACM4, PDC, MC1R, and RAG2 for 384 individuals of all known Mediterranean Tarentola species, so that their evolutionary history could be assessed. Results Of all three generated genealogies (combined mtDNA, combined nDNA, and mtDNA+nDNA we prefer the phylogenetic relationships obtained when all genetic markers are combined. A total of 133 individuals, and 2,901 bp of sequence length, were used in this analysis. The phylogeny obtained for Tarentola presents deep branches, with T. annularis, T. ephippiata and T. chazaliae occupying a basal position and splitting from the remaining species around 15.38 Mya. Tarentola boehmei is sister to all other Mediterranean species, from which it split around 11.38 Mya. There are also two other major groups: 1 the T. mauritanica complex present in North Africa and Europe; and 2 the clade formed by the T. fascicularis/deserti complex, T. neglecta and T. mindiae, occurring only in North Africa. The cladogenesis between these two groups occurred around 8.69 Mya, coincident with the late Miocene. Contrary to what was initially proposed, T. neglecta and T. mindiae are sister taxa to both T. fascicularis and T. deserti. Conclusions At least in the Iberian Peninsula and Northwest Africa, the lineages obtained have some

  18. A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus: an evolutionary history of camelidae

    Directory of Open Access Journals (Sweden)

    Meng He

    2007-07-01

    Full Text Available Abstract Background The family Camelidae that evolved in North America during the Eocene survived with two distinct tribes, Camelini and Lamini. To investigate the evolutionary relationship between them and to further understand the evolutionary history of this family, we determined the complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus, the only wild survivor of the Old World camel. Results The mitochondrial genome sequence (16,680 bp from C. bactrianus ferus contains 13 protein-coding, two rRNA, and 22 tRNA genes as well as a typical control region; this basic structure is shared by all metazoan mitochondrial genomes. Its protein-coding region exhibits codon usage common to all mammals and possesses the three cryptic stop codons shared by all vertebrates. C. bactrianus ferus together with the rest of mammalian species do not share a triplet nucleotide insertion (GCC that encodes a proline residue found only in the nd1 gene of the New World camelid Lama pacos. This lineage-specific insertion in the L. pacos mtDNA occurred after the split between the Old and New World camelids suggests that it may have functional implication since a proline insertion in a protein backbone usually alters protein conformation significantly, and nd1 gene has not been seen as polymorphic as the rest of ND family genes among camelids. Our phylogenetic study based on complete mitochondrial genomes excluding the control region suggested that the divergence of the two tribes may occur in the early Miocene; it is much earlier than what was deduced from the fossil record (11 million years. An evolutionary history reconstructed for the family Camelidae based on cytb sequences suggested that the split of bactrian camel and dromedary may have occurred in North America before the tribe Camelini migrated from North America to Asia. Conclusion Molecular clock analysis of complete mitochondrial genomes from C. bactrianus ferus and L

  19. First endemic freshwaterGammarusfrom Crete and its evolutionary history-an integrative taxonomy approach.

    Science.gov (United States)

    Hupało, Kamil; Mamos, Tomasz; Wrzesińska, Weronika; Grabowski, Michał

    2018-01-01

    The Mediterranean islands are known as natural laboratories of evolution with a high level of endemic biodiversity. However, most biodiversity assessments have focused mainly on terrestrial and marine fauna, leaving the freshwater animals aside. Crete is one of the largest islands in the Mediterranean Basin, with a long history of isolation from the continental mainland. Gammarid amphipods are often dominant in macrozoobenthic communities in European inland waters. They are widely used in biomonitoring and exotoxicological studies. Herein, we describe Gammarus plaitisi sp. nov., endemic to Cretan streams, based on morphological characters and a set of molecular species delimitation methods using mitochondrial cytochrome oxidase subunit I and 16S rRNA genes as well as nuclear 28S rDNA, ITS1 and EF1-alpha genes. The divergence of the new species is strongly connected with the geological history of the island supporting its continental origin.

  20. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

    OpenAIRE

    Putnam, Hollie M.; Adams, Diane K.; Zelzion, Ehud; Wagner, Nicole E.; Qiu, Huan; Mass, Tali; Falkowski, Paul G.; Gates, Ruth D.; Bhattacharya, Debashish

    2017-01-01

    We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtD...

  1. Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

    KAUST Repository

    Choat, John. H.

    2012-09-05

    Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well-supported clades with mid Pliocene/Pleistocene diversification. Twenty-two reciprocally monophyletic sister-species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London.

  2. Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants

    Directory of Open Access Journals (Sweden)

    Maria S. Krasnikova

    2013-01-01

    Full Text Available PCR-based approach was used as a phylogenetic profiling tool to probe genomic DNA samples from representatives of evolutionary distant moss taxa, namely, classes Bryopsida, Tetraphidopsida, Polytrichopsida, Andreaeopsida, and Sphagnopsida. We found relatives of all Physcomitrella patens miR390 and TAS3-like loci in these plant taxa excluding Sphagnopsida. Importantly, cloning and sequencing of Marchantia polymorpha genomic DNA showed miR390 and TAS3-like sequences which were also found among genomic reads of M. polymorpha at NCBI database. Our data suggest that the ancient plant miR390-dependent TAS molecular machinery firstly evolved to target AP2-like mRNAs in Marchantiophyta and only then both ARF- and AP2-specific mRNAs in mosses. The presented analysis shows that moss TAS3 families may undergone losses of tasiAP2 sites during evolution toward ferns and seed plants. These data confirm that miR390-guided genes coding for ARF- and AP2-specific ta-siRNAs have been gradually changed during land plant evolution.

  3. Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

    Directory of Open Access Journals (Sweden)

    Vanessa Rodrigues Paixão-Côrtes

    Full Text Available Paired box (PAX genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.

  4. Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history.

    Science.gov (United States)

    Sansom, Robert S; Randle, Emma; Donoghue, Philip C J

    2015-02-07

    The fossil record of early vertebrates has been influential in elucidating the evolutionary assembly of the gnathostome bodyplan. Understanding of the timing and tempo of vertebrate innovations remains, however, mired in a literal reading of the fossil record. Early jawless vertebrates (ostracoderms) exhibit restriction to shallow-water environments. The distribution of their stratigraphic occurrences therefore reflects not only flux in diversity, but also secular variation in facies representation of the rock record. Using stratigraphic, phylogenetic and palaeoenvironmental data, we assessed the veracity of the fossil records of the jawless relatives of jawed vertebrates (Osteostraci, Galeaspida, Thelodonti, Heterostraci). Non-random models of fossil recovery potential using Palaeozoic sea-level changes were used to calculate confidence intervals of clade origins. These intervals extend the timescale for possible origins into the Upper Ordovician; these estimates ameliorate the long ghost lineages inferred for Osteostraci, Galeaspida and Heterostraci, given their known stratigraphic occurrences and stem-gnathostome phylogeny. Diversity changes through the Silurian and Devonian were found to lie within the expected limits predicted from estimates of fossil record quality indicating that it is geological, rather than biological factors, that are responsible for shifts in diversity. Environmental restriction also appears to belie ostracoderm extinction and demise rather than competition with jawed vertebrates.

  5. Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.

    Science.gov (United States)

    Zhang, W Q; Zhang, M H

    2013-09-03

    Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.

  6. Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis

    Directory of Open Access Journals (Sweden)

    Klingenspor Martin

    2009-01-01

    Full Text Available Abstract Background Uncoupling protein 1 (UCP1 is a mitochondrial anion carrier, expressed in brown adipose tissue (BAT of Eutherians. UCP1 is responsible for uncoupling mitochondrial proton transport from the production of ATP, thereby dissipating heat; it is essential for non-shivering thermogenesis (NST in mammalian BAT. UCP1 orthologs have been identified in non-Eutherian mammals, fish and amphibians. Yet, UCP1 has a unique function in Eutherians in that it is necessary in the production of heat (NST. As such, this study aims to determine the evolutionary mode of UCP1 in Eutherians, where there is clear evidence of UCP1-dependent NST in BAT. Results Models of adaptive evolution through phylogenetic analysis of amino acid sequences by maximum likelihood were implemented to determine the mode of UCP1 protein evolution in Eutherians. An increase in the rate of amino acid substitutions on the branch leading to Eutherians is observed, but is best explained by relaxed constraints, not positive selection. Further, evidence for branch and site heterogeneity in selection pressures, as well as divergent selection pressures between UCP1 and its paralogs (UCP2-3 is observed. Conclusion We propose that the unique thermogenic function of UCP1 in Eutherians may be best explained by neutral processes. Along with other evidence, this suggests that the primary biochemical properties of UCP1 may not differ between Eutherians and non-Eutherians.

  7. Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases.

    Science.gov (United States)

    Cahn, Jackson K B; Brinkmann-Chen, Sabine; Buller, Andrew R; Arnold, Frances H

    2016-07-01

    The duplication of protein structural domains has been proposed as a common mechanism for the generation of new protein folds. A particularly interesting case is the class II ketol-acid reductoisomerase (KARI), which putatively arose from an ancestral class I KARI by duplication of the C-terminal domain and corresponding loss of obligate dimerization. As a result, the class II enzymes acquired a deeply embedded figure-of-eight knot. To test this evolutionary hypothesis we constructed a novel class II KARI by duplicating the C-terminal domain of a hyperthermostable class I KARI. The new protein is monomeric, as confirmed by gel filtration and X-ray crystallography, and has the deeply knotted class II KARI fold. Surprisingly, its catalytic activity is nearly unchanged from the parent KARI. This provides strong evidence in support of domain duplication as the mechanism for the evolution of the class II KARI fold and demonstrates the ability of domain duplication to generate topological novelty in a function-neutral manner. © 2015 The Protein Society.

  8. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species.

    Science.gov (United States)

    Zhang, Shao-Qian; Che, Li-Heng; Li, Yun; Dan Liang; Pang, Hong; Ślipiński, Adam; Zhang, Peng

    2018-01-15

    Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic. The species-poor Nosodendridae is robustly recovered in a novel position sister to Staphyliniformia, Bostrichiformia, and Cucujiformia. Our divergence time analyses suggest that the crown group of extant beetles occurred ~297 million years ago (Mya) and that ~64% of families originated in the Cretaceous. Most of the herbivorous families experienced a significant increase in diversification rate during the Cretaceous, thus suggesting that the rise of angiosperms in the Cretaceous may have been an 'evolutionary impetus' driving the hyperdiversity of herbivorous beetles.

  9. Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

    Science.gov (United States)

    Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

    2017-10-03

    Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

  10. Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes

    Science.gov (United States)

    Ulvskov, Peter; Paiva, Dionisio Soares; Domozych, David; Harholt, Jesper

    2013-01-01

    The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved. In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from the Rhodophyta and Virideplantae and the well-defined CAZy database on glycosyltransferases were included in the analysis. The number of glycosyltransferases found in the Rhodophyta and Chlorophyta are generally much lower then in land plants (Embryophyta). Three specific features exhibited by land plants increase the number of glycosyltransferases in their genomes: (1) cell wall biosynthesis, the more complex land plant cell walls require a larger number of glycosyltransferases for biosynthesis, (2) a richer set of protein glycosylation, and (3) glycosylation of secondary metabolites, demonstrated by a large proportion of family GT1 being involved in secondary metabolite biosynthesis. In a comparative analysis of polysaccharide biosynthesis amongst the taxa of this study, clear distinctions or similarities were observed in (1) N-linked protein glycosylation, i.e., Chlorophyta has different mannosylation and glucosylation patterns, (2) GPI anchor biosynthesis, which is apparently missing in the Rhodophyta and truncated in the Chlorophyta, (3) cell wall biosynthesis, where the land plants have unique cell wall related polymers not found in green and red algae, and (4) O-linked glycosylation where comprehensive orthology was observed in glycosylation between the Chlorophyta and land plants but not between the target proteins. PMID:24146880

  11. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1 gene family.

    Directory of Open Access Journals (Sweden)

    Mia T Levine

    Full Text Available Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.

  12. Being cosmopolitan: evolutionary history and phylogeography of a specialized raptor, the Osprey Pandion haliaetus.

    Science.gov (United States)

    Monti, Flavio; Duriez, Olivier; Arnal, Véronique; Dominici, Jean-Marie; Sforzi, Andrea; Fusani, Leonida; Grémillet, David; Montgelard, Claudine

    2015-11-17

    The Osprey (Pandion haliaetus) is one of only six bird species with an almost world-wide distribution. We aimed at clarifying its phylogeographic structure and elucidating its taxonomic status (as it is currently separated into four subspecies). We tested six biogeographical scenarios to explain how the species' distribution and differentiation took place in the past and how such a specialized raptor was able to colonize most of the globe. Using two mitochondrial genes (cyt b and ND2), the Osprey appeared structured into four genetic groups representing quasi non-overlapping geographical regions. The group Indo-Australasia corresponds to the cristatus ssp, as well as the group Europe-Africa to the haliaetus ssp. In the Americas, we found a single lineage for both carolinensis and ridgwayi ssp, whereas in north-east Asia (Siberia and Japan), we discovered a fourth new lineage. The four lineages are well differentiated, contrasting with the low genetic variability observed within each clade. Historical demographic reconstructions suggested that three of the four lineages experienced stable trends or slight demographic increases. Molecular dating estimates the initial split between lineages at about 1.16 Ma ago, in the Early Pleistocene. Our biogeographical inference suggests a pattern of colonization from the American continent towards the Old World. Populations of the Palearctic would represent the last outcomes of this colonization. At a global scale the Osprey complex may be composed of four different Evolutionary Significant Units, which should be treated as specific management units. Our study brought essential genetic clarifications, which have implications for conservation strategies in identifying distinct lineages across which birds should not be artificially moved through exchange/reintroduction schemes.

  13. Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid Nudibranchs

    Science.gov (United States)

    Johnson, Rebecca Fay; Gosliner, Terrence M.

    2012-01-01

    Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names. PMID:22506002

  14. Comparison of loline alkaloid gene clusters across fungal endophytes: predicting the co-regulatory sequence motifs and the evolutionary history.

    Science.gov (United States)

    Kutil, Brandi L; Greenwald, Charles; Liu, Gang; Spiering, Martin J; Schardl, Christopher L; Wilkinson, Heather H

    2007-10-01

    LOL, a fungal secondary metabolite gene cluster found in Epichloë and Neotyphodium species, is responsible for production of insecticidal loline alkaloids. To analyze the genetic architecture and to predict the evolutionary history of LOL, we compared five clusters from four fungal species (single clusters from Epichloë festucae, Neotyphodium sp. PauTG-1, Neotyphodium coenophialum, and two clusters we previously characterized in Neotyphodium uncinatum). Using PhyloCon to compare putative lol gene promoter regions, we have identified four motifs conserved across the lol genes in all five clusters. Each motif has significant similarity to known fungal transcription factor binding sites in the TRANSFAC database. Conservation of these motifs is further support for the hypothesis that the lol genes are co-regulated. Interestingly, the history of asexual Neotyphodium spp. includes multiple interspecific hybridization events. Comparing clusters from three Neotyphodium species and E. festucae allowed us to determine which Epichloë ancestors are the most likely contributors of LOL in these asexual species. For example, while no present day Epichloë typhina isolates are known to produce lolines, our data support the hypothesis that the E. typhina ancestor(s) of three asexual endophyte species contained a LOL gene cluster. Thus, these data support a model of evolution in which the polymorphism in loline alkaloid production phenotypes among endophyte species is likely due to the loss of the trait over time.

  15. Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success.

    Science.gov (United States)

    Peters, Ralph S; Niehuis, Oliver; Gunkel, Simon; Bläser, Marcel; Mayer, Christoph; Podsiadlowski, Lars; Kozlov, Alexey; Donath, Alexander; van Noort, Simon; Liu, Shanlin; Zhou, Xin; Misof, Bernhard; Heraty, John; Krogmann, Lars

    2017-12-13

    Chalcidoidea are a megadiverse group of mostly parasitoid wasps of major ecological and economical importance that are omnipresent in almost all extant terrestrial habitats. The timing and pattern of chalcidoid diversification is so far poorly understood and has left many important questions on the evolutionary history of Chalcidoidea unanswered. In this study, we infer the early divergence events within Chalcidoidea and address the question of whether or not ancestral chalcidoids were small egg parasitoids. We also trace the evolution of some key traits: jumping ability, development of enlarged hind femora, and associations with figs. Our phylogenetic inference is based on the analysis of 3,239 single-copy genes across 48 chalcidoid wasps and outgroups representatives. We applied an innovative a posteriori evaluation approach to molecular clock-dating based on nine carefully validated fossils, resulting in the first molecular clock-based estimation of deep Chalcidoidea divergence times. Our results suggest a late Jurassic origin of Chalcidoidea, with a first divergence of morphologically and biologically distinct groups in the early to mid Cretaceous, between 129 and 81 million years ago (mya). Diversification of most extant lineages happened rapidly after the Cretaceous in the early Paleogene, between 75 and 53 mya. The inferred Chalcidoidea tree suggests a transition from ancestral minute egg parasitoids to larger-bodied parasitoids of other host stages during the early history of chalcidoid evolution. The ability to jump evolved independently at least three times, namely in Eupelmidae, Encyrtidae, and Tanaostigmatidae. Furthermore, the large-bodied strongly sclerotized species with enlarged hind femora in Chalcididae and Leucospidae are not closely related. Finally, the close association of some chalcidoid wasps with figs, either as pollinators, or as inquilines/gallers or as parasitoids, likely evolved at least twice independently: in the Eocene, giving rise

  16. The tree as evolutionary icon: TREE in the Natural History Museum, London.

    Science.gov (United States)

    Hellström, Nils Petter

    2011-01-01

    As part of the Darwin celebrations in 2009, the Natural History Museum in London unveiled TREE, the first contemporary artwork to win a permanent place in the Museum. While the artist claimed that the inspiration for TREE came from Darwin's famous notebook sketch of branching evolution, sometimes referred to as his "tree of life" drawing, this article emphasises the apparent incongruity between Darwin's sketch and the artist's design -- best explained by other, complementary sources of inspiration. In the context of the Museum's active participation in struggles over science and religion, the effect of the new artwork is contradictory. TREE celebrates Darwinian evolutionism, but it resonates with deep-rooted, mythological traditions of tree symbolism to do so. This complicates the status of the Museum space as one of disinterested, secular science, but it also contributes, with or without the intentions of the Museum's management, to consolidate two sometimes conflicting strains within the Museum's history. TREE celebrates human effort, secular science and reason -- but it also evokes long-standing mythological traditions to inspire reverence and remind us of our humble place in the world.

  17. Patterns of Evolutionary Trajectories and Domestication History within the Genus Hordeum Assessed by REMAP Markers.

    Science.gov (United States)

    Bonchev, Georgi; Dusinský, Roman; Hauptvogel, Pavol; Švec, Miroslav

    2017-03-01

    The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley. The obtained data are consistent with the current taxonomic status within the genus Hordeum. Similar level of genetic diversity was observed between the wild and the domesticated barley accessions suggesting that transposable elements` activity and accumulation may counteract the decrease of genome-wide diversity following domestication. In addition, eco-geographical sub-genome pools of the cultivated barley were identified in support to the theory of multiple origins of domestication within the genus Hordeum. We also provide conclusions about the relationship between accessions of different species and the putative routes of barley domestication. In conclusion, the retrotransposon BARE-1 stands as a reliable and perspective DNA marker for the assessment of the phylogenetic and domestication history in the genus Hordeum and other crop species.

  18. Different Histories, Different Destinies‒Impact of Evolutionary History and Population Genetic Structure on Extinction Risk of the Adriatic Spined Loaches (Genus Cobitis; Cypriniformes, Actinopterygii.

    Directory of Open Access Journals (Sweden)

    Ivana Buj

    Full Text Available The region of Balkans is often considered as an ichthyologic "hot spot", with a great number of species and high portion of endemics living in fresh waters in a relatively small area. The Adriatic watershed in Croatia and Herzegovina is inhabited by six spined loach species (genus Cobitis whose extinction risk estimations were based solely on their extent of occurrence (and/or area of occupancy and its fragmentation, and conservation proposals do not consider diversity below species level. In this investigation we employed molecular genetic methods to describe present genetic structure of the Adriatic spined loaches and reveal their demographic history. The divergence of the Adriatic lineages inside the genus Cobitis started in Miocene and lasted until Pleistocene epoch. Geological events responsible for shaping recent diversity of spined loaches in the Adriatic basin are: the Dinarid Mountains upwelling, the evolution of Dinaric Lake system, local tectonic activity, river connections during glaciations and differences in sea level. Even though all the investigated species inhabit karstic rivers located in the same geographic area and that were subject of similar geological events, the results obtained reveal great differences in their genetic diversity and structure and point out the necessity of different conservation measures to ensure their future viability. High level of genetic polymorphism is characteristic for species located more to the south. Two species comprised of more than one population have completely different intraspecific structure; populations of C. illyrica are genetically distinct and represent separate evolutionary significant units, whereas intraspecific structure of C. narentana corresponds to metapopulational pattern. Without population genetic data, evolutionary significant units could be easily misidentified. Furthermore, the obtained results affirm that population genetic measurements are able to detect differences

  19. Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

    Directory of Open Access Journals (Sweden)

    White Brian

    2009-01-01

    Full Text Available Abstract Background Of the > 2000 serovars of Salmonella enterica subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, S. enterica serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi. Results We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2 identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes. Conclusion Recombination and pseudogene-formation have been

  20. Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history.

    Science.gov (United States)

    Rosauer, Dan; Laffan, Shawn W; Crisp, Michael D; Donnellan, Stephen C; Cook, Lyn G

    2009-10-01

    We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.

  1. Evolutionary thinking

    Science.gov (United States)

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  2. A short history of evolutionary theory Uma breve história da teoria evolutiva

    Directory of Open Access Journals (Sweden)

    Edson Perreira da Silva

    2001-12-01

    Full Text Available The history of the Theory of Evolution has been told a number of times by historians, philosophers, professors, writers, scientists and so on. However, many of these versions differ from or even contradict one another. In this article, the history of the Theory of Evolution is retold according to a dialectical-materialistic perspective. It analyzes the historical contradictions between Darwinian evolution theory and Mendel's model, the background that led to the synthetic theory of evolution, the debate carried out by classic schools and the result of synthesis, as well as the still current debate between Neutralism and Selectionism. Finally, it also discusses the interpretative model used ("an idiosyncratic dialectic materialism", mainly in relation with Popper's and Kuhn's models.A história da teoria evolutiva tem sito contada inúmeras vezes por historiadores, filósofos, professores, escritores, cientistas etc. Contudo, muitas destas versões diferem entre si ou mesmo se contradizem. Neste trabalho, a história da teoria evolutiva é recontada a partir de uma perspectiva materialista dialética. São analisadas as contradições históricas entre a teoria evolutiva darwiniana e o modelo mendeliano, o caminho para a teoria sintética da evolução, o debate entre as escolas clássica e do balanco que sucedeu a síntese, bem como o debate, ainda atual, entre neutralismo e selecionismo. Ao final, o modelo interpretativo utilizado ("um materialismo dialético idiossincrático" é discutido, principalmente, em relação aos modelos popperiano e kuhniano.

  3. Pollutant dehalogenation capability may depend on the trophic evolutionary history of the organism: PBDEs in freshwater food webs.

    Science.gov (United States)

    Bartrons, Mireia; Grimalt, Joan O; de Mendoza, Guillermo; Catalan, Jordi

    2012-01-01

    Organohalogen compounds are some of the most notorious persistent pollutants disturbing the Earth biosphere. Although human-made, these chemicals are not completely alien to living systems. A large number of natural organohalogens, part of the secondary metabolism, are involved in chemical trophic interactions. Surprisingly, the relationship between organisms' trophic position and synthetic organohalogen biotransformation capability has not been investigated. We studied the case for polybromodiphenyl ethers (PBDE), a group of flame-retardants of widespread use in the recent years, in aquatic food webs from remote mountain lakes. These relatively simple ecosystems only receive pollution by atmospheric transport. A large predominance of the PBDE congener currently in use in Europe, BDE-209, largely dominated the PBDE composition of the basal resources of the food web. In contrast, primary consumers (herbivores and detritivores) showed a low proportion of BDE-209, and dominance of several less brominated congeners (e.g. BDE-100, BDE47). Secondary consumers (predators) showed large biomagnification of BDE-209 compare to other congeners. Finally, top predator fish characterized by low total PBDE concentrations. Examination of the bromine stable isotopic composition indicates that primary consumers showed higher PBDE biotransformation capability than secondary consumers. We suggest that the evolutionary response of primary consumers to feeding deterrents would have pre-adapted them for PBDE biotransformation. The observed few exceptions, some insect taxa, can be interpreted in the light of the trophic history of the evolutionary lineage of the organisms. Bromine isotopic composition in fish indicates that low PBDE values are due to not only biotransformation but also to some other process likely related to transport. Our finding illustrates that organohalogen compounds may strongly disturb ecosystems even at low concentrations, since the species lacking or having scarce

  4. Pollutant dehalogenation capability may depend on the trophic evolutionary history of the organism: PBDEs in freshwater food webs.

    Directory of Open Access Journals (Sweden)

    Mireia Bartrons

    Full Text Available Organohalogen compounds are some of the most notorious persistent pollutants disturbing the Earth biosphere. Although human-made, these chemicals are not completely alien to living systems. A large number of natural organohalogens, part of the secondary metabolism, are involved in chemical trophic interactions. Surprisingly, the relationship between organisms' trophic position and synthetic organohalogen biotransformation capability has not been investigated. We studied the case for polybromodiphenyl ethers (PBDE, a group of flame-retardants of widespread use in the recent years, in aquatic food webs from remote mountain lakes. These relatively simple ecosystems only receive pollution by atmospheric transport. A large predominance of the PBDE congener currently in use in Europe, BDE-209, largely dominated the PBDE composition of the basal resources of the food web. In contrast, primary consumers (herbivores and detritivores showed a low proportion of BDE-209, and dominance of several less brominated congeners (e.g. BDE-100, BDE47. Secondary consumers (predators showed large biomagnification of BDE-209 compare to other congeners. Finally, top predator fish characterized by low total PBDE concentrations. Examination of the bromine stable isotopic composition indicates that primary consumers showed higher PBDE biotransformation capability than secondary consumers. We suggest that the evolutionary response of primary consumers to feeding deterrents would have pre-adapted them for PBDE biotransformation. The observed few exceptions, some insect taxa, can be interpreted in the light of the trophic history of the evolutionary lineage of the organisms. Bromine isotopic composition in fish indicates that low PBDE values are due to not only biotransformation but also to some other process likely related to transport. Our finding illustrates that organohalogen compounds may strongly disturb ecosystems even at low concentrations, since the species lacking

  5. Evolutionary history of callose synthases in terrestrial plants with emphasis on proteins involved in male gametophyte development.

    Directory of Open Access Journals (Sweden)

    Lenka Záveská Drábková

    Full Text Available Callose is a plant-specific polysaccharide (β-1,3-glucan playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family. We performed thorough comparative analyses of callose synthase family proteins from major plant lineages to determine their evolutionary history across the plant kingdom. A total of 1211 candidate CalS sequences were identified and compared amongst diverse taxonomic groups of plants, from bryophytes to angiosperms. Phylogenetic analyses identified six main clades of CalS proteins and suggested duplications during the evolution of specialised functions. Twelve family members had previously been identified in Arabidopsis thaliana. We focused on five CalS subfamilies directly linked to pollen function and found that proteins expressed in pollen evolved twice. CalS9/10 and CalS11/12 formed well-defined clades, whereas pollen-specific CalS5 was found within subfamilies that mostly did not express in mature pollen vegetative cell, although were found in sperm cells. Expression of five out of seven mature pollen-expressed CalS genes was affected by mutations in bzip transcription factors. Only three subfamilies, CalS5, CalS10, and CalS11, however, formed monophyletic, mostly conserved clades. The pairs CalS9/CalS10, CalS11/CalS12 and CalS3 may have diverged after angiosperms diversified from lycophytes and bryophytes. Our analysis of fully sequenced plant proteins identified new evolutionary lineages of callose synthase

  6. Evolutionary history of callose synthases in terrestrial plants with emphasis on proteins involved in male gametophyte development

    Science.gov (United States)

    Honys, David

    2017-01-01

    Callose is a plant-specific polysaccharide (β-1,3-glucan) playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS) and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family. We performed thorough comparative analyses of callose synthase family proteins from major plant lineages to determine their evolutionary history across the plant kingdom. A total of 1211 candidate CalS sequences were identified and compared amongst diverse taxonomic groups of plants, from bryophytes to angiosperms. Phylogenetic analyses identified six main clades of CalS proteins and suggested duplications during the evolution of specialised functions. Twelve family members had previously been identified in Arabidopsis thaliana. We focused on five CalS subfamilies directly linked to pollen function and found that proteins expressed in pollen evolved twice. CalS9/10 and CalS11/12 formed well-defined clades, whereas pollen-specific CalS5 was found within subfamilies that mostly did not express in mature pollen vegetative cell, although were found in sperm cells. Expression of five out of seven mature pollen-expressed CalS genes was affected by mutations in bzip transcription factors. Only three subfamilies, CalS5, CalS10, and CalS11, however, formed monophyletic, mostly conserved clades. The pairs CalS9/CalS10, CalS11/CalS12 and CalS3 may have diverged after angiosperms diversified from lycophytes and bryophytes. Our analysis of fully sequenced plant proteins identified new evolutionary lineages of callose synthase subfamilies and has

  7. Population Structure, Genetic Diversity, and Evolutionary History ofKleinia neriifolia(Asteraceae) on the Canary Islands.

    Science.gov (United States)

    Sun, Ye; Vargas-Mendoza, Carlos F

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  8. Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species

    Directory of Open Access Journals (Sweden)

    Linhong Teng

    2017-08-01

    Full Text Available Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS. About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.

  9. The evolutionary history of parasitic gastropods and their coral hosts in the Indo-Pacific

    NARCIS (Netherlands)

    Gittenberger, Adriaan

    2006-01-01

    This thesis deals with the associations between parasitic snails and their mushroom coral hosts. Gittenberger has spent 800 hours under water and searched about 60,000 coral discs for these parasites. He dived in Egypt, the Maldives, Thailand, Malaysia, Japan, Palau, the Philippines, Indonesia and

  10. Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes.

    Science.gov (United States)

    Bittner, Lucie; Payri, Claude E; Maneveldt, Gavin W; Couloux, Arnaud; Cruaud, Corinne; de Reviers, Bruno; Le Gall, Line

    2011-12-01

    Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'.

    Science.gov (United States)

    Buckley, Michael

    2015-05-07

    Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the 'native' South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian 'condylarths', which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the 'native' South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene-Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography-tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.

  12. Ancient collagen reveals evolutionary history of the endemic South American ‘ungulates’

    Science.gov (United States)

    Buckley, Michael

    2015-01-01

    Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs. PMID:25833851

  13. Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci.

    Science.gov (United States)

    Kates, Heather R; Soltis, Pamela S; Soltis, Douglas E

    2017-06-01

    Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. The mathematical modelling of plant behaviour: an evolutionary history and forward projection: Pt. 3

    International Nuclear Information System (INIS)

    Whitmarsh-Everiss, M.J.

    1993-01-01

    The two previous articles in this series considered the evolution of analogue and hybrid computing techniques using examples from Magnox and advanced gas cooled reactor design. The parallel deployment and development of digital computing was discussed in relation to the simulation languages of the day which culminated in the formal release of the Plant Modelling Systems Program, PMSP. It is now proposed to trace the history from 1980 to the present day and discuss the highly sophisticated interactive digital computing environment known as the Plant Design Analyser. A backward step will be taken in time to look at the parallel and evolving design of Plant Operator Training Simulators. Once again, the development of these facilities had to track the evolving computer architectures and developments in computing science. During this period modelling disciplines and methodologies became formalised and were enshrined in elaborate Computer Aided Design Suites. However, they were consolidated at the end of our story. It is first our intention to discuss the simulation language PMSP as this is the foundation of the explanation which follows. (author)

  15. High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania.

    Directory of Open Access Journals (Sweden)

    Marco Salemi

    2008-01-01

    Full Text Available HIV-1 epidemic in Western Europe is largely due to subtype B. Little is known about the HIV-1 in Eastern Europe, but a few studies have shown that non-B subtypes are quite common. In Albania, where a recent study estimated a ten-fold increase of AIDS incidence during the last six years, subtype A and B account for 90% of the know infections.We investigated the demographic history of HIV-1 subtype A and B in Albania by using a statistical framework based on coalescent theory and phylogeography. High-resolution phylogenetic and molecular clock analysis showed a limited introduction to the Balkan country of subtype A during the late 1980s followed by an epidemic outburst in the early 1990 s. In contrast, subtype B was apparently introduced multiple times between the mid-1970s and mid-1980s. Both subtypes are growing exponentially, although the HIV-1A epidemic displays a faster growth rate, and a significantly higher basic reproductive number R(0. HIV-1A gene flow occurs primarily from the capital Tirane, in the center of the country, to the periphery, while HIV-1B flow is characterized by a balanced exchange between center and periphery. Finally, we calculated that the actual number of infections in Albania is at least two orders of magnitude higher than previously thought.Our analysis demonstrates the power of recently developed computational tools to investigate molecular epidemiology of pathogens, and emphasize the complex factors involved in the establishment of HIV-1 epidemics. We suggest that a significant correlation exists between HIV-1 exponential spread and the socio-political changes occurred during the Balkan wars. The fast growth of a relatively new non-B epidemic in the Balkans may have significant consequences for the evolution of HIV-1 epidemiology in neighboring countries in Eastern and Western Europe.

  16. A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.

    Directory of Open Access Journals (Sweden)

    Chaochao Yan

    Full Text Available The lineage of the Bar-backed Partridge (Arborophila brunneopectus was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML and Bayesian inference (BI analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5. The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3 found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

  17. Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia.

    Directory of Open Access Journals (Sweden)

    Sebastien Breurec

    Full Text Available The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.

  18. Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

    Science.gov (United States)

    Corbi, Jonathan; Dutheil, Julien Y; Damerval, Catherine; Tenaillon, Maud I; Manicacci, Domenica

    2012-03-01

    ADP-glucose pyrophosphorylase (AGPase) is a key enzyme of starch biosynthesis. In the green plant lineage, it is composed of two large (LSU) and two small (SSU) sub-units encoded by paralogous genes, as a consequence of several rounds of duplication. First, our aim was to detect specific patterns of molecular evolution following duplication events and the divergence between monocotyledons and dicotyledons. Secondly, we investigated coevolution between amino acids both within and between sub-units. A phylogeny of each AGPase sub-unit was built using all gymnosperm and angiosperm sequences available in databases. Accelerated evolution along specific branches was tested using the ratio of the non-synonymous to the synonymous substitution rate. Coevolution between amino acids was investigated taking into account compensatory changes between co-substitutions. We showed that SSU paralogues evolved under high functional constraints during angiosperm radiation, with a significant level of coevolution between amino acids that participate in SSU major functions. In contrast, in the LSU paralogues, we identified residues under positive selection (1) following the first LSU duplication that gave rise to two paralogues mainly expressed in angiosperm source and sink tissues, respectively; and (2) following the emergence of grass-specific paralogues expressed in the endosperm. Finally, we found coevolution between residues that belong to the interaction domains of both sub-units. Our results support the view that coevolution among amino acid residues, especially those lying in the interaction domain of each sub-unit, played an important role in AGPase evolution. First, within SSU, coevolution allowed compensating mutations in a highly constrained context. Secondly, the LSU paralogues probably acquired tissue-specific expression and regulatory properties via the coevolution between sub-unit interacting domains. Finally, the pattern we observed during LSU evolution is consistent

  19. Mars: The evolutionary history of the northern lowlands based on crater counting and geologic mapping

    Science.gov (United States)

    Werner, S. C.; Tanaka, K. L.; Skinner, J. A.

    2011-09-01

    The geologic history of planetary surfaces is most effectively determined by joining geologic mapping and crater counting which provides an iterative, qualitative and quantitative method for defining relative ages and absolute model ages. Based on this approach, we present spatial and temporal details regarding the evolution of the Martian northern plains and surrounding regions. The highland-lowland boundary (HLB) formed during the pre-Noachian and was subsequently modified through various processes. The Nepenthes Mensae unit along the northern margins of the cratered highlands, was formed by HLB scarp-erosion, deposition of sedimentary and volcanic materials, and dissection by surface runoff between 3.81 and 3.65 Ga. Ages for giant polygons in Utopia and Acidalia Planitiae are ˜ 3.75 Ga and likely reflect the age of buried basement rocks. These buried lowland surfaces are comparable in age to those located closer to the HLB, where a much thinner, post-HLB deposit is mapped. The emplacement of the most extensive lowland surfaces ended between 3.75 and 3.4 Ga, based on densities of craters generally >3km in diameter. Results from the polygonal terrain support the existence of a major lowland depocenter shortly after the pre-Noachian formation of the northern lowlands. In general, northern plains surfaces show gradually younger ages at lower elevations, consistent local to regional unit emplacement and resurfacing between 3.6 and 2.6 Ga. Elevation levels and morphology are not necessarily related, and variations in ages within the mapped units are found, especially in units formed and modified by multiple geological processes. Regardless, most of the youngest units in the northern lowlands are considered to be lavas, polar ice, or thick mantle deposits, arguing against the ocean theory during the Amazonian Period (younger than about 3.15 Ga). All ages measured in the closest vicinity of the steep dichotomy escarpment are also 3.7 Ga or older. The formation ages of

  20. The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

    Science.gov (United States)

    Chen, Bor-Sen; Ho, Shih-Ju

    2014-01-01

    In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

  1. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    Science.gov (United States)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical

  2. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.

    Science.gov (United States)

    Prajapati, Surendra K; Joshi, Hema; Carlton, Jane M; Rizvi, M Alam

    2013-01-01

    The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.

  3. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.

    Directory of Open Access Journals (Sweden)

    Surendra K Prajapati

    Full Text Available The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75 from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years and long-term population history (79,235 to 104,008 of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes to that inferred from mitochondrial genome diversity.

  4. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes.

    Science.gov (United States)

    Rousseau-Gueutin, M; Gaston, A; Aïnouche, A; Aïnouche, M L; Olbricht, K; Staudt, G; Richard, L; Denoyes-Rothan, B

    2009-06-01

    Phylogenetic utility of two nuclear genes (GBSSI-2 and DHAR) was explored in genus Fragaria in order to clarify phylogenetic relationships among taxa and to elucidate the origin of the polyploid species. Orthology of the amplified products was assessed by several methods. Our results strongly suggest the loss of one GBSSI duplicated copy (GBSSI-1) in the Fragariinae subtribe. Phylogenetic analyses provided new insights into the evolutionary history of Fragaria, such as evidence supporting the presence of three main diploid genomic pools in the genus and demonstrating the occurrence of independent events of polyploidisation. In addition, the data provide evidence supporting an allopolyploid origin of the hexaploid F. moschata, and the octoploids F. chiloensis, F. iturupensis and F. virginiana. Accordingly, a new pattern summarizing our present knowledge on the Fragaria evolutionary history is proposed. Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes.

  5. Evolutionary history of Ichthyosaura alpestris (Caudata, Salamandridae) inferred from the combined analysis of nuclear and mitochondrial markers.

    Science.gov (United States)

    Recuero, Ernesto; Buckley, David; García-París, Mario; Arntzen, Jan W; Cogălniceanu, Dan; Martínez-Solano, Iñigo

    2014-12-01

    ) the remaining populations, including subspecies I. a. serdara, I. a. reiseri and I. a. montenegrina and part of subspecies I. a. alpestris, plus samples from Vlasina. Our time estimates are consistent with ages based on the fossil record and suggest a widespread distribution for the I. alpestris ancestor, with the split of the major eastern and western lineages during the Miocene, in the Tortonian. Our study provides a solid, comprehensive background on the evolutionary history of the species based on the most complete combined (mtDNA+nDNA+allozymes) dataset to date. The combination of the historical perspective provided by coalescent-based analyses of mitochondrial and nuclear DNA variation with individual-based multilocus assignment methods based on multiple nuclear markers (allozymes) also allowed identification of instances of discordance across markers that highlight the complexity and dynamism of past and ongoing evolutionary processes in the species. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Inferring the evolutionary history of Indian Plasmodium vivax from population genetic analyses of multilocus nuclear DNA fragments.

    Science.gov (United States)

    Gupta, Bhavna; Srivastava, Nalini; DAS, Aparup

    2012-04-01

    The human malaria parasite Plasmodium vivax is globally widespread, causing high malaria morbidity. As P. vivax is highly endemic to India, and previous reports indicate genetic homogeneity in population samples, we tested the hypothesis of no genetic structuring in Indian P. vivax. Further, based on the reports of increasing incidence of Plasmodium falciparum infection in comparison with P. vivax in recent years in India, it was important to understand whether reduction in population size has resulted in decrease in P. vivax infection rate in India. For this, we utilized recently developed putatively neutral markers from chromosome 13 of P. vivax to score single nucleotide polymorphisms in 126 P. vivax isolates collected from 10 different places in India. The overall results indicated that Indian P. vivax bears high nucleotide diversity within population samples but moderate amount of genetic differentiation between population samples. STRUCTURE analysis grouped 10 population samples into three clusters based on the proportion of the genetic ancestries in each population. However, the pattern of clustering does not correlate with sampling locations in India. Furthermore, analyses of past demographic events indicated reduction in population size in majority of population samples, but when isolates from all the 10 samples were considered as a single population, the data fit to the demographic equilibrium model. All these observations clearly indicate that Indian P. vivax presents complex evolutionary history but possesses several features of being a part of ancestral distribution range of this species. © 2012 Blackwell Publishing Ltd.

  7. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Science.gov (United States)

    2011-01-01

    Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups. PMID:21745361

  8. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau.

    Science.gov (United States)

    Qu, Y; Lei, F; Zhang, R; Lu, X

    2010-01-01

    along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.

  9. Evolutionary history of the grey-faced Sengi, Rhynchocyon udzungwensis, from Tanzania: a molecular and species distribution modelling approach.

    Directory of Open Access Journals (Sweden)

    Lucinda P Lawson

    Full Text Available Rhynchocyon udzungwensis is a recently described and poorly understood sengi (giant elephant-shrew endemic to two small montane forests in Southern Tanzania, and surrounded in lower forests by R. cirnei reichardi. In this study, we investigate the molecular genetic relationship between R. udzungwensis and R. c. reichardi, and the possible role that shifting species distributions in response to climate fluctuations may have played in shaping their evolutionary history. Rhynchocyon udzungwensis and R. c. reichardi individuals were sampled from five localities for genetic analyses. Three mitochondrial and two nuclear loci were used to construct species trees for delimitation and to determine whether introgression was detectable either from ancient or ongoing hybridization. All species-tree results show R. udzungwensis and R. c. reichardi as distinct lineages, though mtDNA shows evidence of introgression in some populations. Nuclear loci of each species were monophyletic, implying introgression is exclusively historical. Because we found evidence of introgression, we used distribution data and species distribution modelling for present, glacial, and interglacial climate cycles to predict how shifting species distributions may have facilitated hybridization in some populations. Though interpretations are affected by the limited range of these species, a likely scenario is that the mtDNA introgression found in eastern mid-elevation populations was facilitated by low numbers of R. udzungwensis that expanded into lowland heavily occupied R. c. reichardi areas during interglacial climate cycles. These results imply that relationships within the genus Rhynchocyon may be confounded by porous species boundaries and introgression, even if species are not currently sympatric.

  10. Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record.

    Science.gov (United States)

    Mahony, Stephen; Foley, Nicole M; Biju, S D; Teeling, Emma C

    2017-03-01

    Molecular dating studies typically need fossils to calibrate the analyses. Unfortunately, the fossil record is extremely poor or presently nonexistent for many species groups, rendering such dating analysis difficult. One such group is the Asian horned frogs (Megophryinae). Sampling all generic nomina, we combined a novel ∼5 kb dataset composed of four nuclear and three mitochondrial gene fragments to produce a robust phylogeny, with an extensive external morphological study to produce a working taxonomy for the group. Expanding the molecular dataset to include out-groups of fossil-represented ancestral anuran families, we compared the priorless RelTime dating method with the widely used prior-based Bayesian timetree method, MCMCtree, utilizing a novel combination of fossil priors for anuran phylogenetic dating. The phylogeny was then subjected to ancestral phylogeographic analyses, and dating estimates were compared with likely biogeographic vicariant events. Phylogenetic analyses demonstrated that previously proposed systematic hypotheses were incorrect due to the paraphyly of genera. Molecular phylogenetic, morphological, and timetree results support the recognition of Megophryinae as a single genus, Megophrys, with a subgenus level classification. Timetree results using RelTime better corresponded with the known fossil record for the out-group anuran tree. For the priorless in-group, it also outperformed MCMCtree when node date estimates were compared with likely influential historical biogeographic events, providing novel insights into the evolutionary history of this pan-Asian anuran group. Given a relatively small molecular dataset, and limited prior knowledge, this study demonstrates that the computationally rapid RelTime dating tool may outperform more popular and complex prior reliant timetree methodologies. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For

  11. Osteological Observations on the Alytid Anura Latonia nigriventer with Comments on Functional Morphology, Biogeography, and Evolutionary History.

    Science.gov (United States)

    Biton, Rebecca; Boistel, Renaud; Rabinovich, Rivka; Gafny, Sarig; Brumfeld, Vlad; Bailon, Salvador

    2016-09-01

    The Hula Painted Frog (Latonia nigriventer) is a rare frog species endemic to the Hula Valley, Israel. The species is the sole relict of a clade that was widespread mainly in Europe from the Oligocene until the beginning of the Pleistocene. The osteological characteristics of L. nigriventer are described based on X-ray microtomography scans of extant specimens and Pleistocene bones from the Hula Valley, to elucidate the evolutionary history of Alytidae and more specifically of Latonia. Based on the osteological description of L. nigriventer, we now better understand the differences, between Latonia and its sister taxon Discoglossus. They differ mainly in their cranial structure with the reinforced skull of Latonia having powerful jaws. Latonia nigriventer can achieve great force while closing its jaws, due to increased adductor muscle insertion surfaces as expressed by the presence of an additional paracoronoid process and an enlarged upper margin of the postero-lateral wall of the lower jaw. In addition, a wider pterygoid fossa and higher canthus postero-lateralis of the frontoparietal, compared to that of Discoglossus, also suggest the presence of well-developed adductor muscles. Furthermore, L. nigriventer have particularly strong skulls as expressed by: long articulations between different skull elements, interdigitation in the contact area between the nasals and between nasals and the frontoparietals, and fused frontoparietals. Both males and females L. nigriventer have very robust forelimbs, as indicated by well-developed medial crests of the humerus. Based on limited eastern Mediterranean paleontological data, we can only suspect that the dispersal of Latonia into the Levant from Asia Minor occurred at some point during the Miocene or later. The first appearance of L. nigriventer in the Hula Valley, its current habitat, dates to approximately 780 thousand years ago at the archaeological site of Gesher Benot Ya'aqov. J. Morphol. 277:1131-1145, 2016. © 2016

  12. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2011-07-01

    Full Text Available Abstract Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a genome segments unshared between B. microti and B. pinnipedialis, b gene deletion/fusion events and c positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.

  13. Phylogeography of Camellia taliensis (Theaceae inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

    Directory of Open Access Journals (Sweden)

    Liu Yang

    2012-06-01

    Full Text Available Abstract Background As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. Results Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314 were almost as high as at PAL (h = 0.836; π = 0.00417. Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989, suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301 provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P  Conclusions We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

  14. Evolutionary History of the Live-Bearing Endemic Allotoca diazi Species Complex (Actinopterygii, Goodeinae): Evidence of Founder Effect Events in the Mexican Pre-Hispanic Period

    OpenAIRE

    Corona-Santiago, Diushi Keri; Doadrio, Ignacio; Dom?nguez-Dom?nguez, Omar

    2015-01-01

    The evolutionary history of Mexican ichthyofauna has been strongly linked to natural events, and the impact of pre-Hispanic cultures is little known. The live-bearing fish species Allotoca diazi, Allotoca meeki and Allotoca catarinae occur in areas of biological, cultural and economic importance in central Mexico: Pátzcuaro basin, Zirahuén basin, and the Cupatitzio River, respectively. The species are closely related genetically and morphologically, and hypotheses have attempted to explain th...

  15. Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production

    NARCIS (Netherlands)

    Mans, R.; Daran, J.G.; Pronk, J.T.

    2018-01-01

    Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical

  16. The evolutionary history of Eugenia sect. Phyllocalyx (Myrtaceae) corroborates historically stable areas in the southern Atlantic forests.

    Science.gov (United States)

    de Oliveira Bünger, Mariana; Fernanda Mazine, Fiorella; Forest, Félix; Leandro Bueno, Marcelo; Renato Stehmann, João; Lucas, Eve J

    2016-12-01

    Eugenia sect. Phyllocalyx Nied. includes 14 species endemic to the Neotropics, mostly distributed in the Atlantic coastal forests of Brazil. Here the first comprehensive phylogenetic study of this group is presented, and this phylogeny is used as the basis to evaluate the recent infrageneric classification in Eugenia sensu lato (s.l.) to test the history of the evolution of traits in the group and test hypotheses associated with the history of this clade. A total of 42 taxa were sampled, of which 14 were Eugenia sect. Phyllocalyx for one nuclear (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, rpl16, trnL-rpl32 and trnQ-rps16). The relationships were reconstructed based on Bayesian analysis and maximum likelihood. Additionally, ancestral area analysis and modelling methods were used to estimate species dispersal, comparing historically climatic stable (refuges) and unstable areas. Maximum likelihood and Bayesian inferences indicate that Eugenia sect. Phyllocalyx is paraphyletic and the two clades recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Cerrado and south-eastern species and a difference in the composition of species from north-eastern and south-eastern Atlantic forest. Refugia and stable areas identified within unstable areas suggest that these areas were important to maintain diversity in the Atlantic forest biodiversity hotspot. This study provides a robust phylogenetic framework to address important historical questions for Eugenia s.l. within an evolutionary context, supporting the need for better taxonomic study of one of the largest genera in the Neotropics. Furthermore, valuable insight is offered into diversification and biome shifts of plant species in the highly environmentally impacted Atlantic forest of South America. Evidence is presented that climate stability in the south-eastern Atlantic forest during the Quaternary contributed to the

  17. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  18. Evolutionary response of the egg hatching date of a herbivorous insect under climate change

    Science.gov (United States)

    van Asch, Margriet; Salis, Lucia; Holleman, Leonard J. M.; van Lith, Bart; Visser, Marcel E.

    2013-03-01

    Under changing climatic conditions, species need to adapt to their new environment. Genetic adaptation is crucial to prevent population extinction but examples where climate change leads to genetic changes in wild populations have been few. The synchronization between the timing of egg hatching of a herbivorous insect, the winter moth (Operophtera brumata), and the seasonal bud burst of its food plant, oak (Quercus robur), has been disrupted by climate change and a quantitative genetic model predicts that selection will delay the egg hatching date. Here we show, using both long-term observational data and experiments, that the egg hatching date has changed genetically, resulting in closer synchrony with oak bud burst. The observed rate of change matches the predicted rate of change of one day per year. Hence, altered selection pressures, caused by environmental change, result in a rapid adaptive response in insect phenology. These genetic changes in a key life-history trait in this herbivorous insect therefore seem to be fast enough to match the climate-change-induced advancement of their host phenology.

  19. Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

    Science.gov (United States)

    Chung, Yujin; Hey, Jody

    2017-06-01

    We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest. Once obtained, a single sample of trees can be used in step 2 to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. Because migration paths are not included in the state space of the MCMC phase, but rather are handled by analytic integration in step 2 of the analysis, the method is scalable to a large number of loci with excellent MCMC mixing properties. With an implementation of the new method in the computer program MIST, we demonstrate the method's accuracy, scalability, and other advantages using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes (P. t.) troglodytes and P. t. verus. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Selection of energy source and evolutionary stable strategies for power plants under financial intervention of government

    Science.gov (United States)

    Hafezalkotob, Ashkan; Mahmoudi, Reza

    2017-09-01

    Currently, many socially responsible governments adopt economic incentives and deterrents to manage environmental impacts of electricity suppliers. Considering the Stackelberg leadership of the government, the government's role in the competition of power plants in an electricity market is investigated. A one-population evolutionary game model of power plants is developed to study how their production strategy depends on tariffs levied by the government. We establish that a unique evolutionary stable strategy (ESS) for the population exists. Numerical examples demonstrate that revenue maximization and environment protection policies of the government significantly affect the production ESS of competitive power plants. The results reveal that the government can introduce a green energy source as an ESS of the competitive power plants by imposing appropriate tariffs.

  1. Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

    Science.gov (United States)

    Xing, Yuanzhi; Deng, Xiaoyi

    2017-11-01

    The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

  2. Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication.

    Directory of Open Access Journals (Sweden)

    Karin Voordeckers

    Full Text Available Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

  3. Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change

    Science.gov (United States)

    Davis, Jenny; Pavlova, Alexandra; Thompson, Ross; Sunnucks, Paul

    2013-01-01

    Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refuges based on our review of the attributes of aquatic habitats and freshwater taxa (fishes and aquatic invertebrates) in arid Australia. We also identify methods of recognizing likely future refugia and approaches to assessing the vulnerability of arid-adapted freshwater biota to a warming and drying climate. Evolutionary refugia in arid areas are characterized as permanent, groundwater-dependent habitats (subterranean aquifers and springs) supporting vicariant relicts and short-range endemics. Ecological refuges can vary across space and time, depending on the dispersal abilities of aquatic taxa and the geographical proximity and hydrological connectivity of aquatic habitats. The most important are the perennial waterbodies (both groundwater and surface water fed) that support obligate aquatic organisms. These species will persist where suitable habitats are available and dispersal pathways are maintained. For very mobile species (invertebrates with an aerial dispersal phase) evolutionary refugia may also act as ecological refuges. Evolutionary refugia are likely future refugia because their water source (groundwater) is decoupled from local precipitation. However, their biota is extremely vulnerable to changes in local conditions because population extinction risks cannot be abated by the dispersal of individuals from other sites. Conservation planning must incorporate a high level of protection for aquifers that support refugial sites. Ecological refuges are vulnerable to changes in regional climate because they have little

  4. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories.

    Science.gov (United States)

    Guthrie, Violeta Beleva; Allen, Jennifer; Camps, Manel; Karchin, Rachel

    2011-09-01

    Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess

  5. Evolutionary history of a widespread Indo-Pacific goby: the role of Pleistocene sea-level changes on demographic contraction/expansion dynamics.

    Science.gov (United States)

    Hoareau, Thierry Bernard; Boissin, Emilie; Berrebi, Patrick

    2012-01-01

    Compared to endemics, widespread species are of particular interest to retrace recent evolutionary history. These species have a large population size which provides a clearer genetic signature of past events. Moreover, their wide geographic range increases the potential occurrence of evolutionary events (expansion, divergence, etc.). Here, we used several coalescent-based methods to disentangle the evolutionary history of a widespread amphidromous goby (Sicyopterus lagocephalus), in the light of sea-level variations during the Pleistocene. Using 75 samples recovered from three biogeographic regions (Western Indian Ocean, Melanesia and Polynesia), we analysed a portion of the cytochromeb gene and confirmed three major haplogroups, each specific to a region. Furthermore, we found that: (1) the Melanesian haplogroup was the oldest while the two peripheral regions hosted daughter haplogroups; (2) two centrifugal colonisation events occurred from Melanesia to the periphery, each synchronised with periods of strong paleo-ENSO episodes; (3) the demographic contraction-expansion events were linked to Pleistocene sea-level changes; (4) Melanesia and Polynesia acted as efficient refuges during the Last Glacial Maximum. These results highlight the importance of studying widespread species to better understand the role of climate changes and paleo-oceanography on the evolution of biodiversity. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

    Directory of Open Access Journals (Sweden)

    Cécile Troupin

    2016-12-01

    Full Text Available The natural evolution of rabies virus (RABV provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

  7. Variations in morphological and life-history traits under extreme ...

    Indian Academy of Sciences (India)

    C than at 32°C in D. ananassae. The genetic variations for all the quantitative and life-history traits were higher at low temperature. Variation in sexual traits was more pronounced as compared with other morphometric traits, which shows that ...

  8. Populations under stress : analysis on the interface between ecology and evolutionary genetics in nematodes

    NARCIS (Netherlands)

    Doroszuk, A.

    2007-01-01

    Human activities increasingly affect the natural environment. Consequently, many organisms are confronted with environmental conditions different from the ones they evolved in and experience stress. Environmental stress affects various levels of biological organization (e.g. cell, life-histories,

  9. The evolutionary origin of somatic cells under the dirty work hypothesis.

    Directory of Open Access Journals (Sweden)

    Heather J Goldsby

    2014-05-01

    Full Text Available Reproductive division of labor is a hallmark of multicellular organisms. However, the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear. Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation. We present evidence in support of this hypothesis gathered using a computational form of experimental evolution. Our digital organisms begin each experiment as undifferentiated multicellular individuals, and can evolve computational functions that improve their rate of reproduction. When such functions are associated with moderate mutagenic effects, we observe the evolution of reproductive division of labor within our multicellular organisms. Specifically, a fraction of the cells remove themselves from consideration as propagules for multicellular offspring, while simultaneously performing a disproportionately large amount of mutagenic work, and are thus classified as soma. As a consequence, other cells are able to take on the role of germ, remaining quiescent and thus protecting their genetic information. We analyze the lineages of multicellular organisms that successfully differentiate and discover that they display unforeseen evolutionary trajectories: cells first exhibit developmental patterns that concentrate metabolic work into a subset of germ cells (which we call "pseudo-somatic cells" and later evolve to eliminate the reproductive potential of these cells and thus convert them to actual soma. We also demonstrate that the evolution of somatic cells enables phenotypic strategies that are otherwise not easily accessible to undifferentiated organisms, though expression of these new phenotypic traits typically includes negative side effects such as aging.

  10. Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria).

    Science.gov (United States)

    Foth, C; Brusatte, S L; Butler, R J

    2012-05-01

    Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological and taxonomic diversity during their 145+ million-year evolutionary history. We characterize broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion data sets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace

  11. Attractive evolutionary equilibria

    NARCIS (Netherlands)

    Joosten, Reinoud A.M.G.; Roorda, Berend

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary

  12. Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

    Science.gov (United States)

    Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

    2012-01-01

    Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

  13. Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of African forests since late Miocene

    Czech Academy of Sciences Publication Activity Database

    Bryja, J.; Šumbera, R.; Kerbis Peterhans, J. C.; Aghová, T.; Bryjová, A.; Mikula, Ondřej; Nicolas, V.; Denys, C.; Verheyen, E.

    2017-01-01

    Roč. 44, č. 1 (2017), s. 182-194 ISSN 0305-0270 Institutional support: RVO:67985904 Keywords : Arvicanthini * coastal forests * late Miocene Subject RIV: EA - Cell Biology OBOR OECD: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology Impact factor: 4.248, year: 2016

  14. Solving the Bilevel Facility Location Problem under Preferences by a Stackelberg-Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    José-Fernando Camacho-Vallejo

    2014-01-01

    Full Text Available This research highlights the use of game theory to solve the classical problem of the uncapacitated facility location optimization model with customer order preferences through a bilevel approach. The bilevel model provided herein consists of the classical facility location problem and an optimization of the customer preferences, which are the upper and lower level problems, respectively. Also, two reformulations of the bilevel model are presented, reducing it into a mixed-integer single-level problem. An evolutionary algorithm based on the equilibrium in a Stackelberg’s game is proposed to solve the bilevel model. Numerical experimentation is performed in this study and the results are compared to benchmarks from the existing literature on the subject in order to emphasize the benefits of the proposed approach in terms of solution quality and estimation time.

  15. An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

    Science.gov (United States)

    Waldispühl, Jérôme; Ponty, Yann

    2011-11-01

    The analysis of the relationship between sequences and structures (i.e., how mutations affect structures and reciprocally how structures influence mutations) is essential to decipher the principles driving molecular evolution, to infer the origins of genetic diseases, and to develop bioengineering applications such as the design of artificial molecules. Because their structures can be predicted from the sequence data only, RNA molecules provide a good framework to study this sequence-structure relationship. We recently introduced a suite of algorithms called RNAmutants which allows a complete exploration of RNA sequence-structure maps in polynomial time and space. Formally, RNAmutants takes an input sequence (or seed) to compute the Boltzmann-weighted ensembles of mutants with exactly k mutations, and sample mutations from these ensembles. However, this approach suffers from major limitations. Indeed, since the Boltzmann probabilities of the mutations depend of the free energy of the structures, RNAmutants has difficulties to sample mutant sequences with low G+C-contents. In this article, we introduce an unbiased adaptive sampling algorithm that enables RNAmutants to sample regions of the mutational landscape poorly covered by classical algorithms. We applied these methods to sample mutations with low G+C-contents. These adaptive sampling techniques can be easily adapted to explore other regions of the sequence and structural landscapes which are difficult to sample. Importantly, these algorithms come at a minimal computational cost. We demonstrate the insights offered by these techniques on studies of complete RNA sequence structures maps of sizes up to 40 nucleotides. Our results indicate that the G+C-content has a strong influence on the size and shape of the evolutionary accessible sequence and structural spaces. In particular, we show that low G+C-contents favor the apparition of internal loops and thus possibly the synthesis of tertiary structure motifs. On

  16. Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens).

    Science.gov (United States)

    Krzemińska, Urszula; Morales, Hernán E; Greening, Chris; Nyári, Árpád S; Wilson, Robyn; Song, Beng Kah; Austin, Christopher M; Sunnucks, Paul; Pavlova, Alexandra; Rahman, Sadequr

    2018-04-01

    The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.

  17. Evolutionary principles and their practical application

    Science.gov (United States)

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

  18. Tree Contractions and Evolutionary Trees

    OpenAIRE

    Kao, Ming-Yang

    2001-01-01

    An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T_1 and ...

  19. Neuroendocrine mechanisms underlying behavioral stability: implications for the evolutionary origin of personality.

    Science.gov (United States)

    Duckworth, Renée A

    2015-12-01

    Personality traits are behaviors that show limited flexibility over time and across contexts, and thus understanding their origin requires an understanding of what limits behavioral flexibility. Here, I suggest that insight into the evolutionary origin of personality traits requires determining the relative importance of selection and constraint in producing limits to behavioral flexibility. Natural selection as the primary cause of limits to behavioral flexibility assumes that the default state of behavior is one of high flexibility and predicts that personality variation arises through evolution of buffering mechanisms to stabilize behavioral expression, whereas the constraint hypothesis assumes that the default state is one of limited flexibility and predicts that the neuroendocrine components that underlie personality variation are those most constrained in flexibility. Using recent work on the neurobiology of sensitive periods and maternal programming of offspring behavior, I show that some of the most stable aspects of the neuroendocrine system are structural components and maternally induced epigenetic effects. Evidence of numerous constraints to changes in structural features of the neuroendocrine system and far fewer constraints to flexibility of epigenetic systems suggests that structural constraints play a primary role in the origin of behavioral stability and that epigenetic programming may be more important in generating adaptive variation among individuals. © 2015 New York Academy of Sciences.

  20. The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

    Science.gov (United States)

    Eckert, Andrew J; Wegrzyn, Jill L; Liechty, John D; Lee, Jennifer M; Cumbie, W Patrick; Davis, John M; Goldfarb, Barry; Loopstra, Carol A; Palle, Sreenath R; Quesada, Tania; Langley, Charles H; Neale, David B

    2013-12-01

    A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.

  1. Evolution of man in the light of molecular genetics: a review. Part I. Our evolutionary history and genomics.

    Science.gov (United States)

    Portin, Petter

    2007-07-01

    The discovery in the mid 1970s of efficient methods of DNA sequencing and their subsequent development into more and more rapid procedures followed by sequencing the genomes of many species, including man in 2001, revolutionised the whole of biology. Remarkably, new light could be cast on the evolutionary relations of different species, and the tempo and mode of evolution within a given species, notably man, could quantitatively be illuminated including ongoing evolution possibly involving also the size of the brains. This review is a short summary of the results of the molecular genetic investigations of human evolution including the time and place of the formation of our species, our evolutionary relation to the closest living species relatives as well as extinct forms of the genus Homo. The nature and amount of genetic polymorphism in man is also considered with special emphasis on the causes of this variation, and the role of natural selection in human evolution. A consensus about the mosaic nature of our genome and the rather dynamic structure of our ancestral population is gradually emerging. The modern gene pool has most likely been contributed to several different ancestral demes either before or after the emergence of the anatomically modern human phenotype in the extent that even the nature of the evolutionary lineage leading to the anatomically modern man as a distinct biological species is disputable. Regulation of the function of genes, as well as the evolution of brains will be dealt with in the second part of this review.

  2. Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization.

    Science.gov (United States)

    Yu, Jingyin; Hu, Fan; Dossa, Komivi; Wang, Zhaokai; Ke, Tao

    2017-06-23

    Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily. We performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea. Using Hidden Markov Model search, we identified 3, 21, 140, 200, 115, 147, and 147 UGTs in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa, Arabidopsis thaliana, B. rapa, and B. oleracea, respectively. Phylogenetic analysis revealed that UGT80 gene family is an ancient gene family, which is shared by all plants and UGT74 gene family is shared by ferns and angiosperms, but the remaining UGT gene families were shared by angiosperms. In dicot lineage, UGTs among three species were classified into three subgroups containing 3, 6, and 12 UGT gene families. Analysis of chromosomal distribution indicates that 98.6 and 71.4% of UGTs were located on B. rapa and B. oleracea pseudo-molecules, respectively. Expansion mechanism analyses uncovered that whole genome duplication event exerted larger influence than tandem duplication on expansion of UGT gene families in B. rapa, and B. oleracea. Analysis of selection forces of UGT orthologous gene pairs in B. rapa, and B. oleracea compared to A. thaliana suggested that orthologous genes in B. rapa, and B. oleracea have undergone negative selection, but there were no significant differences between A. thaliana -B. rapa and A. thaliana -B. oleracea lineages. Our comparisons of expression profiling illustrated that UGTs in B. rapa performed more

  3. Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau.

    Science.gov (United States)

    Zhao, Zhe; Li, Shuqiang

    2017-11-01

    Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic

  4. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).

    Science.gov (United States)

    Botero-Castro, Fidel; Tilak, Marie-ka; Justy, Fabienne; Catzeflis, François; Delsuc, Frédéric; Douzery, Emmanuel J P

    2013-12-01

    Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of

  5. The topology of the possible: formal spaces underlying patterns of evolutionary change.

    Science.gov (United States)

    Stadler, B M; Stadler, P F; Wagner, G P; Fontana, W

    2001-11-21

    The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped with a notion of distance, for example, a Euclidean vector space. Recent computational work on a biophysical genotype-phenotype model based on the folding of RNA sequences into secondary structures suggests a rather different picture. If phenotypes are organized according to genetic accessibility, the resulting space lacks a metric and is formalized by an unfamiliar structure, known as a pre-topology. Patterns of phenotypic evolution-such as punctuation, irreversibility, modularity--result naturally from the properties of this space. The classical framework, however, addresses these patterns by exclusively invoking natural selection on suitably imposed fitness landscapes. We propose to extend the explanatory level for phenotypic evolution from fitness considerations alone to include the topological structure of phenotype space as induced by the genotype-phenotype map. We introduce the mathematical concepts and tools necessary to formalize the notion of accessibility pre-topology relative to which we can speak of continuity in the genotype-phenotype map and in evolutionary trajectories. We connect the factorization of a pre-topology into a product space with the notion of phenotypic character and derive a condition for factorization. Based on anecdotal evidence from the RNA model, we conjecture that this condition is not globally fulfilled, but rather confined to regions where the genotype-phenotype map is continuous. Equivalently, local regions of genotype space on which the map is discontinuous are associated with the loss of character autonomy. This is consistent with the importance of these regions for phenotypic innovation. The intention of the present paper is to offer a perspective, a framework to implement this perspective, and a few results illustrating how this framework can

  6. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history evolution, the evolutionary genetics of biological clocks, and small population and meta population dynamics.

  7. 78 FR 50136 - Notice of Information Collection Under Emergency Review: Medical History and Examination for...

    Science.gov (United States)

    2013-08-16

    ... of Information Collection Under Emergency Review: Medical History and Examination for Foreign Service... submit comments by any of the following methods: Web: Persons with access to the Internet may use the... of Information Collection: Medical History and Examination for Foreign Service. OMB Control Number...

  8. Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea.

    Science.gov (United States)

    Petitjean, Céline; Moreira, David; López-García, Purificación; Brochier-Armanet, Céline

    2012-11-26

    In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants). Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses. Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs) to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea. We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.

  9. Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea

    Directory of Open Access Journals (Sweden)

    Petitjean Céline

    2012-11-01

    Full Text Available Abstract Background In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants. Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses. Results Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea. Conclusions We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.

  10. Evolutionary response of the egg hatching date of a herbivorous insect under climate change

    NARCIS (Netherlands)

    van Asch, Margriet; Salis, Lucia; Holleman, Leonard J. M.; van Lith, Bart; Visser, Marcel E.

    Under changing climatic conditions, species need to adapt to their new environment. Genetic adaptation is crucial to prevent population extinction(1) but examples where climate change leads to genetic changes in wild populations have been few(2,3). The synchronization between the timing of egg

  11. Evolutionary response of the egg hatching date of a herbivorous insect under climate change

    NARCIS (Netherlands)

    Van Asch, M.; Salis, L.; Holleman, L.J.M.; van Lith, B.; Visser, M.E.

    2013-01-01

    Under changing climatic conditions, species need to adapt to their new environment. Genetic adaptation is crucial to prevent population extinction1 but examples where climate change leads to genetic changes in wild populations have been few2, 3. The synchronization between the timing of egg hatching

  12. Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

    Directory of Open Access Journals (Sweden)

    Ding Cun-Bang

    2009-10-01

    Full Text Available Abstract Background Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene. Results Two homoeologues of the Acc1 gene were isolated from nearly all the sampled Leymus species using allele-specific primer and were analyzed with those from 35 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1 Leymus is closely related to Psathyrostachys, Agropyron, and Eremopyrum; (2 Psathyrostachys juncea is an ancestral Ns-genome donor of Leymus species; (3 the Xm genome in Leymus may be originated from an ancestral lineage of Agropyron and Eremopyrum triticeum; (4 the Acc1 sequences of Leymus species from the Qinghai-Tibetan plateau are evolutionarily distinct; (5 North America Leymus species might originate from colonization via the Bering land bridge; (6 Leymus originated about 11-12MYA in Eurasia, and adaptive radiation might have occurred in Leymus during the period of 3.7-4.3 MYA and 1.7-2.1 MYA. Conclusion Leymus species have allopolyploid origin. It is hypothesized that the adaptive radiation of Leymus species might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters in Leymus. Our results shed new light on our

  13. Do the historical biogeography and evolutionary history of the digenean Margotrema spp. across central Mexico mirror those of their freshwater fish hosts (Goodeinae?

    Directory of Open Access Journals (Sweden)

    Andrés Martínez-Aquino

    Full Text Available Host-parasite systems provide an ideal platform to study evolution at different levels, including codivergence in a historical biogeography context. In this study we aim to describe biogeographic and codivergent patterns and associated processes of the Goodeinae freshwater fish and their digenean parasite (Margotrema spp. over the last 6.5 Ma (million years, identifying the main factors (host and/or hydrogeomorphology that influenced the evolution of Margotrema. We obtained a species tree for Margotrema spp. using DNA sequence data from mitochondrial and nuclear molecular markers (COI and ITS1, respectively and performed molecular dating to discern divergence events within the genus. The dispersal-extinction-cladogenesis (DEC model was used to describe the historical biogeography of digeneans and applied to cophylogenetic analyses of Margotrema and their goodeine hosts. Our results showed that the evolutionary history of Margotrema has been shaped in close association with its geographic context, especially with the geological history of central Mexico during the Pleistocene. Host-specificity has been established at three levels of historical association: a Species-Species, represented by Xenotaenia resolanae-M. resolanae exclusively found in the Cuzalapa River Basin; b Species-Lineage, represented by Characodon audax-M. bravoae Lineage II, exclusive to the Upper and Middle Mezquital River Basin, and c Tribe-Lineage, including two instances of historical associations among parasites and hosts at the taxonomical level of tribe, one represented by Ilyodontini-M. bravoae Lineage I (distributed across the Ayuquila and Balsas River Basins, and another comprised of Girardinichthyini/Chapalichthyini-M. bravoae Lineage III, found only in the Lerma River Basin. We show that the evolutionary history of the parasites is, on several occasions, in agreement with the phylogenetic and biogeographic history of their hosts. A series of biogeographic and host

  14. Brief Communication: Quantitative- and molecular-genetic differentiation in humans and chimpanzees: implications for the evolutionary processes underlying cranial diversification.

    Science.gov (United States)

    Weaver, Timothy D

    2014-08-01

    Estimates of the amount of genetic differentiation in humans among major geographic regions (e.g., Eastern Asia vs. Europe) from quantitative-genetic analyses of cranial measurements closely match those from classical- and molecular-genetic markers. Typically, among-region differences account for ∼10% of the total variation. This correspondence is generally interpreted as evidence for the importance of neutral evolutionary processes (e.g., genetic drift) in generating among-region differences in human cranial form, but it was initially surprising because human cranial diversity was frequently assumed to show a strong signature of natural selection. Is the human degree of similarity of cranial and DNA-sequence estimates of among-region genetic differentiation unusual? How do comparisons with other taxa illuminate the evolutionary processes underlying cranial diversification? Chimpanzees provide a useful starting point for placing the human results in a broader comparative context, because common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the extant species most closely related to humans. To address these questions, I used 27 cranial measurements collected on a sample of 861 humans and 263 chimpanzees to estimate the amount of genetic differentiation between pairs of groups (between regions for humans and between species or subspecies for chimpanzees). Consistent with previous results, the human cranial estimates are quite similar to published DNA-sequence estimates. In contrast, the chimpanzee cranial estimates are much smaller than published DNA-sequence estimates. It appears that cranial differentiation has been limited in chimpanzees relative to humans. © 2014 Wiley Periodicals, Inc.

  15. Data on the evolutionary history of the V(DJ recombination-activating protein 1 – RAG1 coupled with sequence and variant analyses

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    2016-09-01

    Full Text Available RAG1 protein is one of the key component of RAG complex regulating the V(DJ recombination. There are only few studies for RAG1 concerning evolutionary history, detailed sequence and mutational hotspots. Herein, we present out datasets used for the recent comprehensive study of RAG1 based on sequence, phylogenetic and genetic variant analyses (Kumar et al., 2015 [1]. Protein sequence alignment helped in characterizing the conserved domains and regions of RAG1. It also aided in unraveling ancestral RAG1 in the sea urchin. Human genetic variant analyses revealed 751 mutational hotspots, located both in the coding and the non-coding regions. For further analysis and discussion, see (Kumar et al., 2015 [1].

  16. Evolutionary history of Calosomina ground beetles (Coleoptera, Carabidae, Carabinae) of the world as deduced from sequence comparisons of the mitochondrial ND 5 gene.

    Science.gov (United States)

    Su, Zhi-Hui; Imura, Yûki; Osawa, Syozo

    2005-11-07

    We deduced the phylogenetic relationships of 54 individuals representing 27 species of the Calosomina (Coleoptera, Carabidae) from various regions of the world from the mitochondrial NADH dehydrogenase subunit 5 (ND 5) gene sequences. The results suggest that these Calosomina radiated into 17 lineages within a short time about 30 million years ago (Mya). Most of the lineages are composed of a single genus containing only one or a few species. In some cases, several species classified into the same genus (e.g., Calosoma maximowiczi, Calos. inquisitor and Calos. frigidum) appear separately in independent lineages, while in others a series of species classified into different genera fall into one lineage (e.g., Chrysostigma calidum, Blaptosoma chihuahua, Microcallisthenes wilkesi and Callisthenes spp.). Based on this molecular phylogeny and morphological data, the probable evolutionary history and mode of morphological differentiation of the Calosomina are discussed.

  17. Genetic diversity, evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa

    NARCIS (Netherlands)

    Bertola, L.D.; Hooft, van W.F.; Vrieling, K.; Weerd, de D.R.U.; York, D.S.; Bauer, H.; Prins, H.H.T.; Funston, P.J.; Haes, de H.A.U.; Leirs, H.; Haeringen, van W.A.; Sogbohossou, E.; Tumenta, P.N.; Iongh, de H.H.

    2011-01-01

    Aim In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique

  18. Evolutionary History of the Live-Bearing Endemic Allotoca diazi Species Complex (Actinopterygii, Goodeinae: Evidence of Founder Effect Events in the Mexican Pre-Hispanic Period.

    Directory of Open Access Journals (Sweden)

    Diushi Keri Corona-Santiago

    Full Text Available The evolutionary history of Mexican ichthyofauna has been strongly linked to natural events, and the impact of pre-Hispanic cultures is little known. The live-bearing fish species Allotoca diazi, Allotoca meeki and Allotoca catarinae occur in areas of biological, cultural and economic importance in central Mexico: Pátzcuaro basin, Zirahuén basin, and the Cupatitzio River, respectively. The species are closely related genetically and morphologically, and hypotheses have attempted to explain their systematics and biogeography. Mitochondrial DNA and microsatellite markers were used to investigate the evolutionary history of the complex. The species complex shows minimal genetic differentiation. The separation of A. diazi and A. meeki was dated to 400-7000 years ago, explained by geological and climate events. A bottleneck and reduction of genetic diversity in Allotoca diazi was detected, attributed to recent climate fluctuations and anthropogenic activity. The isolation of A. catarinae occurred ~1900 years ago. No geological events are documented in the area during this period, but the date is contemporary with P'urhépecha culture settlements. This founder effect represents the first evidence of fish species translocation by a pre-Hispanic culture of Mexico. The response of the complex to climate fluctuation, geological changes and human activity in the past and the future according to the ecological niches predictions indicates areas of vulnerability and important information for conservation. The new genetic information showed that the Allotoca diazi complex consist of two genetic groups with an incomplete lineage sorting pattern: Pátzcuaro and Zirahuén lakes, and an introduced population in the Cupatitzio River.

  19. Evolutionary History of the Live-Bearing Endemic Allotoca diazi Species Complex (Actinopterygii, Goodeinae): Evidence of Founder Effect Events in the Mexican Pre-Hispanic Period.

    Science.gov (United States)

    Corona-Santiago, Diushi Keri; Doadrio, Ignacio; Domínguez-Domínguez, Omar

    2015-01-01

    The evolutionary history of Mexican ichthyofauna has been strongly linked to natural events, and the impact of pre-Hispanic cultures is little known. The live-bearing fish species Allotoca diazi, Allotoca meeki and Allotoca catarinae occur in areas of biological, cultural and economic importance in central Mexico: Pátzcuaro basin, Zirahuén basin, and the Cupatitzio River, respectively. The species are closely related genetically and morphologically, and hypotheses have attempted to explain their systematics and biogeography. Mitochondrial DNA and microsatellite markers were used to investigate the evolutionary history of the complex. The species complex shows minimal genetic differentiation. The separation of A. diazi and A. meeki was dated to 400-7000 years ago, explained by geological and climate events. A bottleneck and reduction of genetic diversity in Allotoca diazi was detected, attributed to recent climate fluctuations and anthropogenic activity. The isolation of A. catarinae occurred ~1900 years ago. No geological events are documented in the area during this period, but the date is contemporary with P'urhépecha culture settlements. This founder effect represents the first evidence of fish species translocation by a pre-Hispanic culture of Mexico. The response of the complex to climate fluctuation, geological changes and human activity in the past and the future according to the ecological niches predictions indicates areas of vulnerability and important information for conservation. The new genetic information showed that the Allotoca diazi complex consist of two genetic groups with an incomplete lineage sorting pattern: Pátzcuaro and Zirahuén lakes, and an introduced population in the Cupatitzio River.

  20. Impacts of Evolutionary History on Endangerment in a Changing Climate: Miocene upwelling, Holocene Pluvial Cycles and Endemics at the Mouth of the Colorado River.

    Science.gov (United States)

    Jacobs, D. K.

    2006-12-01

    The environmental conditions communities experienced during their diversification and recent geologic history informs us as to which environmental changes are most likely to impact species in those communities. Three examples follow: 1) Recent compilation of molecular and paleontological data document that higher aspects of the trophic chain in the Pacific Northwest, including the salmon genus Onchoyrhynchus, alcid birds (Auks & Puffins) and crabs of the genus Cancer speciated dramatically in response to enhanced upwelling of the mid Miocene (Jacobs et al. 2004). Consistent with this evolutionary origin, population dynamics and endangerment of these taxa are associated with the changing productivity regime of the Pacific as well as more direct human impacts. 2) Pluvials in the Eurasian and African continent respond to the precession cycle, as a result wetland habitats were much more expansive in the early and middle Holocene. Late Holocene wetland habitat contraction combines with increasing anthropogenic manipulation of these cyclically limited hydrologic resources to yield a suite of endangered taxa across these continents as is statistically documented by analysis of Redbook data. 3) Our recent work documents the evolution of endemic fish and Molluscan taxa in association with the Colorado River Delta. These endemic taxa are then vulnerable to the to impacts on the Colorado Delta where anthropogenic use of water resources combine with the threat of climate provide combined threats to this ecosystem. The Environmental/Evolutionary history of lineages clearly has strong implications for how anthropogenic changes impacts and endangers those lineages. Jacobs D.K. et al. Annu. Rev. Earth Planet. Sci. 2004. 32:601 52

  1. Testing the evolutionary and biogeographical history of Glypthelmins (Digenea: Plagiorchiida), a parasite of anurans, through a simultaneous analysis of molecular and morphological data.

    Science.gov (United States)

    Razo-Mendivil, Ulises; de León, Gerardo Pérez-Ponce

    2011-05-01

    The genus Glypthelmins includes some of the most common digeneans inhabiting the intestine of anurans in the Americas. Phylogenetic analyses of eight species of Glypthelmins and five outgroups, using 26 morphological characters and sequences of cox1, 18S, 5.8S, 28S genes and ITS2 were performed. Additionally, 2 species for which no molecular data have been obtained were included in the analyses. Following a simultaneous analysis approach and using different methods of phylogenetic inference we obtained a phylogenetic tree where the eight studied species conform a monophyletic clade which is well supported by Bremer support, bootstrap, and posterior probabilities. The mapping of morphological characters showed that traits such as serrate scale-like spines, bipartite seminal vesicle, metraterm running dorsal to the cirrus pouch, and ovary sinistral are unequivocal synapomorphies that support the monophyly of Glypthelmins. Phylogenetic hypothesis based on combined data sets was used to re-evaluate the evolutionary and biogeographical history of this group of digeneans. New information provided in this study, in the context of a more robust analytical method allowed us to corroborate that members of the "Rana pipiens" group were the plesiomorphic group of hosts for Glypthelmins, with two host switching events occurring from the "Rana pipiens" group to the "Rana palmipes" group and to Hylidae during the evolutionary history of this group of parasites, and the origin of the group is proposed in Nearctic frogs, with a colonization of Neotropical hosts represented by a monophyletic clade constituted by G. brownorumae, G. facioi, and G. tuxtlasensis. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

    Directory of Open Access Journals (Sweden)

    Kim Kyung Mo

    2012-01-01

    Full Text Available Abstract Background The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya. However, the use of molecular sequence information for deep phylogenetic analyses is limited by mutational saturation, differential evolutionary rates, lack of sequence site independence, and other biological and technical constraints. In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration. Results Here we build phylogenies that describe the evolution of proteins and proteomes. These phylogenetic trees are derived from a genomic census of protein domains defined at the fold family (FF level of structural classification. Phylogenomic trees of FF structures were reconstructed from genomic abundance levels of 2,397 FFs in 420 proteomes of free-living organisms. These trees defined timelines of domain appearance, with time spanning from the origin of proteins to the present. Timelines are divided into five different evolutionary phases according to patterns of sharing of FFs among superkingdoms: (1 a primordial protein world, (2 reductive evolution and the rise of Archaea, (3 the rise of Bacteria from the common ancestor of Bacteria and Eukarya and early development of the three superkingdoms, (4 the rise of Eukarya and widespread organismal diversification, and (5 eukaryal diversification. The relative ancestry of the FFs shows that reductive evolution by domain loss is dominant in the first three phases and is responsible for both the diversification of life from a universal cellular ancestor and the appearance of superkingdoms. On the other hand, domain gains are predominant in the last two phases and are responsible for organismal diversification, especially in Bacteria and Eukarya. Conclusions The evolution of functions that are

  3. Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex

    Directory of Open Access Journals (Sweden)

    Stewart Alan V

    2010-10-01

    Full Text Available Abstract Background The agriculturally important pasture grass tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum (Schreb. Darbysh. is an outbreeding allohexaploid, that may be more accurately described as a species complex consisting of three major (Continental, Mediterranean and rhizomatous morphotypes. Observation of hybrid infertility in some crossing combinations between morphotypes suggests the possibility of independent origins from different diploid progenitors. This study aims to clarify the evolutionary relationships between each tall fescue morphotype through phylogenetic analysis using two low-copy nuclear genes (encoding plastid acetyl-CoA carboxylase [Acc1] and centroradialis [CEN], the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS and the chloroplast DNA (cpDNA genome-located matK gene. Other taxa within the closely related Lolium-Festuca species complex were also included in the study, to increase understanding of evolutionary processes in a taxonomic group characterised by multiple inter-specific hybridisation events. Results Putative homoeologous sequences from both nuclear genes were obtained from each polyploid species and compared to counterparts from 15 diploid taxa. Phylogenetic reconstruction confirmed F. pratensis and F. arundinacea var. glaucescens as probable progenitors to Continental tall fescue, and these species are also likely to be ancestral to the rhizomatous morphotype. However, these two morphotypes are sufficiently distinct to be located in separate clades based on the ITS-derived data set. All four of the generated data sets suggest independent evolution of the Mediterranean and Continental morphotypes, with minimal affinity between cognate sequence haplotypes. No obvious candidate progenitor species for Mediterranean tall fescues were identified, and only two putative sub-genome-specific haplotypes were identified for this morphotype. Conclusions This study describes the first

  4. Child mortality estimation: consistency of under-five mortality rate estimates using full birth histories and summary birth histories.

    Directory of Open Access Journals (Sweden)

    Romesh Silva

    Full Text Available Given the lack of complete vital registration data in most developing countries, for many countries it is not possible to accurately estimate under-five mortality rates from vital registration systems. Heavy reliance is often placed on direct and indirect methods for analyzing data collected from birth histories to estimate under-five mortality rates. Yet few systematic comparisons of these methods have been undertaken. This paper investigates whether analysts should use both direct and indirect estimates from full birth histories, and under what circumstances indirect estimates derived from summary birth histories should be used.Usings Demographic and Health Surveys data from West Africa, East Africa, Latin America, and South/Southeast Asia, I quantify the differences between direct and indirect estimates of under-five mortality rates, analyze data quality issues, note the relative effects of these issues, and test whether these issues explain the observed differences. I find that indirect estimates are generally consistent with direct estimates, after adjustment for fertility change and birth transference, but don't add substantial additional insight beyond direct estimates. However, choice of direct or indirect method was found to be important in terms of both the adjustment for data errors and the assumptions made about fertility.Although adjusted indirect estimates are generally consistent with adjusted direct estimates, some notable inconsistencies were observed for countries that had experienced either a political or economic crisis or stalled health transition in their recent past. This result suggests that when a population has experienced a smooth mortality decline or only short periods of excess mortality, both adjusted methods perform equally well. However, the observed inconsistencies identified suggest that the indirect method is particularly prone to bias resulting from violations of its strong assumptions about recent mortality

  5. Islands in the desert: Species delimitation and evolutionary history of Pseudotetracha tiger beetles (Coleoptera: Cicindelidae: Megacephalini) from Australian salt lakes.

    Science.gov (United States)

    López-López, Alejandro; Hudson, Peter; Galián, José

    2016-08-01

    The Australian salt lakes are a natural archipelago-like laboratory for investigating evolutionary and population processes. Their environmental conditions have not undergone relevant changes since the aridification of Australia 10-5 million years ago. The genus Pseudotetracha, a group of nocturnal tiger beetles found on these remote salt lakes, includes 20 described species. Recent studies based on molecular markers and cytogenetics hinted at the existence of cryptic species within this group. Here we use various species delimitation algorithms to detect a high number of cryptic and undescribed taxa, and challenge the validity of the taxonomic characters traditionally used for discerning species in this group. Our analyses show that the divergence dates of the clades, between 10 and 5 million years ago, correspond to the period in which Australia was undergoing an aridification process that probably isolated the ancestral Pseudotetracha populations to individual lakes or palaeodrainage basins. This implies an important role of the isolation, produced by the aridification of Australia, in the speciation and divergence of Pseudotetracha, which underwent a remarkable radiation as the populations became geographically restricted. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores.

    Science.gov (United States)

    Kim, Soonok; Cho, Yun Sung; Bhak, Jong; O'Brian, Stephen J; Yeo, Joo-Hong

    2017-01-01

    Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. [BMB Reports 2017; 50(1): 3-4].

  7. Evolutionary history of the PER3 variable number of tandem repeats (VNTR): idiosyncratic aspect of primate molecular circadian clock.

    Science.gov (United States)

    Sabino, Flávia Cal; Ribeiro, Amanda Oliveira; Tufik, Sérgio; Torres, Laila Brito; Oliveira, José Américo; Mello, Luiz Eugênio Araújo Moraes; Cavalcante, Jeferson Souza; Pedrazzoli, Mario

    2014-01-01

    The PER3 gene is one of the clock genes, which function in the core mammalian molecular circadian system. A variable number of tandem repeats (VNTR) locus in the 18th exon of this gene has been strongly associated to circadian rhythm phenotypes and sleep organization in humans, but it has not been identified in other mammals except primates. To better understand the evolution and the placement of the PER3 VNTR in a phylogenetical context, the present study enlarges the investigation about the presence and the structure of this variable region in a large sample of primate species and other mammals. The analysis of the results has revealed that the PER3 VNTR occurs exclusively in simiiforme primates and that the number of copies of the primitive unit ranges from 2 to 11 across different primate species. Two transposable elements surrounding the 18th exon of PER3 were found in primates with published genome sequences, including the tarsiiforme Tarsius syrichta, which lacks the VNTR. These results suggest that this VNTR may have evolved in a common ancestor of the simiiforme branch and that the evolutionary copy number differentiation of this VNTR may be associated with primate simiiformes sleep and circadian phenotype patterns.

  8. Evolutionary history of the PER3 variable number of tandem repeats (VNTR: idiosyncratic aspect of primate molecular circadian clock.

    Directory of Open Access Journals (Sweden)

    Flávia Cal Sabino

    Full Text Available The PER3 gene is one of the clock genes, which function in the core mammalian molecular circadian system. A variable number of tandem repeats (VNTR locus in the 18th exon of this gene has been strongly associated to circadian rhythm phenotypes and sleep organization in humans, but it has not been identified in other mammals except primates. To better understand the evolution and the placement of the PER3 VNTR in a phylogenetical context, the present study enlarges the investigation about the presence and the structure of this variable region in a large sample of primate species and other mammals. The analysis of the results has revealed that the PER3 VNTR occurs exclusively in simiiforme primates and that the number of copies of the primitive unit ranges from 2 to 11 across different primate species. Two transposable elements surrounding the 18th exon of PER3 were found in primates with published genome sequences, including the tarsiiforme Tarsius syrichta, which lacks the VNTR. These results suggest that this VNTR may have evolved in a common ancestor of the simiiforme branch and that the evolutionary copy number differentiation of this VNTR may be associated with primate simiiformes sleep and circadian phenotype patterns.

  9. Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae family.

    Science.gov (United States)

    Perazzolli, Michele; Malacarne, Giulia; Baldo, Angela; Righetti, Laura; Bailey, Aubrey; Fontana, Paolo; Velasco, Riccardo; Malnoy, Mickael

    2014-01-01

    The family of resistance gene analogues (RGAs) with a nucleotide-binding site (NBS) domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh.) cultivar 'Golden Delicious'. This represents 1.51% of the total number of predicted genes for this cultivar. Several evolutionary features are pronounced in M. domestica, including a high fraction (80%) of RGAs occurring in clusters. This suggests frequent tandem duplication and ectopic translocation events. Of the identified RGAs, 56% are located preferentially on six chromosomes (Chr 2, 7, 8, 10, 11, and 15), and 25% are located on Chr 2. TIR-NBS and non-TIR-NBS classes of RGAs are primarily exclusive of different chromosomes, and 99% of non-TIR-NBS RGAs are located on Chr 11. A phylogenetic reconstruction was conducted to study the evolution of RGAs in the Rosaceae family. More than 1400 RGAs were identified in six species based on their NBS domain, and a neighbor-joining analysis was used to reconstruct the phylogenetic relationships among the protein sequences. Specific phylogenetic clades were found for RGAs of Malus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, and Prunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.

  10. 'Candidatus Megaira polyxenophila' gen. nov., sp. nov.: considerations on evolutionary history, host range and shift of early divergent rickettsiae.

    Directory of Open Access Journals (Sweden)

    Martina Schrallhammer

    Full Text Available "Neglected Rickettsiaceae" (i.e. those harboured by non-hematophagous eukaryotic hosts display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora; furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta. Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.

  11. The wild type as concept and in experimental practice: A history of its role in classical genetics and evolutionary theory.

    Science.gov (United States)

    Holmes, Tarquin

    2017-06-01

    Wild types in genetics are specialised strains of laboratory experimental organism which principally serve as standards against which variation is measured. As selectively inbred lineages highly isolated from ancestral wild populations, there appears to be little wild or typical about them. I will nonetheless argue that they have historically been successfully used as stand-ins for nature, allowing knowledge produced in the laboratory to be extrapolated to the natural world. In this paper, I will explore the 19th century origins of the wild type concept, the theoretical and experimental innovations which allowed concepts and organisms to move from wild nature to laboratory domestication c. 1900 (resulting in the production of standardised lab strains), and the conflict among early geneticists between interactionist and atomist accounts of wild type, which would eventually lead to the conceptual disintegration of wild types and the triumph of genocentrism and population genetics. I conclude by discussing how the strategy of using wild type strains to represent nature in the lab has nonetheless survived the downfall of the wild type concept and continues to provide, significant limitations acknowledged, an epistemically productive means of investigating heredity and evolutionary variation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Characterization of resistance gene analogues (RGAs in apple (Malus × domestica Borkh. and their evolutionary history of the Rosaceae family.

    Directory of Open Access Journals (Sweden)

    Michele Perazzolli

    Full Text Available The family of resistance gene analogues (RGAs with a nucleotide-binding site (NBS domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh. cultivar 'Golden Delicious'. This represents 1.51% of the total number of predicted genes for this cultivar. Several evolutionary features are pronounced in M. domestica, including a high fraction (80% of RGAs occurring in clusters. This suggests frequent tandem duplication and ectopic translocation events. Of the identified RGAs, 56% are located preferentially on six chromosomes (Chr 2, 7, 8, 10, 11, and 15, and 25% are located on Chr 2. TIR-NBS and non-TIR-NBS classes of RGAs are primarily exclusive of different chromosomes, and 99% of non-TIR-NBS RGAs are located on Chr 11. A phylogenetic reconstruction was conducted to study the evolution of RGAs in the Rosaceae family. More than 1400 RGAs were identified in six species based on their NBS domain, and a neighbor-joining analysis was used to reconstruct the phylogenetic relationships among the protein sequences. Specific phylogenetic clades were found for RGAs of Malus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, and Prunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.

  13. Fast computation of a string duplication history under no-breakpoint-reuse

    Science.gov (United States)

    Brejová, Broňa; Kravec, Martin; Landau, Gad M.; Vinař, Tomáš

    2014-01-01

    In this paper, we provide an O(n log2 n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. The motivation of this problem stems from computational biology, in particular, from analysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but, in our scenario, the start of the history is not fixed, but chosen to minimize the distance measure. PMID:24751867

  14. Stellar models simulating the disk-locking mechanism and the evolutionary history of the Orion Nebula cluster and NGC 2264

    Science.gov (United States)

    Landin, N. R.; Mendes, L. T. S.; Vaz, L. P. R.; Alencar, S. H. P.

    2016-02-01

    Context. Rotational evolution in young stars is described by pre-main sequence evolutionary tracks including non-gray boundary conditions, rotation, conservation of angular momentum, and simulations of disk-locking. Aims: By assuming that disk-locking is the regulation mechanism for the stellar angular velocity during the early stages of pre-main sequence evolution, we use our rotating models and observational data to constrain disk lifetimes (Tdisk) of a representative sample of low-mass stars in two young clusters, the Orion Nebula cluster (ONC) and NGC 2264, and to better understand their rotational evolution. Methods: The period distributions of the ONC and NGC 2264 are known to be bimodal and to depend on the stellar mass. To follow the rotational evolution of these two clusters' stars, we generated sets of evolutionary tracks from a fully convective configuration with low central temperatures (before D- and Li-burning). We assumed that the evolution of fast rotators can be represented by models considering conservation of angular momentum during all stages and of moderate rotators by models considering conservation of angular velocity during the first stages of evolution. With these models we estimate a mass and an age for all stars. Results: The resulting mass distribution for the bulk of the cluster population is in the ranges of 0.2-0.4 M⊙ and 0.1-0.6 M⊙ for the ONC and NGC 2264, respectively. For the ONC, we assume that the secondary peak in the period distribution is due to high-mass objects still locked in their disks, with a locking period (Plock) of ~8 days. For NGC 2264 we make two hypotheses: (1) the stars in the secondary peak are still locked with Plock = 5 days, and (2) NGC 2264 is in a later stage in the rotational evolution. Hypothesis 2 implies in a disk-locking scenario with Plock = 8 days, a disk lifetime of 1 Myr and, after that, constant angular momentum evolution. We then simulated the period distribution of NGC 2264 when the mean age

  15. Tracing hepatitis B virus (HBV genotype B5 (formerly B6 evolutionary history in the circumpolar Arctic through phylogeographic modelling

    Directory of Open Access Journals (Sweden)

    Remco Bouckaert

    2017-08-01

    Full Text Available Background Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence with hepatitis B virus (HBV, with subgenotype B5 (formerly B6 unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. Methods To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2 using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10−5 substitutions/site/year. Results Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901], HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic. Discussion HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

  16. Evolutionary history and leaf succulence as explanations for medicinal use in aloes and the global popularity of Aloe vera.

    Science.gov (United States)

    Grace, Olwen M; Buerki, Sven; Symonds, Matthew R E; Forest, Félix; van Wyk, Abraham E; Smith, Gideon F; Klopper, Ronell R; Bjorå, Charlotte S; Neale, Sophie; Demissew, Sebsebe; Simmonds, Monique S J; Rønsted, Nina

    2015-02-26

    Aloe vera supports a substantial global trade yet its wild origins, and explanations for its popularity over 500 related Aloe species in one of the world's largest succulent groups, have remained uncertain. We developed an explicit phylogenetic framework to explore links between the rich traditions of medicinal use and leaf succulence in aloes. The phylogenetic hypothesis clarifies the origins of Aloe vera to the Arabian Peninsula at the northernmost limits of the range for aloes. The genus Aloe originated in southern Africa ~16 million years ago and underwent two major radiations driven by different speciation processes, giving rise to the extraordinary diversity known today. Large, succulent leaves typical of medicinal aloes arose during the most recent diversification ~10 million years ago and are strongly correlated to the phylogeny and to the likelihood of a species being used for medicine. A significant, albeit weak, phylogenetic signal is evident in the medicinal uses of aloes, suggesting that the properties for which they are valued do not occur randomly across the branches of the phylogenetic tree. Phylogenetic investigation of plant use and leaf succulence among aloes has yielded new explanations for the extraordinary market dominance of Aloe vera. The industry preference for Aloe vera appears to be due to its proximity to important historic trade routes, and early introduction to trade and cultivation. Well-developed succulent leaf mesophyll tissue, an adaptive feature that likely contributed to the ecological success of the genus Aloe, is the main predictor for medicinal use among Aloe species, whereas evolutionary loss of succulence tends to be associated with losses of medicinal use. Phylogenetic analyses of plant use offer potential to understand patterns in the value of global plant diversity.

  17. Fitness costs associated with unnecessary virulence factors and life history traits: evolutionary insights from the potato late blight pathogen Phytophthora infestans

    Directory of Open Access Journals (Sweden)

    Corbi Roselyneère

    2010-09-01

    Full Text Available Abstract Background In gene-for-gene models of plant-pathogen interactions, the existence of fitness costs associated with unnecessary virulence factors still represents an issue, both in evolutionary biology and agricultural sciences. Measuring such costs experimentally has proven difficult, especially in pathogens not readily amenable to genetic transformation, since the creation of isogenic lines differing only by the presence or absence of avirulence genes cannot be achieved in many organisms. Here, we circumvented this difficulty by comparing fitness traits in groups of Phytophthora infestans isolates sharing the same multilocus fingerprint, but differing by their virulence/avirulence spectrum. Results Fitness was assessed from calculations derived from the basic reproduction number, combining several life history traits (latent period, spore density and lesion growth rate evaluated on leaflets of the potato cultivar Bintje, which is free of resistance genes. A statistically significant fitness cost was found in isolates virulent to the R10 resistance gene. That cost was due to a lower spore production in virulent isolates; however, the latent period was shorter in virulent isolates. Similar trends, although not statistically significant, were observed for the other genes tested. Conclusion The data likely reflect the adaptive response of the pathogen to the cost associated with virulence. They suggest strong trade-offs between life history traits related to pathogenicity and adaptive biology of pathogens.

  18. The First Joke: Exploring the Evolutionary Origins of Humor

    Directory of Open Access Journals (Sweden)

    Joseph Polimeni

    2006-01-01

    Full Text Available Humor is a complex cognitive function which often leads to laughter. Contemporary humor theorists have begun to formulate hypotheses outlining the possible innate cognitive structures underlying humor. Humor's conspicuous presence in the behavioral repertoire of humankind invites adaptive explanations. This article explores the possible adaptive features of humor and ponders its evolutionary path through hominid history. Current humor theories and previous evolutionary ideas on humor are reviewed. In addition, scientific fields germane to the evolutionary study of humor are examined: animal models, genetics, children's humor, humor in pathological conditions, neurobiology, humor in traditional societies and cognitive archeology. Candidate selection pressures and associated evolutionary mechanisms are considered. The authors conclude that several evolutionary-related topics such as the origins of language, cognition underlying spiritual feelings, hominid group size, and primate teasing could have special relevance to the origins of humor.

  19. The mean and variance of climate change in the oceans: hidden evolutionary potential under stochastic environmental variability in marine sticklebacks.

    Science.gov (United States)

    Shama, Lisa N S

    2017-08-21

    Increasing climate variability may pose an even greater risk to species than climate warming because temperature fluctuations can amplify adverse impacts of directional warming on fitness-related traits. Here, the influence of directional warming and increasing climate variability on marine stickleback fish (Gasterosteus aculeatus) offspring size variation was investigated by simulating changes to the mean and variance of ocean temperatures predicted under climate change. Reproductive traits of mothers and offspring size reaction norms across four climate scenarios were examined to assess the roles of standing genetic variation, transgenerational and within-generation plasticity in adaptive potential. Mothers acclimated to directional warming produced smaller eggs than mothers in constant, ambient temperatures, whereas mothers in a predictably variable environment (weekly change between temperatures) produced a range of egg sizes, possibly reflecting a diversified bet hedging strategy. Offspring size post-hatch was mostly influenced by genotype by environment interactions and not transgenerational effects. Offspring size reaction norms also differed depending on the type of environmental predictability (predictably variable vs. stochastic), with offspring reaching the largest sizes in the stochastic environment. Release of cryptic genetic variation for offspring size in the stochastic environment suggests hidden evolutionary potential in this wild population to respond to changes in environmental predictability.

  20. The Evolutionary History of MAPL (Mitochondria-Associated Protein Ligase and Other Eukaryotic BAM/GIDE Domain Proteins.

    Directory of Open Access Journals (Sweden)

    Jeremy G Wideman

    Full Text Available MAPL (mitochondria-associated protein ligase, also called MULAN/GIDE/MUL1 is a multifunctional mitochondrial outer membrane protein found in human cells that contains a unique BAM (beside a membrane domain and a C-terminal RING-finger domain. MAPL has been implicated in several processes that occur in animal cells such as NF-kB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. Previous studies demonstrated that the BAM domain is present in diverse organisms in which most of these processes do not occur, including plants, archaea, and bacteria. Thus the conserved function of MAPL and its BAM domain remains an open question. In order to gain insight into its conserved function, we investigated the evolutionary origins of MAPL by searching for homologues in predicted proteomes of diverse eukaryotes. We show that MAPL proteins with a conserved BAM-RING architecture are present in most animals, protists closely related to animals, a single species of fungus, and several multicellular plants and related green algae. Phylogenetic analysis demonstrated that eukaryotic MAPL proteins originate from a common ancestor and not from independent horizontal gene transfers from bacteria. We also determined that two independent duplications of MAPL occurred, one at the base of multicellular plants and another at the base of vertebrates. Although no other eukaryote genome examined contained a verifiable MAPL orthologue, BAM domain-containing proteins were identified in the protists Bigelowiella natans and Ectocarpus siliculosis. Phylogenetic analyses demonstrated that these proteins are more closely related to prokaryotic BAM proteins and therefore likely arose from independent horizontal gene transfers from bacteria. We conclude that MAPL proteins with BAM-RING architectures have been present in the holozoan and viridiplantae lineages since their very beginnings

  1. Tracing the trans-pacific evolutionary history of a domesticated Seaweed (Gracilaria chilensis with archaeological and genetic data.

    Directory of Open Access Journals (Sweden)

    Marie-Laure Guillemin

    Full Text Available The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile.

  2. Tracing the trans-pacific evolutionary history of a domesticated Seaweed (Gracilaria chilensis) with archaeological and genetic data.

    Science.gov (United States)

    Guillemin, Marie-Laure; Valero, Myriam; Faugeron, Sylvain; Nelson, Wendy; Destombe, Christophe

    2014-01-01

    The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile.

  3. New light on the evolutionary history of the common goby (Pomatoschistus microps with an emphasis on colonization processes in the Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Christelle Tougard

    Full Text Available Through the study of the phylogeographic structure and demographic history of the common goby, Pomatoschistus microps, the influence of Quaternary climatic changes on the evolutionary history of coastal and marine fishes is investigated. Because of its sedentary life cycle in Mediterranean lagoons, it is also a good model to study more specifically if the formation of lagoons during the Holocene had an impact on population structure and demography. Mitochondrial sequences of Northeastern Atlantic and Western Mediterranean specimens were used for phylogenetic reconstructions as well as divergence time estimates, demographic history and population structure analyses. Pomatoschistus microps was a highly supported monophyletic clade including four lineages. It may have appeared 77,000 yr ago, and the divergence of its lineages likely occured shortly thereafter (between 61,000 and 54,000 yr. Most lineages had polytomic topologies, low nucleotide diversity and demographic analyses providing evidence of population expansion. Each lineage was characterized by a large number of private haplotypes. Most haplotypes found in Mediterranean localities were endemic, and one was dominant. Complex reticulated relationships connecting North European, Atlantic and Mediterranean haplotypes were observed. Moderate to high population structure was underlined. Contrary to previous published studies, no significant differentiation was observed between Atlantic and Mediterranean populations, indicating that the Gibraltar Strait is not a phylogeographic break for P. microps. Indeed, molecular dating combined with the tree topologies, phylogeographic and demographic analyses as well as high haplotype diversity underline a recent and rapid population divergence during the last glacial. However, population structure indicates that differentiation is an ongoing process. From an ancestral population trapped in the Atlantic, this goby colonized first northern Europe and later

  4. An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae.

    Science.gov (United States)

    Blanquart, François; Lehtinen, Sonja; Fraser, Christophe

    2017-05-31

    The frequency of resistance to antibiotics in Streptococcus pneumoniae has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates in phase with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.

  5. Multi-gene phylogenetic analyses reveal species limits, phylogeographic patterns, and evolutionary histories of key morphological traits in Entoloma (Agaricales, Basidiomycota).

    Science.gov (United States)

    Morgado, L N; Noordeloos, M E; Lamoureux, Y; Geml, J

    2013-12-01

    Species from Entoloma subg. Entoloma are commonly recorded from both the Northern and Southern Hemispheres and, according to literature, most of them have at least Nearctic-Palearctic distributions. However, these records are based on morphological analysis, and studies relating morphology, molecular data and geographical distribution have not been reported. In this study, we used phylogenetic species recognition criteria through gene genealogical concordance (based on nuclear ITS, LSU, rpb2 and mitochondrial SSU) to answer specific questions considering species limits in Entoloma subg. Entoloma and their geographic distribution in Europe, North America and Australasia. The studied morphotaxa belong to sect. Entoloma, namely species like the notorious poisonous E. sinuatum (E. lividum auct.), E. prunuloides (type-species of sect. Entoloma), E. nitidum and the red-listed E. bloxamii. With a few exceptions, our results reveal strong phylogeographical partitions that were previously not known. For example, no collection from Australasia proved to be conspecific with the Northern Hemisphere specimens. Almost all North American collections represent distinct and sister taxa to the European ones. And even within Europe, new lineages were uncovered for the red-listed E. bloxamii, which were previously unknown due to a broad morphological species concept. Our results clearly demonstrate the power of the phylogenetic species concept to reveal evolutionary units, to redefine the morphological limits of the species addressed and to provide insights into the evolutionary history of key morphological characters for Entoloma systematics. New taxa are described, and new combinations are made, including E. fumosobrunneum, E. pseudoprunuloides, E. ochreoprunuloides and E. caesiolamellatum. Epitypes are selected for E. prunuloides and E. bloxamii. In addition, complete descriptions are given of some other taxa used in this study for which modern descriptions are lacking, viz. E

  6. Exploring climate niches of ponderosa pine (Pinus ponderosa Douglas ex Lawson) haplotypes in the western United States: Implications for evolutionary history and conservation

    Science.gov (United States)

    Shinneman, Douglas; Means, Robert E.; Potter, Kevin M.; Hipkins, Valerie D.

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with

  7. Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers.

    Science.gov (United States)

    Østbye, K; Bernatchez, L; Naesje, T F; Himberg, K-J M; Hindar, K

    2005-12-01

    We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500-5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.

  8. Exploring Climate Niches of Ponderosa Pine (Pinus ponderosa Douglas ex Lawson) Haplotypes in the Western United States: Implications for Evolutionary History and Conservation.

    Science.gov (United States)

    Shinneman, Douglas J; Means, Robert E; Potter, Kevin M; Hipkins, Valerie D

    2016-01-01

    Ponderosa pine (Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific (P. p. var. ponderosa) and Rocky Mountain (P. p. var. scopulorum) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P. p. vars. ponderosa and scopulorum, respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with discrete

  9. Diversity and Evolutionary Histories of Human Coronaviruses NL63 and 229E Associated with Acute Upper Respiratory Tract Symptoms in Kuala Lumpur, Malaysia.

    Science.gov (United States)

    Al-Khannaq, Maryam Nabiel; Ng, Kim Tien; Oong, Xiang Yong; Pang, Yong Kek; Takebe, Yutaka; Chook, Jack Bee; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2016-05-04

    The human alphacoronaviruses HCoV-NL63 and HCoV-229E are commonly associated with upper respiratory tract infections (URTI). Information on their molecular epidemiology and evolutionary dynamics in the tropical region of southeast Asia however is limited. Here, we analyzed the phylogenetic, temporal distribution, population history, and clinical manifestations among patients infected with HCoV-NL63 and HCoV-229E. Nasopharyngeal swabs were collected from 2,060 consenting adults presented with acute URTI symptoms in Kuala Lumpur, Malaysia, between 2012 and 2013. The presence of HCoV-NL63 and HCoV-229E was detected using multiplex polymerase chain reaction (PCR). The spike glycoprotein, nucleocapsid, and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. A total of 68/2,060 (3.3%) subjects were positive for human alphacoronavirus; HCoV-NL63 and HCoV-229E were detected in 45 (2.2%) and 23 (1.1%) patients, respectively. A peak in the number of HCoV-NL63 infections was recorded between June and October 2012. Phylogenetic inference revealed that 62.8% of HCoV-NL63 infections belonged to genotype B, 37.2% was genotype C, while all HCoV-229E sequences were clustered within group 4. Molecular dating analysis indicated that the origin of HCoV-NL63 was dated to 1921, before it diverged into genotype A (1975), genotype B (1996), and genotype C (2003). The root of the HCoV-229E tree was dated to 1955, before it diverged into groups 1-4 between the 1970s and 1990s. The study described the seasonality, molecular diversity, and evolutionary dynamics of human alphacoronavirus infections in a tropical region. © The American Society of Tropical Medicine and Hygiene.

  10. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

    Science.gov (United States)

    Li, Cai; Zhang, Yong; Li, Jianwen; Kong, Lesheng; Hu, Haofu; Pan, Hailin; Xu, Luohao; Deng, Yuan; Li, Qiye; Jin, Lijun; Yu, Hao; Chen, Yan; Liu, Binghang; Yang, Linfeng; Liu, Shiping; Zhang, Yan; Lang, Yongshan; Xia, Jinquan; He, Weiming; Shi, Qiong; Subramanian, Sankar; Millar, Craig D; Meader, Stephen; Rands, Chris M; Fujita, Matthew K; Greenwold, Matthew J; Castoe, Todd A; Pollock, David D; Gu, Wanjun; Nam, Kiwoong; Ellegren, Hans; Ho, Simon Yw; Burt, David W; Ponting, Chris P; Jarvis, Erich D; Gilbert, M Thomas P; Yang, Huanming; Wang, Jian; Lambert, David M; Wang, Jun; Zhang, Guojie

    2014-01-01

    Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

  11. Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest

    Science.gov (United States)

    Ribeiro, R A; Lemos-Filho, J P; Ramos, A C S; Lovato, M B

    2011-01-01

    The Brazilian rosewood (Dalbergia nigra) is an endangered tree endemic to the central Brazilian Atlantic Forest, one of the world's most threatened biomes. The population diversity, phylogeographic structure and demographic history of this species were investigated using the variation in the chloroplast DNA (cpDNA) sequences of 185 individuals from 19 populations along the geographical range of the species. Fifteen haplotypes were detected in the analysis of 1297 bp from two non-coding sequences, trnV-trnM and trnL. We identified a strong genetic structure (FST=0.62, Pclimatic changes in the central part of the Atlantic forest, with cycles of forest expansion and contraction, may have led to repeated vicariance events, resulting in the genetic differentiation of these groups. Based on comparisons among the populations of large reserves and small, disturbed fragments of the same phylogeographic group, we also found evidence of recent anthropogenic effects on genetic diversity. The results were also analysed with the aim of contributing to the conservation of D. nigra. We suggest that the three phylogeographic groups could be considered as three distinct management units. Based on the genetic diversity and uniqueness of the populations, we also indicate priority areas for conservation. PMID:20517347

  12. High incidence of interchromosomal transpositions in the evolutionary history of a subset of or genes in Drosophila.

    Science.gov (United States)

    Conceição, Inês C; Aguadé, Montserrat

    2008-04-01

    In insects, the odorant receptor (Or) multigene family is an intermediate-sized family with genes present in all chromosomes, indicating that duplication followed by interchromosomal transposition played an important role in the early stages of the family evolution. Here, we have explored the occurrence of interchromosomal transpositions in more recent stages through the comparative analysis of a subset of Or genes in Drosophila, where the gene content of chromosomal arms is highly conserved. The studied subset consisted of 11 Or genes located on the left arm of chromosome 3 (Muller's D element) in D. melanogaster. Our study focused on the number and chromosomal arm location of these members of the family across the 12 Drosophila species with complete genome sequences. In contrast to previous results from in situ hybridization comparative mapping that were mainly based on single-copy genes, our study, based on members of a multigene family of moderate size, revealed repeated interchromosomal transposition events and a complex history of some of the studied genes.

  13. Testing evolutionary theories of menopause.

    Science.gov (United States)

    Shanley, Daryl P; Sear, Rebecca; Mace, Ruth; Kirkwood, Thomas B L

    2007-12-07

    Why do women cease fertility rather abruptly through menopause at an age well before generalized senescence renders child rearing biologically impossible? The two main evolutionary hypotheses are that menopause serves either (i) to protect mothers from rising age-specific maternal mortality risks, thereby protecting their highly dependent younger children from death if the mother dies or (ii) to provide post-reproductive grandmothers who enhance their inclusive fitness by helping to care and provide for their daughters' children. Recent theoretical work indicates that both factors together are necessary if menopause is to provide an evolutionary advantage. However, these ideas need to be tested using detailed data from actual human life histories lived under reasonably 'natural' conditions; for obvious reasons, such data are extremely scarce. We here describe a study based on a remarkably complete dataset from The Gambia. The data provided quantitative estimates for key parameters for the theoretical model, which were then used to assess the actual effects on fitness. Empirically based numerical analysis of this nature is essential if the enigma of menopause is to be explained satisfactorily in evolutionary terms. Our results point to the distinctive (and perhaps unique) role of menopause in human evolution and provide important support for the hypothesized evolutionary significance of grandmothers.

  14. History-dependent coupled growth of creep damage under variable stress conditions

    Science.gov (United States)

    Kawai, M.

    1998-08-01

    A multiaxial constitutive model is presented for the description of the history-dependent inelastic and damage behavior of polycrystalline metallic materials in the high-temperature range under variable loading conditions. A particular emphasis is placed on a new formulation for the history-dependent material degradation which is based on a coupling between hardening and damage. The total damage is given by the sum of damage components which have different history dependence. The associated continuum damage variables are defined through their evolution equations coupled with hardening parameters involved with a kinematic hardening model. The non-classical coupling between hardening and damage is incorporated into the modified kinematic hardening model which has. been developed for describing the complicated hardening and softening behavior under repeated stress changes. Numerical simulations for different material parameters show that the proposed damage-coupled constitutive model can predict an acceleration as well as a deceleration of creep damage growth due to stress variations.

  15. New fossils from the Paleogene of central Libya illuminate the evolutionary history of endemic African anomaluroid rodents

    Directory of Open Access Journals (Sweden)

    Pauline eCoster

    2015-10-01

    Full Text Available Anomaluroid rodents show interesting biogeographic and macroevolutionary patterns, although their fossil record is meager and knowledge of the natural history of extant members of the clade remains inadequate. Living anomaluroids (Anomaluridae are confined to equatorial parts of western and central Africa, but the oldest known fossil anomaluroid (Pondaungimys comes from the late middle Eocene of Myanmar. The first appearance of anomaluroids in the African fossil record coincides with the first appearances of hystricognathous rodents and anthropoid primates there. Both of the latter taxa are widely acknowledged to have originated in Asia, suggesting that anomaluroids may show a concordant biogeographic pattern. Here we describe two new taxa of African Paleogene anomaluroids from sites in the Sirt Basin of central Libya. These include a new Eocene species of the nementchamyid genus Kabirmys, which ranks among the oldest African anomaluroids recovered to date, and a new genus and species of Anomaluridae from the early Oligocene, which appears to be closely related to extant Zenkerella, the only living non-volant anomalurid. Phylogenetic analyses incorporating the new Libyan fossils suggest that anomaluroids are not specially related to Zegdoumyidae, which are the only African rodents known to antedate the first appearance of anomaluroids there. The evolution of gliding locomotion in Anomaluridae appears to conflict with traditional assessments of relationships among living anomalurid taxa. If the historically accepted division of Anomaluridae into Anomalurinae (extant and Miocene Anomalurus and Miocene Paranomalurus and Zenkerellinae (extant and Miocene Zenkerella and extant Idiurus is correct, then either gliding locomotion evolved independently in Anomalurinae and Idiurus or non-volant Zenkerella evolved from a gliding ancestor. Anatomical data related to gliding in Anomaluridae are more consistent with a nontraditional systematic arrangement

  16. The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage

    Directory of Open Access Journals (Sweden)

    Kotal M

    2008-08-01

    Full Text Available Abstract Background The "out of Africa" model postulating single "southern route" dispersal posits arrival of "Anatomically Modern Human" to Indian subcontinent around 66–70 thousand years before present (kyBP. However the contributions and legacy of these earliest settlers in contemporary Indian populations, owing to the complex past population dynamics and later migrations has been an issue of controversy. The high frequency of mitochondrial lineage "M2" consistent with its greater age and distribution suggests that it may represent the phylogenetic signature of earliest settlers. Accordingly, we attempted to re-evaluate the impact and contribution of earliest settlers in shaping the genetic diversity and structure of contemporary Indian populations; using our newly sequenced 72 and 4 published complete mitochondrial genomes of this lineage. Results The M2 lineage, harbouring two deep rooting subclades M2a and M2b encompasses approximately one tenth of the mtDNA pool of studied tribes. The phylogeographic spread and diversity indices of M2 and its subclades among the tribes of different geographic regions and linguistic phyla were investigated in detail. Further the reconstructed demographic history of M2 lineage as a surrogate of earliest settlers' component revealed that the demographic events with pronounced regional variations had played pivotal role in shaping the complex net of populations phylogenetic relationship in Indian subcontinent. Conclusion Our results suggest that tribes of southern and eastern region along with Dravidian and Austro-Asiatic speakers of central India are the modern representatives of earliest settlers of subcontinent. The Last Glacial Maximum aridity and post LGM population growth mechanised some sort of homogeneity and redistribution of earliest settlers' component in India. The demic diffusion of agriculture and associated technologies around 3 kyBP, which might have marginalized hunter-gatherer, is

  17. Evolutionary history of a vanishing radiation: isolation-dependent persistence and diversification in Pacific Island partulid tree snails.

    Science.gov (United States)

    Lee, Taehwan; Li, Jingchun; Churchill, Celia K C; Foighil, Diarmaid Ó

    2014-09-24

    Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. Our goal was to investigate broad scale (range wide) and fine scale (within-Society Islands) molecular phylogenetic relationships of the two widespread genera, Partula and Samoana. What can such data tell us regarding the genesis of such divergent generic distribution patterns, and nominal species diversity levels across Oceania? Museum, captive (zoo) and contemporary field specimens enabled us to genotype 54 of the ~120 recognized species, including many extinct or extirpated taxa, from 14 archipelagoes. The genera Partula and Samoana are products of very distinct diversification processes. Originating at the western edge of the familial range, the derived genus Samoana is a relatively recent arrival in the far eastern archipelagoes (Society, Austral, Marquesas) where it exhibits a stepping-stone phylogenetic pattern and has proven adept at both intra-and inter- archipelago colonization. The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. The central importance of isolation for partulid lineage persistence and diversification is evident in time-calibrated phylogenetic trees that show that remote archipelagoes least impacted by continental biotas bear the oldest clades and/or the most speciose radiations. In contemporary Oceania, that isolation is being progressively undermined and these tree snails are now directly exposed to introduced continental predators

  18. Transcriptome analysis deciphers evolutionary mechanisms underlying genetic differentiation between coastal and offshore anchovy populations in the Bay of Biscay

    KAUST Repository

    Montes, Iratxe

    2016-09-13

    Morphometry and otolith microchemistry point to the existence of two populations of the European anchovy (Engraulis encrasicolus) in the Bay of Biscay: one in open seawaters, and a yet unidentified population in coastal waters. To test this hypothesis, we assembled a large number of samples from the region, including 587 juveniles and spawning adults from offshore and coastal waters, and 264 fish from other locations covering most of the species’ European range. These samples were genotyped for 456 exonic SNPs that provide a robust way to decipher adaptive processes in these populations. Two genetically differentiated populations of anchovy inhabit the Bay of Biscay with different population dynamics: (1) a large offshore population associated with marine waters included in the wide-shelf group, and (2) a coastal metapopulation adapted to estuarine environments in the Bay of Biscay and North Sea included in the narrow-shelf group. Transcriptome analysis identified neutral and adaptive evolutionary processes underlying differentiation between these populations. Reduced gene flow between offshore and coastal populations in the Bay of Biscay appears to result from divergence between two previously isolated gene pools adapted to contrasting habitats and now in secondary contact. Eleven molecular markers appear to mark divergent selection between the ecotypes, and a majority of these markers are associated with salinity variability. Ecotype differences at two outlier genes, TSSK6 and basigin, may hinder gamete compatibility between the ecotypes and reinforce reproductive isolation. Additionally, possible convergent evolution between offshore and coastal populations in the Bay of Biscay has been detected for the syntaxin1B-otoferlin gene system, which is involved in the control of larval buoyancy. Further study of exonic markers opens the possibility of understanding the mechanisms of adaptive divergence between European anchovy populations. © 2016, Springer

  19. Cognitive Processes Underlying Women's Risk Judgments: Associations with Sexual Victimization History and Rape Myth Acceptance

    Science.gov (United States)

    Yeater, Elizabeth A.; Treat, Teresa A.; Viken, Richard J.; McFall, Richard M.

    2010-01-01

    Objective: This study evaluated the effects of sexual victimization history, rape myth acceptance, implicit attention, and recent learning on the cognitive processes underlying undergraduate women's explicit risk judgments. Method: Participants were 194 undergraduate women between 18 and 24 years of age. The sample was ethnically diverse and…

  20. Evolutionary history of the fish genus Astyanax Baird & Girard (1854) (Actinopterygii, Characidae) in Mesoamerica reveals multiple morphological homoplasies.

    Science.gov (United States)

    Ornelas-García, Claudia Patricia; Domínguez-Domínguez, Omar; Doadrio, Ignacio

    2008-12-22

    Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution. Analysis of the entire mitochondrial cytochrome b (Cytb) gene in 208 individuals from 147 localities and of a subset of individuals for three mitochondrial genes (Cytb, 16 S, and COI) and a single nuclear gene (RAG1) yielded similar topologies, recovering six major groups with significant phylogeographic structure. Populations from North America and Upper Central America formed a monophyletic group, while Middle Central America showed evidence of rapid radiation with incompletely resolved relationships. Lower Central America lineages showed a fragmented structure, with geographically restricted taxa showing high levels of molecular divergence. All Bramocharax samples grouped with their sympatric Astyanax lineages (in some cases even with allopatric Astyanax populations), with less than 1% divergence between them. These results suggest a homoplasic nature to the trophic specializations associated with Bramocharax ecomorphs, which seem to have arisen independently in different Astyanax lineages. We observed higher taxonomic diversity compared to previous phylogenetic studies of the Astyanax genus. Colonization of Mesoamerica by Astyanax before the final closure of the Isthmus of Panama (3.3 Mya) explains the deep level of divergence detected in Lower Central America. The colonization of Upper Mesoamerica apparently

  1. Evolutionary history of the fish genus Astyanax Baird & Girard (1854 (Actinopterygii, Characidae in Mesoamerica reveals multiple morphological homoplasies

    Directory of Open Access Journals (Sweden)

    Doadrio Ignacio

    2008-12-01

    Full Text Available Abstract Background Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution. Results Analysis of the entire mitochondrial cytochrome b (Cytb gene in 208 individuals from 147 localities and of a subset of individuals for three mitochondrial genes (Cytb, 16 S, and COI and a single nuclear gene (RAG1 yielded similar topologies, recovering six major groups with significant phylogeographic structure. Populations from North America and Upper Central America formed a monophyletic group, while Middle Central America showed evidence of rapid radiation with incompletely resolved relationships. Lower Central America lineages showed a fragmented structure, with geographically restricted taxa showing high levels of molecular divergence. All Bramocharax samples grouped with their sympatric Astyanax lineages (in some cases even with allopatric Astyanax populations, with less than 1% divergence between them. These results suggest a homoplasic nature to the trophic specializations associated with Bramocharax ecomorphs, which seem to have arisen independently in different Astyanax lineages. We observed higher taxonomic diversity compared to previous phylogenetic studies of the Astyanax genus. Colonization of Mesoamerica by Astyanax before the final closure of the Isthmus of Panama (3.3 Mya explains the deep level of divergence detected in Lower Central America. The

  2. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

    KAUST Repository

    Bernal, Moisés A.

    2016-11-22

    Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

  3. On the Evolutionary History of Uleiella chilensis, a Smut Fungus Parasite of Araucaria araucana in South America: Uleiellales ord. nov. in Ustilaginomycetes.

    Directory of Open Access Journals (Sweden)

    Kai Riess

    Full Text Available The evolutionary history, divergence times and phylogenetic relationships of Uleiella chilensis (Ustilaginomycotina, smut fungi associated with Araucaria araucana were analysed. DNA sequences from multiple gene regions and morphology were analysed and compared to other members of the Basidiomycota to determine the phylogenetic placement of smut fungi on gymnosperms. Divergence time estimates indicate that the majority of smut fungal orders diversified during the Triassic-Jurassic period. However, the origin and relationships of several orders remain uncertain. The most recent common ancestor between Uleiella chilensis and Violaceomyces palustris has been dated to the Lower Cretaceous. Comparisons of divergence time estimates between smut fungi and host plants lead to the hypothesis that the early Ustilaginomycotina had a saprobic lifestyle. As there are only two extant species of Araucaria in South America, each hosting a unique Uleiella species, we suggest that either coevolution or a host shift followed by allopatric speciation are the most likely explanations for the current geographic restriction of Uleiella and its low diversity. Phylogenetic and age estimation analyses, ecology, the unusual life-cycle and the peculiar combination of septal and haustorial characteristics support Uleiella chilensis as a distinct lineage among the Ustilaginomycotina. Here, we describe a new ustilaginomycetous order, the Uleiellales to accommodate Uleiella. Within the Ustilaginomycetes, Uleiellales are sister taxon to the Violaceomycetales.

  4. On the Evolutionary History of Uleiella chilensis, a Smut Fungus Parasite of Araucaria araucana in South America: Uleiellales ord. nov. in Ustilaginomycetes.

    Science.gov (United States)

    Riess, Kai; Schön, Max E; Lutz, Matthias; Butin, Heinz; Oberwinkler, Franz; Garnica, Sigisfredo

    2016-01-01

    The evolutionary history, divergence times and phylogenetic relationships of Uleiella chilensis (Ustilaginomycotina, smut fungi) associated with Araucaria araucana were analysed. DNA sequences from multiple gene regions and morphology were analysed and compared to other members of the Basidiomycota to determine the phylogenetic placement of smut fungi on gymnosperms. Divergence time estimates indicate that the majority of smut fungal orders diversified during the Triassic-Jurassic period. However, the origin and relationships of several orders remain uncertain. The most recent common ancestor between Uleiella chilensis and Violaceomyces palustris has been dated to the Lower Cretaceous. Comparisons of divergence time estimates between smut fungi and host plants lead to the hypothesis that the early Ustilaginomycotina had a saprobic lifestyle. As there are only two extant species of Araucaria in South America, each hosting a unique Uleiella species, we suggest that either coevolution or a host shift followed by allopatric speciation are the most likely explanations for the current geographic restriction of Uleiella and its low diversity. Phylogenetic and age estimation analyses, ecology, the unusual life-cycle and the peculiar combination of septal and haustorial characteristics support Uleiella chilensis as a distinct lineage among the Ustilaginomycotina. Here, we describe a new ustilaginomycetous order, the Uleiellales to accommodate Uleiella. Within the Ustilaginomycetes, Uleiellales are sister taxon to the Violaceomycetales.

  5. The tale of a modern animal plague: Tracing the evolutionary history and determining the time-scale for foot and mouth disease virus

    International Nuclear Information System (INIS)

    Tully, Damien C.; Fares, Mario A.

    2008-01-01

    Despite significant advances made in the understanding of its epidemiology, foot and mouth disease virus (FMDV) is among the most unexpected agricultural devastating plagues. While the disease manifests itself as seven immunologically distinct strains their origin, population dynamics, migration patterns and divergence times remain unknown. Herein we have assembled a comprehensive data set of gene sequences representing the global diversity of the disease and inferred the time-scale and evolutionary history for FMDV. Serotype-specific rates of evolution and divergence times were estimated using a Bayesian coalescent framework. We report that an ancient precursor FMDV gave rise to two major diversification events spanning a relatively short interval of time. This radiation event is estimated to have taken place towards the end of the 17th and the beginning of the 18th century giving us the present circulating Euro-Asiatic and South African viral strains. Furthermore our results hint that Europe acted as a possible hub for the disease from where it successfully dispersed elsewhere via exploration and trading routes

  6. The tale of a modern animal plague: tracing the evolutionary history and determining the time-scale for foot and mouth disease virus.

    Science.gov (United States)

    Tully, Damien C; Fares, Mario A

    2008-12-20

    Despite significant advances made in the understanding of its epidemiology, foot and mouth disease virus (FMDV) is among the most unexpected agricultural devastating plagues. While the disease manifests itself as seven immunologically distinct strains their origin, population dynamics, migration patterns and divergence times remain unknown. Herein we have assembled a comprehensive data set of gene sequences representing the global diversity of the disease and inferred the time-scale and evolutionary history for FMDV. Serotype-specific rates of evolution and divergence times were estimated using a Bayesian coalescent framework. We report that an ancient precursor FMDV gave rise to two major diversification events spanning a relatively short interval of time. This radiation event is estimated to have taken place towards the end of the 17th and the beginning of the 18th century giving us the present circulating Euro-Asiatic and South African viral strains. Furthermore our results hint that Europe acted as a possible hub for the disease from where it successfully dispersed elsewhere via exploration and trading routes.

  7. Coral Bleaching Susceptibility Is Decreased following Short-Term (1–3 Year Prior Temperature Exposure and Evolutionary History

    Directory of Open Access Journals (Sweden)

    Joshua A. Haslun

    2011-01-01

    Full Text Available Coral exposed to short periods of temperature stress (≥1.0°C above mean monthly maximum and/or increased frequencies of high temperatures may bolster resilience to global warming associated with climate change. We compared Montastraea cavernosa (Linnaeus, 1767; Cnidaria, Scleractinia, Faviidae from the Florida Keys National Marine Sanctuary (FKNMS and the Flower Garden Banks National Marine Sanctuary (FGBNMS. Thermal stress has been reported frequently within the FKNMS; however, corals in the FGBNMS experience nominal exposures to similar stressors. Corals were exposed to three temperatures (27°C, 31°C, and 35°C for 72 h. Colonies from the FKNMS lost significantly fewer viable and necrotic zooxanthellae under conditions of acute stress (35°C than the FGBNMS colonies. This indicates that the FKNMS corals are less temperature-sensitive than those in the FGBNMS. The observed differences point to greater prior temperature exposure and adaptation in the former versus the latter site when correlated to previous years of thermal exposure.

  8. Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

    Science.gov (United States)

    Minias, Piotr; Bateson, Zachary W.; Whittingham, Linda A.; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O.

    2016-01-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

  9. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.

    Science.gov (United States)

    Hsiang, Allison Y; Field, Daniel J; Webster, Timothy H; Behlke, Adam D B; Davis, Matthew B; Racicot, Rachel A; Gauthier, Jacques A

    2015-05-20

    The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K

  10. Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia.

    Science.gov (United States)

    Al-Khannaq, Maryam Nabiel; Ng, Kim Tien; Oong, Xiang Yong; Pang, Yong Kek; Takebe, Yutaka; Chook, Jack Bee; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2016-02-25

    Despite the worldwide circulation of human coronavirus OC43 (HCoV-OC43) and HKU1 (HCoV-HKU1), data on their molecular epidemiology and evolutionary dynamics in the tropical Southeast Asia region is lacking. The study aimed to investigate the genetic diversity, temporal distribution, population history and clinical symptoms of betacoronavirus infections in Kuala Lumpur, Malaysia between 2012 and 2013. A total of 2,060 adults presented with acute respiratory symptoms were screened for the presence of betacoronaviruses using multiplex PCR. The spike glycoprotein, nucleocapsid and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. A total of 48/2060 (2.4 %) specimens were tested positive for HCoV-OC43 (1.3 %) and HCoV-HKU1 (1.1 %). Both HCoV-OC43 and HCoV-HKU1 were co-circulating throughout the year, with the lowest detection rates reported in the October-January period. Phylogenetic analysis of the spike gene showed that the majority of HCoV-OC43 isolates were grouped into two previously undefined genotypes, provisionally assigned as novel lineage 1 and novel lineage 2. Sign of natural recombination was observed in these potentially novel lineages. Location mapping showed that the novel lineage 1 is currently circulating in Malaysia, Thailand, Japan and China, while novel lineage 2 can be found in Malaysia and China. Molecular dating showed the origin of HCoV-OC43 around late 1950s, before it diverged into genotypes A (1960s), B (1990s), and other genotypes (2000s). Phylogenetic analysis revealed that 27.3 % of the HCoV-HKU1 strains belong to genotype A while 72.7 % belongs to genotype B. The tree root of HCoV-HKU1 was similar to that of HCoV-OC43, with the tMRCA of genotypes A and B estimated around the 1990s and 2000s, respectively. Correlation of HCoV-OC43 and HCoV-HKU1 with the severity of respiratory symptoms was not observed. The present study reported the molecular complexity and evolutionary dynamics of human

  11. Evolutionary History of Ascomyceteous Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Riley, Robert; Salamov, Asaf; Goker, Markus; Klenk, Hans-Peter; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor; Jeffries, Thomas W.

    2014-06-06

    Yeasts are important for many industrial and biotechnological processes and show remarkable diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. A comparison of these with several other previously published yeast genomes have added increased confidence to the phylogenetic positions of previously poorly placed species including Saitoella complicata, Babjeviella inositovora and Metschnikowia bicuspidata. Phylogenetic analysis also showed that yeasts with alternative nuclear codon usage where CUG encodes serine instead of leucine are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes with Lipomyces starkeyi and the previously published Pneumocystis jirovecii being notable exceptions. Intron analysis suggests that early diverging species have more introns. We also observed a large number of unclassified lineage specific non-simple repeats in these genomes.

  12. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  13. Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep.

    Science.gov (United States)

    Demirci, Sevgin; Koban Baştanlar, Evren; Dağtaş, Nihan Dilşad; Pişkin, Evangelia; Engin, Atilla; Ozer, Füsun; Yüncü, Eren; Doğan, Sükrü Anıl; Togan, Inci

    2013-01-01

    In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).

  14. Evolutionary history and population genetic structure of the endemic tree frog Hyla tsinlingensis (Amphibia: Anura: Hylidae) inferred from mitochondrial gene analysis.

    Science.gov (United States)

    Zhang, Yan-Hua; Zhao, Yan-Yu; Li, Xue-Ying; Li, Xiao-Chen

    2016-01-01

    The influence of topography and Pleistocenic climatic fluctuations on the population genetic structure of amphibians in the Tsinling-Dabieshan Mountains of China is poorly investigated. Hyla tsinlingensis is a tree frog endemic to the Tsinling-Dabieshan Mountains, with a restricted and patchy distribution that is currently shrinking. We speculated on the evolutionary history of amphibians in this region by studying the population genetic structure of H. tsinlingensis. Using a total of 212 samples, 32 haplotypes and four haplogroups were found in the present study. Population genetic structure showed significant differentiation (F(ST)) between most populations of H. tsinlingensis in the Tsinling-Dabieshan Mountains. An analysis of molecular variance (AMOVA) suggested that most of the observed genetic variation occurs between the two regions (the Tsinling and Dabieshan Mountains). Mantel tests indicated that the genetic divergence was induced through isolation by distance. Using Monmonier's maximum difference algorithm to predict the genetic barrier, two putative barriers in gene flow that separate lineages of H. tsinlingensis were identified. Mismatch distribution and neutrality tests found a sudden population expansion in all haplogroups except the Tsinling population and total population. This population expansion was identified between 0.5 Myr to 0.1 Myr (Quaternary) by Bayesian skyline plot (BSP). Divergence dating indicated the divergence time between the Tsinling population and Dabieshan population to be 3.26 MYA (Pliocene). In conclusion, the topography of the Tsinling and Dabieshan Mountains exerts a significant impact on the population genetic structure of H. tsinlingensis, and climatic oscillations during glacial periods in the Quaternary affected the distribution of H. tsinlingensis.

  15. Evolutionary history of HIV-1 subtype B and CRF01_AE transmission clusters among men who have sex with men (MSM) in Kuala Lumpur, Malaysia.

    Science.gov (United States)

    Ng, Kim Tien; Ong, Lai Yee; Lim, Sin How; Takebe, Yutaka; Kamarulzaman, Adeeba; Tee, Kok Keng

    2013-01-01

    HIV-1 epidemics among men who have sex with men (MSM) continue to expand in developed and developing countries. Although HIV infection in MSM is amongst the highest of the key affected populations in many countries in Southeast Asia, comprehensive molecular epidemiological study of HIV-1 among MSM remains inadequate in the region including in Malaysia. Here, we reported the phylodynamic profiles of HIV-1 genotypes circulating among MSM population in Kuala Lumpur, Malaysia. A total of n = 459 newly-diagnosed treatment-naïve consenting subjects were recruited between March 2006 and August 2012, of whom 87 (18.9%) were self-reported MSM. Transmitted drug resistance mutations were absent in these isolates. Cumulatively, phylogenetic reconstructions of the pro-rt gene (HXB2∶2253-3275) showed that HIV-1 subtype B and CRF01_AE were predominant and contributed to approximately 80% of the total HIV-1 infection among MSM. In addition to numerous unique transmission lineages within these genotypes, twelve monophyletic transmission clusters of different sizes (2-7 MSM sequences, supported by posterior probability value of 1) were identified in Malaysia. Bayesian coalescent analysis estimated that the divergence times for these clusters were mainly dated between 1995 and 2005 with four major transmission clusters radiating at least 12 years ago suggesting that active spread of multiple sub-epidemic clusters occurred during this period. The changes in effective population size of subtype B showed an exponential growth within 5 years between 1988 and 1993, while CRF01_AE lineage exhibited similar expansion between 1993 and 2003. Our study provides the first insight of the phylodynamic profile of HIV-1 subtype B and CRF01_AE circulating among MSM population in Kuala Lumpur, Malaysia, unravelling the importance of understanding transmission behaviours as well as evolutionary history of HIV-1 in assessing the risk of outbreak or epidemic expansion.

  16. Evolutionary history of HIV-1 subtype B and CRF01_AE transmission clusters among men who have sex with men (MSM in Kuala Lumpur, Malaysia.

    Directory of Open Access Journals (Sweden)

    Kim Tien Ng

    Full Text Available HIV-1 epidemics among men who have sex with men (MSM continue to expand in developed and developing countries. Although HIV infection in MSM is amongst the highest of the key affected populations in many countries in Southeast Asia, comprehensive molecular epidemiological study of HIV-1 among MSM remains inadequate in the region including in Malaysia. Here, we reported the phylodynamic profiles of HIV-1 genotypes circulating among MSM population in Kuala Lumpur, Malaysia. A total of n = 459 newly-diagnosed treatment-naïve consenting subjects were recruited between March 2006 and August 2012, of whom 87 (18.9% were self-reported MSM. Transmitted drug resistance mutations were absent in these isolates. Cumulatively, phylogenetic reconstructions of the pro-rt gene (HXB2∶2253-3275 showed that HIV-1 subtype B and CRF01_AE were predominant and contributed to approximately 80% of the total HIV-1 infection among MSM. In addition to numerous unique transmission lineages within these genotypes, twelve monophyletic transmission clusters of different sizes (2-7 MSM sequences, supported by posterior probability value of 1 were identified in Malaysia. Bayesian coalescent analysis estimated that the divergence times for these clusters were mainly dated between 1995 and 2005 with four major transmission clusters radiating at least 12 years ago suggesting that active spread of multiple sub-epidemic clusters occurred during this period. The changes in effective population size of subtype B showed an exponential growth within 5 years between 1988 and 1993, while CRF01_AE lineage exhibited similar expansion between 1993 and 2003. Our study provides the first insight of the phylodynamic profile of HIV-1 subtype B and CRF01_AE circulating among MSM population in Kuala Lumpur, Malaysia, unravelling the importance of understanding transmission behaviours as well as evolutionary history of HIV-1 in assessing the risk of outbreak or epidemic expansion.

  17. Modeling evolutionary games in populations with demographic structure

    DEFF Research Database (Denmark)

    Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

    2015-01-01

    interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

  18. "Small size" in the Philippine human fossil record: is it meaningful for a better understanding of the evolutionary history of the negritos?

    Science.gov (United States)

    Détroit, Florent; Corny, Julien; Dizon, Eusebio Z; Mijares, Armand S

    2013-01-01

    "Pygmy populations" are recognized in several places over the world, especially in Western Africa and in Southeast Asia (Philippine "negritos," for instance). Broadly defined as "small-bodied Homo sapiens" (compared with neighboring populations), their origins and the nature of the processes involved in the maintenance of their phenotype over time are highly debated. Major results have been recently obtained from population genetics on present-day negrito populations, but their evolutionary history remains largely unresolved. We present and discuss the Upper Pleistocene human remains recovered from Tabon Cave and Callao Cave in the Philippines, which are potentially highly relevant to these research questions. Human fossils have been recovered in large numbers from Tabon Cave (Palawan Island) but mainly from reworked and mixed sediments from several archaeological layers. We review and synthesize the long and meticulous collaborative work done on the archives left from the 1960s excavations and on the field. The results demonstrate the long history of human occupations in the cave, since at least ~30,000 BP. The examination of the Tabon human remains shows a large variability: large and robust for one part of the sample, and small and gracile for the other part. The latter would fit quite comfortably within the range of variation of Philippine negritos. Farther north, on Luzon Island, the human third metatarsal recently recovered from Callao Cave and dated to ~66,000 BP is now the oldest direct evidence of human presence in the Philippines. Previous data show that, compared with H. sapiens (including Philippine negritos), this bone presents a very small size and several unusual morphological characteristics. We present a new analytical approach using three-dimensional geometric morphometrics for comparing the Callao fossil to a wide array of extant Asian mammals, including nonhuman primates and H. sapiens. The results demonstrate that the shape of the Callao

  19. Expansion of biological pathways based on evolutionary inference.

    Science.gov (United States)

    Li, Yang; Calvo, Sarah E; Gutman, Roee; Liu, Jun S; Mootha, Vamsi K

    2014-07-03

    The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild.

    Science.gov (United States)

    Buoro, M; Prévost, E; Gimenez, O

    2012-10-01

    The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life-history components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  1. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

  2. A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history.

    Science.gov (United States)

    Bhullar, Bhart-Anjan S; Morris, Zachary S; Sefton, Elizabeth M; Tok, Atalay; Tokita, Masayoshi; Namkoong, Bumjin; Camacho, Jasmin; Burnham, David A; Abzhanov, Arhat

    2015-07-01

    The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches. We approached the problem of the mechanism behind this innovation using an approach bridging paleontology, comparative anatomy, and experimental developmental biology. First, we used fossil and extant data to show the beak is distinctive in consisting of fused premaxillae that are geometrically distinct from those of ancestral archosaurs. To elucidate underlying developmental mechanisms, we examined candidate gene expression domains in the embryonic face: the earlier frontonasal ectodermal zone (FEZ) and the later midfacial WNT-responsive region, in birds and several reptiles. This permitted the identification of an autapomorphic median gene expression region in Aves. To test the mechanism, we used inhibitors of both pathways to replicate in chicken the ancestral amniote expression. Altering the FEZ altered later WNT responsiveness to the ancestral pattern. Skeletal phenotypes from both types of experiments had premaxillae that clustered geometrically with ancestral fossil forms instead of beaked birds. The palatal region was also altered to a more ancestral phenotype. This is consistent with the fossil record and with the tight functional association of avian premaxillae and palate in forming a kinetic beak. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  3. Evolutionary Processes and Mental Deficiency

    Science.gov (United States)

    Spitz, Herman H.

    1973-01-01

    The author hypothesizes that central nervous system damage of deficiency associated with mental retardation affects primarily those cortical processes which developed at a late stage in man's evolutionary history. (Author)

  4. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  5. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

    Directory of Open Access Journals (Sweden)

    Nakhleh Luay

    2008-07-01

    Full Text Available Abstract Background Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT, hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX. Results In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1 evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2 evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3 evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4 evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees. Conclusion The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in

  6. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.

    Science.gov (United States)

    Than, Cuong; Ruths, Derek; Nakhleh, Luay

    2008-07-28

    Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX. In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks - trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees. The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the

  7. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  8. Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

    Science.gov (United States)

    Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

    2017-10-01

    Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

  9. East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

    Directory of Open Access Journals (Sweden)

    De Bruyn Alexandre

    2012-11-01

    Full Text Available Abstract Background Cassava (Manihot esculenta is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD. Caused by a complex of bipartite cassava mosaic geminiviruses (CMG species (Family: Geminivirideae; Genus: Begomovirus CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO islands. Results The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV. Phylogeographic analyses suggest that CMG’s presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Conclusions Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain

  10. Geological and climatic changes in quaternary shaped the evolutionary history of Calibrachoa heterophylla, an endemic South-Atlantic species of petunia.

    Science.gov (United States)

    Mäder, Geraldo; Fregonezi, Jéferson N; Lorenz-Lemke, Aline P; Bonatto, Sandro L; Freitas, Loreta B

    2013-08-29

    The glacial and interglacial cycles that characterized the Quaternary greatly affected the distribution and genetic diversity of plants. In the Neotropics, few phylogeographic studies have focused on coastal species outside of the Atlantic Rainforest. Climatic and sea level changes during the Quaternary played an important role in the evolutionary history of many organisms found in coastal regions. To contribute to a better understanding of plant evolution in this environment in Southern South America, we focused on Calibrachoa heterophylla (Solanaceae), an endemic and vulnerable wild petunia species from the South Atlantic Coastal Plain (SACP). We assessed DNA sequences from two cpDNA intergenic spacers and analyzed them using a phylogeographic approach. The present phylogeographic study reveals the influence of complex geologic and climatic events on patterns of genetic diversification. The results indicate that C. heterophylla originated inland and subsequently colonized the SACP; the data show that the inland haplogroup is more ancient than the coastal one and that the inland was not affected by sea level changes in the Quaternary. The major diversification of C. heterophylla that occurred after 0.4 Myr was linked to sea level oscillations in the Quaternary, and any diversification that occurred before this time was obscured by marine transgressions that occurred before the coastal sand barrier's formation. Results of the Bayesian skyline plot showed a recent population expansion detected in C. heterophylla seems to be related to an increase in temperature and humidity that occurred at the beginning of the Holocene. The geographic clades have been formed when the coastal plain was deeply dissected by paleochannels and these correlate very well with the distributional limits of the clades. The four major sea transgressions formed a series of four sand barriers parallel to the coast that progressively increased the availability of coastal areas after the

  11. Life history responses to irradiance at the early seedling stage of Picea omorika (Pančić) Purkyňe: adaptiveness and evolutionary limits

    Science.gov (United States)

    Tucić, Branka; Pemac, Danijela; Dučić, Jelena

    2005-05-01

    A multivariate selection analysis has been implemented for testing the adaptiveness of life history plasticity to irradiance during the seedling establishment in Picea omorika plants raised in a growth-room. Siblings of a synthetic population comprising 21 families from six natural populations were exposed to contrasting light levels to explore variation in phenotypic expression of three seedling traits: days from germination to cotyledon opening (DGTOC), days from cotyledon opening to epicotyl appearance (DCTOE), and epicotyl length at 6 weeks (EPL6). Ambient light conditions significantly affected DCTOE and EPL6, but not DGTOC. Phenotypic selection analysis revealed that DGTOC was under negative directional selection in both radiation environments, suggesting that canalization of DGTOC was promoted across different light conditions, as well as that the observed pattern of canalization might be regarded as adaptive. DCTOE was also found to be under negative directional selection in both light treatments, but the plastic responses of this trait were opposite to the values favoured by selection within environments. Since there was evidence for selection against plasticity in DCTOE, the pattern of plastic responses in DCTOE to variation in light conditions could be diagnosed as maladaptive. Multiple regression analysis revealed a cost of canalization in DGTOC regardless of light environment, as well as a cost of plasticity in DCTOE under high light intensity. All genetic correlations across light environments were significantly different from unity, indicating the existence of heritable variation for plasticity in these traits. However, since DGTOC and DCTOE were involved in a genetic trade-off with respect to both trait mean and plasticity, these early life histories would never reach their optimal values across radiation environments.

  12. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...... of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  13. CLASH's life history foundations [commentary on Van Lange et al., 2017

    NARCIS (Netherlands)

    Frankenhuis, W.E.; Fenneman, J.; Gelder, J.L. van; Godoy, I.

    2017-01-01

    We recommend extending CLASH by incorporating two evolutionary accounts of the shift toward fast life histories under harsh, unpredictable conditions. These accounts, if integrated with CLASH, make different predictions about the distributions of aggression and violence within and between societies.

  14. YI Kwang Su's Love and history records of modern hospital under the japanese colonial period.

    Science.gov (United States)

    Lee, Byoung Hoon

    2016-12-01

    This article aims to evaluate and analyze the description of the modern hospital as history record, which appeared in YI Kwang Su's novel Love. This novel has mentioned in detail western style clinic, Bukgando Catholic hospital, tuberculosis sanitarium as its main space. Modern hospitals are depicted in the novel has a great significance in historical aspect as well as in literary aspect. The most data on modern hospital is laws, statistics and newspaper archives. These materials are a great help to understand the history and status of the modern hospital. Literary description here is important materials, that specific to reconstruct the appearance of the modern hospital at that time. Literary representations infuse life into the history record. In this regard, Love has special meaning in the history of Korean modern literature. Before anything else, doctor AN Bin's clinic as a first space of the novel vividly shows the reality of the Western style clinic and a general practitioner under the colonial period. The establishment of the hospital was based on 「Rules on private hospital」 declared by the Japanese Government General of Korea in 1919. According to this Rules, a private clinic's founder had to submit the documents to the director of police affairs, in which all the details were written. It included name of hospital, site location and size, floor plan of a nearby building, each size of patient's rooms, number of steps and emergency exit, bath, toilet, disinfecting room. AN Bin's clinic was a private hospital with the requirements in the rules. The descriptions of this clinic re-created real situation of private hospitals, specifically scale of hospital, interior space, conditions of patient's room at the time. The second modern hospital in the novel is Bukgando Catholic hospital. There is a lot more materials on medical activity and hospital of protestant churches than we thought. But we do not have a lot of information on catholic church's medical

  15. Diversification within the Spiny Throated Reed Frog complex (H. tanneri and H. minutissimus, H. spinigularis): untangling evolutionary history among closely related lineages

    Science.gov (United States)

    Super-species complexes, where lineages are morphological similarity but evolutionary divergent, are a particularly interesting biological phenomena in terms of understanding the process of diversification. The signal of selection is less swamped by secondary divergence and spatial relocation than i...

  16. Materials Science Experiments Under Microgravity - A Review of History, Facilities, and Future Opportunities

    Science.gov (United States)

    Stenzel, Ch.

    2012-01-01

    Materials science experiments have been a key issue already since the early days of research under microgravity conditions. A microgravity environment facilitates processing of metallic and semiconductor melts without buoyancy driven convection and sedimentation. Hence, crystal growth of semiconductors, solidification of metallic alloys, and the measurement of thermo-physical parameters are the major applications in the field of materials science making use of these dedicated conditions in space. In the last three decades a large number of successful experiments have been performed, mainly in international collaborations. In parallel, the development of high-performance research facilities and the technological upgrade of diagnostic and stimuli elements have also contributed to providing optimum conditions to perform such experiments. A review of the history of materials science experiments in space focussing on the development of research facilities is given. Furthermore, current opportunities to perform such experiments onboard ISS are described and potential future options are outlined.

  17. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

    Science.gov (United States)

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-03-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

  18. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  19. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    , they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...

  20. TAS3 miR390-dependent loci in non-vascular land plants: towards a comprehensive reconstruction of the gene evolutionary history

    Directory of Open Access Journals (Sweden)

    Sergey Y. Morozov

    2018-04-01

    Full Text Available Trans-acting small interfering RNAs (ta-siRNAs are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant non-vascular plant taxa such as Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in plant classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified charophyte alga sequences coding for SUPPRESSOR OF GENE SILENCING 3 (SGS3, which is required for generation of ta-siRNAs in plants, and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants.

  1. Evolutionary robotics

    Indian Academy of Sciences (India)

    In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to ...

  2. An evolutionary perspective for contemporary psychiatric research.

    Science.gov (United States)

    Alleva, Enrico; Branchi, Igor

    2011-01-01

    Behaviour represents the ultimate output of the brain and is characterized by a high level of inter-individual variability. On the one hand, taking into account evolutionary history and adaptive significance of behavioural responses allows to design experimental protocols that improve both data quality and interpretation. On the other hand, a multilevel approach, which analyses factors ranging from the genetic set up to the socioeconomic status, leads to a more comprehensive and effective investigation of mechanisms underlying brain function. Exploitation of this approach in clinical studies may provide new strategies to more precisely investigate psychiatric disorders.

  3. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... was to define a major transition by identifying a pattern that is common across an otherwise diverse set of ... been many major evolutionary events that this definition of a transition excludes. The evolution of ...... fragmentation periodic, or brings it under endogenous con- trol. So the mechanisms are far from ...

  4. Summary history of domestic uranium procurement under US Atomic Energy Commission contracts. Final report

    International Nuclear Information System (INIS)

    Albrethsen, H. Jr.; McGinley, F.E.

    1982-09-01

    During the period 1947 through 1970, the Atomic Energy Commission (AEC) fostered the rapid development and expansion of the domestic uranium mining and milling industry by providing a market for uranium. Some thirty-two mills were constructed during that period to produce U 3 O 8 concentrates for sale to the AEC. In addition, there were various pilot plants, concentrators, upgraders, heap leach, and solution mining facilities that operated during the period. The purpose of this report is to compile a short narrative history of the AEC's uranium concentrate procurement program and to describe briefly each of the operations that produced uranium for sale to the AEC. Contractual arrangements are described and data are given on quantities of U 3 O 8 purchased and prices paid. Similar data are included for V 2 O 5 , where applicable. Mill and other plant operating data were also compiled from old AEC records. These latter data were provided by the companies, as a contractual requirement, during the period of operation under AEC contracts. Additionally, an effort was made to determine the present status of each facility by reference to other recently published reports. No sites were visited nor were the individual reports reviewed by the companies, many of which no longer exist. The authors relied almost entirely on published information for descriptions of facilities and milling processes utilized

  5. A stochastic, evolutionary model for range shifts and richness on tropical elevational gradients under Quaternary glacial cycles.

    Science.gov (United States)

    Colwell, Robert K; Rangel, Thiago F

    2010-11-27

    Quaternary glacial-interglacial cycles repeatedly forced thermal zones up and down the slopes of mountains, at all latitudes. Although no one doubts that these temperature cycles have left their signature on contemporary patterns of geography and phylogeny, the relative roles of ecology and evolution are not well understood, especially for the tropics. To explore key mechanisms and their interactions in the context of chance events, we constructed a geographical range-based, stochastic simulation model that incorporates speciation, anagenetic evolution, niche conservatism, range shifts and extinctions under late Quaternary temperature cycles along tropical elevational gradients. In the model, elevational patterns of species richness arise from the differential survival of founder lineages, consolidated by speciation and the inheritance of thermal niche characteristics. The model yields a surprisingly rich variety of realistic patterns of phylogeny and biogeography, including close matches to a variety of contemporary elevational richness profiles from an elevational transect in Costa Rica. Mountaintop extinctions during interglacials and lowland extinctions at glacial maxima favour mid-elevation lineages, especially under the constraints of niche conservatism. Asymmetry in temperature (greater duration of glacial than of interglacial episodes) and in lateral area (greater land area at low than at high elevations) have opposing effects on lowland extinctions and the elevational pattern of species richness in the model--and perhaps in nature, as well.

  6. Life history of the terrestrial snail Ovachlamys fulgens (Stylommatophora: Helicarionidae under laboratory conditions

    Directory of Open Access Journals (Sweden)

    Zaidett Barrientos

    1998-06-01

    Full Text Available Aspects of the biology of Ovachlamys fulgens (Gude 1900 were studied under laboratory conditions in Costa Rica for 16 months. The lifespan of this snail in captivity was about nine months (N= 22 and it could lay viable eggs without mating (N= 40. Oviposition began 42 days after eclosion, when shell diameter averaged 5.12 mm (N= 24. Clutches had about three eggs each (N= 252. One clutch was laid daily over periods of one to four days, with intervals of one to two days (N= 252. Age, shell diameter and clutch size were positively correlated (N= 1097 as were shell diameter of adult, egg diameter and shell diameter of the offspring (N= 136. Oviposition took place between crevices of the soil and in the leaf litter. Eggs had a soft egg shell and were laid semi-hydrated; they hydrated by absorbing water from the surroundings (N= 21. This strategy may be the evolutionary compromise between a mechanical limitation (small body size and the advantage of producing bigger eggs with a larger amount of nutritive substances. At room temperature (mean = 21°C egg eclosion took place in 14 days (N= 67 and in 11 days at 28 °C (N= 32. Egg shell dissolution was not uniform (N= 107, it began in a local area, that usually was the side on which it rested (N= 46. The fact that eggs with and without an embryo (N= 5 underwent the same process of egg shell's calcium dissolution suggested a chemical mechanism. Embryos did not induce the process, but accelerated it. Egg viability was decreased by the tannins of the surrounding leaf litter (N= 50. Juveniles could feed on leaves of Persea americana (Lauraceae (N= 299.Durante 16 meses se estudió en laboratorio la biología básica de Ovachlamys fulgens en Costa Rica. Esta especie se reprodujo sin copular (N= 40 y su longevidad fue de nueve meses (N= 22. La oviposición inició a los 42 días de haber eclosionado y con 5.12 mm de diámetro de concha (N= 24. Los huevos fueron depositados en camadas diarias de alrededor de tres

  7. Evolutionary Finance

    OpenAIRE

    Igor V. Evstigneev; Thorsten Hens; Klaus Reiner Schenk-Hoppé

    2008-01-01

    Evolutionary finance studies the dynamic interaction of investment strategies in financial markets. This market interaction generates a stochastic wealth dynamics on a heterogenous population of traders through the fluctuation of asset prices and their random payoffs. Asset prices are endogenously determined through short-term market clearing. Investors' portfolio choices are characterized by investment strategies which provide a descriptive model of decision behavior. The mathematical framew...

  8. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  9. Human asparaginyl-tRNA synthetase: molecular cloning and the inference of the evolutionary history of Asx-tRNA synthetase family.

    Science.gov (United States)

    Shiba, K; Motegi, H; Yoshida, M; Noda, T

    1998-11-15

    We have cloned and sequenced a cDNA encoding human cytoplasmic asparaginyl-tRNA synthetase (AsnRS). The N-terminal appended domain of 112 amino acid represents the signature sequence for the eukaryotic AsnRS and is absent from archaebacterial or eubacterial enzymes. The canonical ortholog for AsnRS is absent from most archaebacterial and some eubacterial genomes, indicating that in those organisms, formation of asparaginyl-tRNA is independent of the enzyme. The high degree of sequence conservation among asparaginyl- and aspartyl-tRNA synthetases (AsxRS) made it possible to infer the evolutionary paths of the two enzymes. The data show the neighbor relationship between AsnRS and eubacterial aspartyl-tRNA synthetase, and support the occurrence of AsnRS early in the course of evolution, which is in contrast to the proposed late occurrence of glutaminyl-tRNA synthetase.

  10. Evolutionary genomics of environmental pollution.

    Science.gov (United States)

    Whitehead, Andrew

    2014-01-01

    Chemical toxins have been a persistent source of evolutionary challenges throughout the history of life, and deep within the genomic storehouse of evolutionary history lay ancient adaptations to diverse chemical poisons. However, the rate of change of contemporary environments mediated by human-introduced pollutants is rapidly screening this storehouse and severely testing the adaptive potential of many species. In this chapter, we briefly review the deep history of evolutionary adaptation to environmental toxins, and then proceed to describe the attributes of stressors and populations that may facilitate contemporary adaptation to pollutants introduced by humans. We highlight that phenotypes derived to enable persistence in polluted habitats may be multi-dimensional, requiring global genome-scale tools and approaches to uncover their mechanistic basis, and include examples of recent progress in the field. The modern tools of genomics offer promise for discovering how pollutants interact with genomes on physiological timescales, and also for discovering what genomic attributes of populations may enable resistance to pollutants over evolutionary timescales. Through integration of these sophisticated genomics tools and approaches with an understanding of the deep historical forces that shaped current populations, a more mature understanding of the mechanistic basis of contemporary ecological-evolutionary dynamics should emerge.

  11. Incorporating Development Into Evolutionary Psychology

    OpenAIRE

    David F. Bjorklund

    2016-01-01

    Developmental thinking is gradually becoming integrated within mainstream evolutionary psychology. This is most apparent with respect to the role of parenting, with proponents of life history theory arguing that cognitive and behavioral plasticity early in life permits children to select different life history strategies, with such strategies being adaptive solutions to different fitness trade-offs. I argue that adaptations develop and are based on the highly plastic nature of infants’ and ch...

  12. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...... anatomical diversity and include the bivalves (scallops, oysters, and clams), gastropods (limpets, snails, and slugs), and cephalopods (squid, cuttlefish, and octopus). This study treats each major taxon and supplies general information as well as overviews of evolution and phylogeny using data from...... different sources--morphological, ultrastructural, molecular, developmental, and from the fossil record....

  13. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system.

    Science.gov (United States)

    Vieira, Filipe G; Rozas, Julio

    2011-01-01

    Chemoreception is a biological process essential for the survival of animals, as it allows the recognition of important volatile cues for the detection of food, egg-laying substrates, mates, or predators, among other purposes. Furthermore, its role in pheromone detection may contribute to evolutionary processes, such as reproductive isolation and speciation. This key role in several vital biological processes makes chemoreception a particularly interesting system for studying the role of natural selection in molecular adaptation. Two major gene families are involved in the perireceptor events of the chemosensory system: the odorant-binding protein (OBP) and chemosensory protein (CSP) families. Here, we have conducted an exhaustive comparative genomic analysis of these gene families in 20 Arthropoda species. We show that the evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes, and independent origins of subfamilies. Taken together, our data clearly support the birth-and-death model for the evolution of these gene families with an overall high gene turnover rate. Moreover, we show that the genome organization of the two families is significantly more clustered than expected by chance and, more important, that this pattern appears to be actively maintained across the Drosophila phylogeny. Finally, we suggest the homologous nature of the OBP and CSP gene families, dating back their most recent common ancestor after the terrestrialization of Arthropoda (380--450 Ma) and we propose a scenario for the origin and diversification of these families.

  14. Determinants of SME credit worthiness under Basel rules: the value of credit history information

    Directory of Open Access Journals (Sweden)

    Francesco Dainelli

    2013-03-01

    Full Text Available The Basel III Accord has reportedly had an impact on SME financing. In this paper, we aim to highlight the determinants of SME credit worthiness. We use credit history in addition to financial ratios and “hybrid” indicators that have been built by mixing credit history with financial statement data. We develop a failure prediction logit model on 187 Italian SMEs. The use of short-term credit lines is the most important variable. Contrary to common understanding, capitalization levels do not affect ratings. Lastly, credit worthiness is sensitive to sale profitability.

  15. Determinants of SME credit worthiness under Basel rules: the value of credit history information

    OpenAIRE

    Francesco Dainelli; Francesco Giunta; Fabrizio Cipollini

    2013-01-01

    The Basel III Accord has reportedly had an impact on SME financing. In this paper, we aim to highlight the determinants of SME credit worthiness. We use credit history in addition to financial ratios and “hybrid” indicators that have been built by mixing credit history with financial statement data. We develop a failure prediction logit model on 187 Italian SMEs. The use of short-term credit lines is the most important variable. Contrary to common understanding, capitalization levels do not a...

  16. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  17. Anxiety: an evolutionary approach.

    OpenAIRE

    Bateson, M; Brilot, B; Nettle, D

    2011-01-01

    Anxiety disorders are among the most common mental illnesses, with huge attendant suffering. Current treatments are not universally effective, suggesting that a deeper understanding of the causes of anxiety is needed. To understand anxiety disorders better, it is first necessary to understand the normal anxiety response. This entails considering its evolutionary function as well as the mechanisms underlying it. We argue that the function of the human anxiety response, and homologues in other ...

  18. The Australian Education Union: A History of Opposing School Choice and School Autonomy Down-Under

    Science.gov (United States)

    Donnelly, Kevin

    2015-01-01

    In this article, I chronicle the recent history of efforts to broaden school choice in the Commonwealth of Australia and the opposition to these efforts put forth by Australia's largest teacher union, the Australian Education Union (AEU). Evidence is presented on the positive effects that flow from the public funding of nongovernment schools and…

  19. Insights into the evolutionary history of tubercle bacilli as disclosed by genetic rearrangements within a PE_PGRS duplicated gene pair

    Directory of Open Access Journals (Sweden)

    Kurepina Natalia

    2006-12-01

    Full Text Available Abstract Background The highly homologous PE_PGRS (Proline-glutamic acid_polymorphic GC-rich repetitive sequence genes are members of the PE multigene family which is found only in mycobacteria. PE genes are particularly abundant within the genomes of pathogenic mycobacteria where they seem to have expanded as a result of gene duplication events. PE_PGRS genes are characterized by their high GC content and extensive repetitive sequences, making them prone to recombination events and genetic variability. Results Comparative sequence analysis of Mycobacterium tuberculosis genes PE_PGRS17 (Rv0978c and PE_PGRS18 (Rv0980c revealed a striking genetic variation associated with this typical tandem duplicate. In comparison to the M. tuberculosis reference strain H37Rv, the variation (named the 12/40 polymorphism consists of an in-frame 12-bp insertion invariably accompanied by a set of 40 single nucleotide polymorphisms (SNPs that occurs either in PE_PGRS17 or in both genes. Sequence analysis of the paralogous genes in a representative set of worldwide distributed tubercle bacilli isolates revealed data which supported previously proposed evolutionary scenarios for the M. tuberculosis complex (MTBC and confirmed the very ancient origin of "M. canettii" and other smooth tubercle bacilli. Strikingly, the identified polymorphism appears to be coincident with the emergence of the post-bottleneck successful clone from which the MTBC expanded. Furthermore, the findings provide direct and clear evidence for the natural occurrence of gene conversion in mycobacteria, which appears to be restricted to modern M. tuberculosis strains. Conclusion This study provides a new perspective to explore the molecular events that accompanied the evolution, clonal expansion, and recent diversification of tubercle bacilli.

  20. Elastic-plastic creep response of structures under composite time history

    International Nuclear Information System (INIS)

    Zudans, Z.

    1975-01-01

    High temperature nuclear reactor components are subject to a complex history of thermal and mechanical loading cycles. To evaluate the adequacy of such components, detailed information on the accumulated inelastic strains and strain cycling is required. This paper presents the theory, describes efficient numerical techniques accounting for plasticity, creep and overall equilibrium, describes the overall structure of the resulting computer program, and demonstrates the capability of the analysis method on a real three-dimensional structure. The new results of this work are the efficient handling of an arbitrary load history, introduction of the 'plastic stress' concept for inelastic computation, novel implementation of classical plasticity with recognition of incrementation conditions for the kinematic hardening, use of the load incrementation algorithm based on the 'plastic stress' concept, and development of a computer code capable of solving practical three-dimensional problems. (Auth.)

  1. Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

    Directory of Open Access Journals (Sweden)

    James Timothy Y

    2009-06-01

    Full Text Available Abstract Background Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32 into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. Results We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. Conclusion We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi

  2. Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses.

    Science.gov (United States)

    Parrent, Jeri Lynn; James, Timothy Y; Vasaitis, Rimvydas; Taylor, Andrew Fs

    2009-06-30

    Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0-12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant

  3. Elastic-plastic-creep response of structures under composite time history of loadings

    International Nuclear Information System (INIS)

    Zudans, Z.

    1975-01-01

    High temperature nuclear reactor components are subject to a complex history of thermal and mechanical loading cycles. To evaluate the adequacy of such components, detailed information on the accumulated inelastic strains and strain cycling is required. This work derives the theory, develops efficient numerical techniques accounting for plasticity, creep and overall equilibrium, describes the overall structure of the resulting computer program, and demonstrates the capability of this analysis on a real structure. (Auth.)

  4. Growth, life history, and species interactions of bluegill sunfish (Lepomis macrochirus) under heavy predation

    Energy Technology Data Exchange (ETDEWEB)

    Belk, Mark Carl [Univ. of Georgia, Athens, GA (United States)

    1992-01-01

    The purpose of this study was, first, to compare growth and life history characteristics of an unfished population of bluegill sunfish (Lepomis macrochirus) in the presence of an abundant predator population to characteristic exhibited by bluegills in typical southeastern US reservoirs where the abundance of predators is reduced, but fishing is increased. The second objective was to determine if differences observed between populations were determined genetically or environmentally.

  5. Geochronological, geochemical, and Nd-Hf isotopic studies of the Qinling Complex, central China: Implications for the evolutionary history of the North Qinling Orogenic Belt

    Directory of Open Access Journals (Sweden)

    Chunrong Diwu

    2014-07-01

    The available data indicate that the NQOB was an independent micro-continent at least prior to the Neoproterozoic, and included a portion of the Grenville orogenic belt during the period of 1.2–0.8 Ga. The NQOB has experienced a unique geological history, which is obviously different from that of the North China Craton (NCC and the Yangtze Craton during the Precambrian. The Neoproterozoic granitoids that intruded the Qinling Complex can be interpreted as the products of assembly of the supercontinent Rodinia. The NQOB was separated from Rodinia at ca. 830–740 Ma. Subsequently, the NQOB moved closer to the northern margin of the NCC, and the initial accretion or collision with the NCC occurred from the late Cambrian to the early Ordovician.

  6. Interpreting Evolutionary Diagrams: When Topology and Process Conflict

    Science.gov (United States)

    Catley, Kefyn M.; Novick, Laura R.; Shade, Courtney K.

    2010-01-01

    The authors argue that some diagrams in biology textbooks and the popular press presented as depicting evolutionary relationships suggest an inappropriate (anagenic) conception of evolutionary history. The goal of this research was to provide baseline data that begin to document how college students conceptualize the evolutionary relationships…

  7. Evolutionary developmental biology its roots and characteristics.

    Science.gov (United States)

    Morange, Michel

    2011-09-01

    The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. The structure of microbial evolutionary theory.

    Science.gov (United States)

    Sapp, J

    2007-12-01

    The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life's history over billions of years, but also in transcending the structure of thought that has shaped evolutionary theory since the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists.

  9. Evolutionary Effects on Morphology and Agronomic Performance of Three Winter Wheat Composite Cross Populations Maintained for Six Years under Organic and Conventional Conditions

    Directory of Open Access Journals (Sweden)

    Sarah Brumlop

    2017-02-01

    Full Text Available Three winter wheat (Triticum aestivum L. composite cross populations (CCPs that had been maintained in repeated parallel populations under organic and conventional conditions from the F5 to the F10 were compared in a two-year replicated field trial under organic conditions. The populations were compared to each other, to a mixture of the parental varieties used to establish the CCPs, and to three winter wheat varieties currently popular in organic farming. Foot and foliar diseases, straw length, ear length, yield parameters, and baking quality parameters were assessed. The overall performance of the CCPs differed clearly from each other due to differences in their parental genetics and not because of their conventional or organic history. The CCPs with high yielding background (YCCPs also yielded higher than the CCPs with a high baking quality background (QCCPs; in the absence of extreme winter stress. The QCCPs performed equally well in comparison to the reference varieties, which were also of high baking quality. Compared to the parental mixture the CCPs proved to be highly resilient, recovering much better from winter kill in winter 2011/12. Nevertheless, they were out yielded by the references in that year. No such differences were seen in 2013, indicating that the CCPs are comparable with modern cultivars in yielding ability under organic conditions. We conclude that—especially when focusing on traits that are not directly influenced by natural selection (e.g. quality traits—the choice of parents to establish a CCP is crucial. In the case of the QCCPs the establishment of a reliable high-quality population worked very well and quality traits were successfully maintained over time. However, in the YCCPs lack of winter hardiness in the YCCP parents also became clearly visible under relevant winter conditions.

  10. Sense of control under uncertainty depends on people's childhood environment: a life history theory approach.

    Science.gov (United States)

    Mittal, Chiraag; Griskevicius, Vladas

    2014-10-01

    Past research found that environmental uncertainty leads people to behave differently depending on their childhood environment. For example, economic uncertainty leads people from poor childhoods to become more impulsive while leading people from wealthy childhoods to become less impulsive. Drawing on life history theory, we examine the psychological mechanism driving such diverging responses to uncertainty. Five experiments show that uncertainty alters people's sense of control over the environment. Exposure to uncertainty led people from poorer childhoods to have a significantly lower sense of control than those from wealthier childhoods. In addition, perceptions of control statistically mediated the effect of uncertainty on impulsive behavior. These studies contribute by demonstrating that sense of control is a psychological driver of behaviors associated with fast and slow life history strategies. We discuss the implications of this for theory and future research, including that environmental uncertainty might lead people who grew up poor to quit challenging tasks sooner than people who grew up wealthy. 2014 APA, all rights reserved

  11. Vitamin D status in under-five children with a history of close tuberculosis contact in Padang, West Sumatra.

    Science.gov (United States)

    Yani, Finny Fitry; Lipoeto, Nur Indrawaty; Supriyatno, Bambang; Darwin, Eryati; Basir, Darfioes

    2017-06-01

    Serum vitamin D influences cellular immunity against Mycobacterium tuberculosis, particularly in under-five children. Vitamin D insufficiency and deficiency as well as tuberculosis (TB) are highly prevalent in Indonesia. This study described the association of serum vitamin D in the incidence of latent TB in under-five children with a history of close TB contact. This cross-sectional study examined 178 under-five children with a history of close TB contact, with 98 index cases from primary health care facilities in Padang. Latent TB was defined based on a positive tuberculin skin test. Serum vitamin D was determined using ELISA method. General characteristics for age, sex, socioeconomic status, contact score, BCG scars, and nutritional status were also collected. Of 168 eligible subjects, 40.5% had latent TB, however no differences between 'latent TB' and 'without latent TB' were observed in participant characteristics. Vitamin D deficiency, insufficiency, and sufficiency were observed in 23.3%, 43.5%, and 33.3% of children, respectively. In general, the 'latent TB' group had lower serum vitamin D than those in the 'without latent TB' group, stratified by age, contact score and nutritional status; however, significant differences were observed in children age <1 years (18.0±2.6 vs 31.2±10.5, respectively, p=0.013). Nevertheless, no associations between the two groups were observed using multivariate analysis. Vitamin D status was not associated with the incidence of latent TB among under-five children with a history of close TB contact, although this may not obtain in children aged <1 year old.

  12. History of childhood abuse, sensation seeking, and intimate partner violence under/not under the influence of a substance: a cross-sectional study in Russia.

    Directory of Open Access Journals (Sweden)

    Weihai Zhan

    Full Text Available To examine correlates of perpetration and victimization of intimate partner violence (IPV under and not under the influence of a substance, we conducted a study among women in Russia.In 2011, a cross-sectional survey was conducted among patients receiving services at a clinic for sexually transmitted infections in St. Petersburg, Russia. Multinomial logistic regression was used for analysis.Of 299 women, 104 (34.8% and 113 (37.8% reported a history of IPV perpetration and victimization, respectively. Nearly half (47.1% of perpetrators and 61.1% of victims reported that the latest IPV event (perpetration and victimization, respectively was experienced under the influence of a substance. Factors independently associated with IPV victimization under the influence of a substance were alcohol misuse and a higher number of lifetime sex partners, whereas only experience of childhood abuse (emotional and physical abuse was independently associated with IPV victimization that did not occur under the influence of a substance. Childhood physical abuse, lower age of first sex, sensation seeking, and alcohol misuse were independently associated with IPV perpetration under the influence of a substance, while only childhood abuse (emotional and physical abuse was independently associated with IPV perpetration that did not occur under the influence of a substance.IPV under and not under the influence of a substance had different correlates (e.g., alcohol misuse and sensation seeking. Despite the strong association between substance use and IPV, experience of childhood abuse is an important predictor of IPV perpetration and victimization in Russia, above and beyond substance use.

  13. Mass killing under the guise of ECT: the darkest chapter in the history of biological psychiatry.

    Science.gov (United States)

    Gazdag, G; Ungvari, G S; Czech, H

    2017-12-01

    Following its inception, electroconvulsive therapy (ECT), rapidly spread all over the world, including Nazi Germany. Paradoxically, at the same time, the euthanasia programme was started in Germany: the extermination of people with intellectual disabilities and severe psychiatric disorders. In Lower Austria, Dr Emil Gelny, who had been granted a specialist qualification in psychiatry after three months of clinical training, took control of two psychiatric hospitals, in Gugging and Mauer-Öhling. In 1944, he began systematically killing patients with an ECT machine, something that was not practised anywhere else before or after, and remains unprecedented in the history of convulsive therapy. He modified an ECT machine, adding extra electrodes, which he fastened onto a victim's wrists and ankles to administer lethal electric shocks.

  14. A Large-scale Survey of CRF55_01B from Men-Who-Have-Sex-with-Men in China: implying the Evolutionary History and Public Health Impact.

    Science.gov (United States)

    Han, Xiaoxu; Takebe, Yutaka; Zhang, Weiqing; An, Minghui; Zhao, Bin; Hu, Qinghai; Xu, Junjie; Wu, Hao; Wu, Jianjun; Lu, Lin; Chen, Xi; Liang, Shu; Wang, Zhe; Yan, Hongjing; Fu, Jihua; Cai, Weiping; Zhuang, Minghua; Liao, Christina; Shang, Hong

    2015-12-15

    The HIV-1 epidemic among men-who-have-sex-with-men (MSM) continues to expand in China, involving the co-circulation of several different lineages of HIV-1 strains, including subtype B and CRF01_AE. This expansion has created conditions that facilitate the generation of new recombinant strains. A molecular epidemiologic survey among MSM in 11 provinces/cities around China was conducted from 2008 to 2013. Based on pol nucleotide sequences, a total of 19 strains (1.95%) belonged to the CRF55_01B were identified from 975 MSM in 7 provinces, with the prevalence range from 1.5% to 12.5%. Near full length genome (NFLG) sequences from six epidemiologically-unlinked MSM were amplified for analyzing evolutionary history, an identical genome structure composed of CRF01_AE and subtype B with four unique recombination breakpoints in the pol region were identified. Bayesian molecular clock analyses for both CRF01_AE and B segments indicated that the estimated time of the most recent common ancestors of CRF55_01B was around the year 2000. Our study found CRF55_01B has spread throughout the most provinces with high HIV-1 prevalence and highlights the importance of continual surveillance of dynamic changes in HIV-1 strains, the emergence of new recombinants, and the need for implementing effective prevention measures specifically targeting the MSM population in China.

  15. PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex.

    Science.gov (United States)

    Cinelli, Tamara; Moscetti, Ilaria; Marchi, Guido

    2014-11-01

    A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.

  16. Fracture criteria under creep with strain history taken into account, and long-term strength modelling

    Science.gov (United States)

    Khokhlov, A. V.

    2009-08-01

    In the present paper, we continue to study the nonlinear constitutive relation (CR) between the stress and strain proposed in [1] to describe one-dimensional isothermal rheological processes in the case of monotone variation of the strain (in particular, relaxation, creep, plasticity, and superplasticity). We show that this CR together with the strain fracture criterion (FC) leads to theoretical long-term strength curves (LSC) with the same qualitative properties as the typical experimental LSC of viscoelastoplastic materials. We propose two parametric families of fracture criteria in the case of monotone uniaxial strain, which are related to the strain fracture criterion (SFC) but take into account the strain increase history and the dependence of the critical strain on the stress. Instead of the current strain, they use other measures of damage related to the strain history by time-dependent integral operators. For any values of the material parameters, analytic studies of these criteria allowed us to find several useful properties, which confirm that they can be used to describe the creep fracture of different materials. In particular, we prove that, together with the proposed constitutive relations, these FC lead to theoretical long-term strength curves (TLSC) with the same qualitative properties as the experimental LSC. It is important that each of the constructed families of FC forms a monotone and continuous scale of criteria (monotonously and continuously depending on a real parameter) that contains the SFC as the limit case. Moreover, the criteria in the first family always provide the fracture time greater than that given by the SFC, the criteria in the second family always provide a smaller fracture time, and the difference can be made arbitrarily small by choosing the values of the control parameter near the scale end. This property is very useful in finding a more accurate adjustment of the model to the existing experimental data describing the

  17. Evolutionary analysis of hepatitis C virus gene sequences from 1953

    Science.gov (United States)

    Gray, Rebecca R.; Tanaka, Yasuhito; Takebe, Yutaka; Magiorkinis, Gkikas; Buskell, Zelma; Seeff, Leonard; Alter, Harvey J.; Pybus, Oliver G.

    2013-01-01

    Reconstructing the transmission history of infectious diseases in the absence of medical or epidemiological records often relies on the evolutionary analysis of pathogen genetic sequences. The precision of evolutionary estimates of epidemic history can be increased by the inclusion of sequences derived from ‘archived’ samples that are genetically distinct from contemporary strains. Historical sequences are especially valuable for viral pathogens that circulated for many years before being formally identified, including HIV and the hepatitis C virus (HCV). However, surprisingly few HCV isolates sampled before discovery of the virus in 1989 are currently available. Here, we report and analyse two HCV subgenomic sequences obtained from infected individuals in 1953, which represent the oldest genetic evidence of HCV infection. The pairwise genetic diversity between the two sequences indicates a substantial period of HCV transmission prior to the 1950s, and their inclusion in evolutionary analyses provides new estimates of the common ancestor of HCV in the USA. To explore and validate the evolutionary information provided by these sequences, we used a new phylogenetic molecular clock method to estimate the date of sampling of the archived strains, plus the dates of four more contemporary reference genomes. Despite the short fragments available, we conclude that the archived sequences are consistent with a proposed sampling date of 1953, although statistical uncertainty is large. Our cross-validation analyses suggest that the bias and low statistical power observed here likely arise from a combination of high evolutionary rate heterogeneity and an unstructured, star-like phylogeny. We expect that attempts to date other historical viruses under similar circumstances will meet similar problems. PMID:23938759

  18. Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms.

    Science.gov (United States)

    Killeen, Joshua; Gougat-Barbera, Claire; Krenek, Sascha; Kaltz, Oliver

    2017-04-01

    Evolutionary rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23 to 32 °C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35, 37 °C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23 °C) and high-temperature (32 °C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9 °C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche. © 2017 John Wiley & Sons Ltd.

  19. Origin of two maxima in specific heat in enthalpy relaxation under thermal history composed of cooling, annealing, and heating.

    Science.gov (United States)

    Sakatsuji, Waki; Konishi, Takashi; Miyamoto, Yoshihisa

    2016-12-01

    The origin of two maxima in specific heat observed at the higher and the lower temperatures in the glass-transition region in the heating process has been studied for polymethyl methacrylate and polyvinyl chloride using differential scanning calorimetry, and the calculation was done using the phenomenological model equation under a thermal history of the typical annealing experiment composed of cooling, annealing, and heating. The higher maximum is observed above the glass-transition temperature, and it remains almost unchanged independent of annealing time t_{a}, while the lower one is observed above an annealing temperature T_{a} and shifts toward the higher one, increasing its magnitude with t_{a}. The analysis by the phenomenological model equation proposed in order to interpret the memory effect in the glassy state clarifies that under a typical annealing history, two maxima in specific heat essentially appear. The shift of the lower maximum toward higher temperatures from above T_{a} is caused by an increase in the amount of relaxation during annealing with t_{a}. The annealing temperature and the amount of relaxation during annealing play a major role in the determination of the number of maxima in the specific heat.

  20. Ecosystem Carbon Budgets under Contrasting Land Use Histories Using Eddy Covariance and Deep Core Methods

    Science.gov (United States)

    Abraha, M.; Gelfand, I.; Hamilton, S. K.; Shao, C.; Su, Y. J.; Robertson, G. P.; Chen, J.

    2016-12-01

    Increasing demand for agricultural production could be met through conversion of uncultivated lands and/or intensification of production on existing agricultural lands, each with distinct implications for ecosystem carbon budgets. We investigated the carbon budget of two intensively managed continuous no-till corn fields with contrasting land use histories over six years using eddy covariance (EC) and deep core methods. One treatment had been managed as Conservation Reserve Program (CRP) grassland for 22 years before conversion, thus representing conversion of uncultivated lands into agriculture, and the other treatment had been managed as conventional agriculture (AGR) in a corn-soybean rotation for several decades before conversion, thus representing agricultural intensification. We hypothesized that the AGR land would sequester more carbon or at least remain neutral owing to the reduced soil disturbance and increased overall productivity of the land following conversion. Accordingly, we expected soil carbon to either increase or remain unchanged compared to its pre-conversion status. We also hypothesized that the CRP grassland converted to no-till would lose carbon to the atmosphere until a new equilibrium is reached owing to the decomposition of the large below- and above-ground plant biomass and soil organic matter that had accumulated during the 22 years of CRP management. Consequently, we anticipated the soil carbon to decrease compared to its pre-conversion status. The EC-derived carbon budget supported our hypothesis in that the former AGR land was on average carbon neutral (-8 g C m-2 yr-1) while the former CRP land emitted 301 g C m-2 yr-1 to the atmosphere over the six year period. In contradiction to the hypothesis, the deep core method indicated that the former AGR land emitted 167 g C m-2 yr-1 to the atmosphere while the former CRP land sequestered 127 g C m-2 yr-1 over the same time period. This could be due to pre-conversion plant biomass and soil

  1. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

  2. Evolutionary history of regeneration in crinoids (Echinodermata).

    Science.gov (United States)

    Gahn, Forest J; Baumiller, Tomasz K

    2010-10-01

    The fossil record indicates that crinoids have exhibited remarkable regenerative abilities since their origin in the Ordovician, abilities that they likely inherited from stem-group echinoderms. Regeneration in extant and fossil crinoids is recognized by abrupt differences in the size of abutting plates, aberrant branching patterns, and discontinuities in carbon isotopes. While recovery is common, not all lost body parts can be regenerated; filling plates and overgrowths are evidence of non-regenerative healing. Considering them as a whole, Paleozoic crinoids exhibit the same range of regenerative and non-regenerative healing as Recent crinoids. For example, Paleozoic and extant crinoids show evidence of crown regeneration and stalk regrowth, which can occur only if the entoneural nerve center (chambered organ) remains intact. One group of Paleozoic crinoids, the camerates, may be an exception in that they probably could not regenerate their complex calyx-plating arrangements, including arm facets, but their calyxes could be healed with reparative plates. With that exception, and despite evidence for increases in predation pressure, there is no compelling evidence that crinoids have changed though time in their ability to recover from wounds. Finally, although crinoid appendages may be lost as a consequence of severe abiotic stress and through ontogenetic development, spatiotemporal changes in the intensity and frequency of biotic interactions, especially direct attacks, are the most likely explanation for observed patterns of regeneration and autotomy in crinoids. © The Author 2010. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.

  3. Evolutionary history of rabies in Ghana.

    Directory of Open Access Journals (Sweden)

    David T S Hayman

    2011-04-01

    Full Text Available Rabies virus (RABV is enzootic throughout Africa, with the domestic dog (Canis familiaris being the principal vector. Dog rabies is estimated to cause 24,000 human deaths per year in Africa, however, this estimate is still considered to be conservative. Two sub-Saharan African RABV lineages have been detected in West Africa. Lineage 2 is present throughout West Africa, whereas Africa 1a dominates in northern and eastern Africa, but has been detected in Nigeria and Gabon, and Africa 1b was previously absent from West Africa. We confirmed the presence of RABV in a cohort of 76 brain samples obtained from rabid animals in Ghana collected over an eighteen-month period (2007-2009. Phylogenetic analysis of the sequences obtained confirmed all viruses to be RABV, belonging to lineages previously detected in sub-Saharan Africa. However, unlike earlier reported studies that suggested a single lineage (Africa 2 circulates in West Africa, we identified viruses belonging to the Africa 2 lineage and both Africa 1 (a and b sub-lineages. Phylogeographic Bayesian Markov chain Monte Carlo analysis of a 405 bp fragment of the RABV nucleoprotein gene from the 76 new sequences derived from Ghanaian animals suggest that within the Africa 2 lineage three clades co-circulate with their origins in other West African countries. Africa 1a is probably a western extension of a clade circulating in central Africa and the Africa 1b virus a probable recent introduction from eastern Africa. We also developed and tested a novel reverse-transcription loop-mediated isothermal amplification (RT-LAMP assay for the detection of RABV in African laboratories. This RT-LAMP was shown to detect both Africa 1 and 2 viruses, including its adaptation to a lateral flow device format for product visualization. These data suggest that RABV epidemiology is more complex than previously thought in West Africa and that there have been repeated introductions of RABV into Ghana. This analysis highlights the potential problems of individual developing nations implementing rabies control programmes in the absence of a regional programme.

  4. YI Kwang Su’s Love and history records of modern hospital under the japanese colonial period

    Directory of Open Access Journals (Sweden)

    Byoung Hoon LEE

    2016-12-01

    Full Text Available This article aims to evaluate and analyze the description of the modern hospital as history record, which appeared in YI Kwang Su’s novel Love. This novel has mentioned in detail western style clinic, Bukgando Catholic hospital, tuberculosis sanitarium as its main space. Modern hospitals are depicted in the novel has a great significance in historical aspect as well as in literary aspect. The most data on modern hospital is laws, statistics and newspaper archives. These materials are a great help to understand the history and status of the modern hospital. Literary description here is important materials, that specific to reconstruct the appearance of the modern hospital at that time. Literary representations infuse life into the history record. In this regard, Love has special meaning in the history of Korean modern literature. Before anything else, doctor AN Bin’s clinic as a first space of the novel vividly shows the reality of the Western style clinic and a general practitioner under the colonial period. The establishment of the hospital was based on 「Rules on private hospital」 declared by the Japanese Government General of Korea in 1919. According to this Rules, a private clinic’s founder had to submit the documents to the director of police affairs, in which all the details were written. It included name of hospital, site location and size, floor plan of a nearby building, each size of patient’s rooms, number of steps and emergency exit, bath, toilet, disinfecting room. AN Bin’s clinic was a private hospital with the requirements in the rules. The descriptions of this clinic re-created real situation of private hospitals, specifically scale of hospital, interior space, conditions of patient’s room at the time. The second modern hospital in the novel is Bukgando Catholic hospital. There is a lot more materials on medical activity and hospital of protestant churches than we thought. But we do not have a lot of information on

  5. Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history.

    Science.gov (United States)

    Klonowska, Agnieszka; Melkonian, Rémy; Miché, Lucie; Tisseyre, Pierre; Moulin, Lionel

    2018-01-30

    Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099-111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica.

  6. Euryhalinity in an evolutionary context

    Science.gov (United States)

    Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.

    2013-01-01

    This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

  7. Incorporating Development Into Evolutionary Psychology

    Directory of Open Access Journals (Sweden)

    David F. Bjorklund

    2016-09-01

    Full Text Available Developmental thinking is gradually becoming integrated within mainstream evolutionary psychology. This is most apparent with respect to the role of parenting, with proponents of life history theory arguing that cognitive and behavioral plasticity early in life permits children to select different life history strategies, with such strategies being adaptive solutions to different fitness trade-offs. I argue that adaptations develop and are based on the highly plastic nature of infants’ and children’s behavior/cognition/brains. The concept of evolved probabilistic cognitive mechanisms is introduced, defined as information processing mechanisms evolved to solve recurrent problems faced by ancestral populations that are expressed in a probabilistic fashion in each individual in a generation and are based on the continuous and bidirectional interaction over time at all levels of organization, from the genetic through the cultural. Early perceptual/cognitive biases result in behavior that, when occurring in a species-typical environment, produce continuous adaptive changes in behavior (and cognition, yielding adaptive outcomes. Examples from social learning and tool use are provided, illustrating the development of adaptations via evolved probabilistic cognitive mechanisms. The integration of developmental concepts into mainstream evolutionary psychology (and evolutionary concepts into mainstream developmental psychology will provide a clearer picture of what it means to be human.

  8. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Evolutionary Biology Today - The Domain of Evolutionary Biology ... Keywords. Evolution; natural selection; biodiversity; fitness; adaptation. Author Affiliations. Amitabh Joshi1. Evolutionary and Organismal Biology Unit Jawaharlal Nehru Centre for Advanced Scientific Research P.Box 6436, Jakkur Bangalore 560 065, India.

  9. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  10. A representation-theoretic approach to the calculation of evolutionary distance in bacteria

    Science.gov (United States)

    Sumner, Jeremy G.; Jarvis, Peter D.; Francis, Andrew R.

    2017-08-01

    In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general maximum likelihood setting, how to use elementary matrix algebra to sidestep intractable combinatorial computations and convert the problem into one of eigenvalue estimation amenable to standard numerical approximation techniques.

  11. Multi types DG expansion dynamic planning in distribution system under stochastic conditions using Covariance Matrix Adaptation Evolutionary Strategy and Monte-Carlo simulation

    International Nuclear Information System (INIS)

    Sadeghi, Mahmood; Kalantar, Mohsen

    2014-01-01

    Highlights: • Defining a DG dynamic planning problem. • Applying a new evolutionary algorithm called “CMAES” in planning process. • Considering electricity price and fuel price variation stochastic conditions. • Scenario generation and reduction with MCS and backward reduction programs. • Considering approximately all of the costs of the distribution system. - Abstract: This paper presents a dynamic DG planning problem considering uncertainties related to the intermittent nature of the DG technologies such as wind turbines and solar units in addition to the stochastic economic conditions. The stochastic economic situation includes the uncertainties related to the fuel and electricity price of each year. The Monte Carlo simulation is used to generate the possible scenarios of uncertain situations and the produced scenarios are reduced through backward reduction program. The aim of this paper is to maximize the revenue of the distribution system through the benefit cost analysis alongside the encouraging and punishment functions. In order to close to reality, the different growth rates for the planning period are selected. In this paper the Covariance Matrix Adaptation Evolutionary Strategy is introduced and is used to find the best planning scheme of the DG units. The different DG types are considered in the planning problem. The main assumption of this paper is that the DISCO is the owner of the distribution system and the DG units. The proposed method is tested on a 9 bus test distribution system and the results are compared with the known genetic algorithm and PSO methods to show the applicability of the CMAES method in this problem

  12. Evolutionary process of deep-sea bathymodiolus mussels.

    Directory of Open Access Journals (Sweden)

    Jun-Ichi Miyazaki

    Full Text Available BACKGROUND: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. METHODOLOGY/PRINCIPAL FINDING: We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI and NADH dehydrogenase subunit 4 (ND4 genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. CONCLUSIONS/SIGNIFICANCE: The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of

  13. Environmental evolutionary graph theory.

    Science.gov (United States)

    Maciejewski, Wes; Puleo, Gregory J

    2014-11-07

    Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have received relatively less attention. Here we present a structured population model where different individuals are best suited to different regions of their environment. The underlying structure is a graph: individuals occupy vertices, which are connected by edges. If an individual is suited for their vertex, they receive an increase in fecundity. This framework allows attention to be restricted to the spatial arrangement of suitable habitat. We prove some basic properties of this model and find some counter-intuitive results. Notably, (1) the arrangement of suitable sites is as important as their proportion, and (2) decreasing the proportion of suitable sites may result in a decrease in the fixation time of an allele. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

    Science.gov (United States)

    Hunt, Tam

    2014-12-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

  15. Life-history traits of Fossaria cubensis (Gastropoda: Lymnaeidae under experimental exposure to Fasciola hepatica (Trematoda: Digenea

    Directory of Open Access Journals (Sweden)

    Gutiérrez Alfredo

    2000-01-01

    Full Text Available The effect of exposing the lymnaeid snail Fossaria cubensis to the trematode Fasciola hepatica on the snail population's life-history traits was studied under laboratory conditions. Exposed individuals showed a lower survival rate than control snails, although from week 7 onward a slower decrease of this parameter in relation to the control group was observed. There were higher values of fecundity rate for the controls compared to the exposed group except during weeks 9, 10, 11 and 12, which was the time that followed the period when almost all of the infected snails died. Both the intrinsic and finite rates of natural increase were significantly higher for the control group, but exposed snails still attained a lower mean generation time. Age-specific trade-offs were found, mainly for the weekly increase in size versus the number of eggs per mass, the weekly increase in size versus the number of viable eggs per mass, the number of masses versus the hatching probability and the number of eggs versus the hatching probability. All these negative associations were significant for juveniles of both control and exposed snails and not for adults; however, exposed young individuals exhibited much higher values of the correlation coefficient than control animals.

  16. Ecological and Evolutionary Effects of Dispersal on Freshwater Zooplankton

    Science.gov (United States)

    Allen, Michael R.

    2009-01-01

    A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate ecology with evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species…

  17. A história ensinada sob o império da memória: questões de História da disciplina History taught under memory empire: discipline history questions

    Directory of Open Access Journals (Sweden)

    Maria Aparecida Leopoldino Tursi Toledo

    2004-01-01

    Full Text Available Este trabalho trata de uma reflexão acerca da história ensinada nas séries iniciais do ensino fundamental na perspectiva da História das disciplinas. O texto procura mostrar a contribuição das atuais pesquisas sobre História e Memória para a compreensão da trajetória desta disciplina escolar a partir do discernimento de ambos os termos no trato de seus percursos disciplinares. Registra que a história ensinada, principalmente nas séries iniciais, esteve dominantemente sob o império da memória não apenas porque havia a compreensão de que o ensino de História se fazia pela memorização de datas e vultos nacionais, mas porque foi a partir do recurso metodológico e historiográfico do século XIX que a História se tornou um meio importante para dispor da memória e converter-se em História nacional.This work deals with the history taught in initial grades of elementary school, under the perspective of history of disciplines. The text intends to show the current researches contribution about history and memory in order to understand this school discipline trajectory discerning both terms and dealing with their disciplinary courses. It registers that the history taught, mainly in initial grades, was dominantly under the memory empire not only due to the view that history teaching was constructed by dates and national important figures memorization, but also because history became an important mean to dispose memory and change into national History through methodological and historiographic resources from the nineteenth century.

  18. Evolutionary heritage influences amazon tree ecology

    NARCIS (Netherlands)

    Souza, De Fernanda Coelho; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J.W.; Chave, Jerome; Galbraith, David R.; Gonzalez, Gabriela Lopez; Mendoza, Abel Monteagudo; Toby Pennington, R.; Poorter, Lourens; Arets, E.J.M.M.; Boot, Rene G.A.; Meer, van der Peter J.

    2016-01-01

    Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of

  19. An Evolutionary Perspective on War Heroism

    NARCIS (Netherlands)

    Rusch, Hannes; Störmer, C.

    2015-01-01

    Humans are one of the most cooperative and altruistic species on the planet. At the same time, humans have a long history of violent and deadly intergroup conflicts or wars. Recently, contemporary evolutionary theorists have revived Charles Darwin’s idea that human in-group altruism and out-group

  20. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

    Science.gov (United States)

    Roux, F; Bergelson, J

    2016-01-01

    In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. © 2016 Elsevier Inc. All rights reserved.

  1. Chemoselective O-acylation of hydroxyamino acids and amino alcohols under acidic reaction conditions: History, scope and applications

    Directory of Open Access Journals (Sweden)

    Tor E. Kristensen

    2015-04-01

    Full Text Available Amino acids, whether natural, semisynthetic or synthetic, are among the most important and useful chiral building blocks available for organic chemical synthesis. In principle, they can function as inexpensive, chiral and densely functionalized starting materials. On the other hand, the use of amino acid starting materials routinely necessitates protective group chemistry, and in reality, large-scale preparations of even the simplest side-chain derivatives of many amino acids often become annoyingly strenuous due to the necessity of employing protecting groups, on one or more of the amino acid functionalities, during the synthetic sequence. However, in the case of hydroxyamino acids such as hydroxyproline, serine, threonine, tyrosine and 3,4-dihydroxyphenylalanine (DOPA, many O-acyl side-chain derivatives are directly accessible via a particularly expedient and scalable method not commonly applied until recently. Direct acylation of unprotected hydroxyamino acids with acyl halides or carboxylic anhydrides under appropriately acidic reaction conditions renders possible chemoselective O-acylation, furnishing the corresponding side-chain esters directly, on multigram-scale, in a single step, and without chromatographic purification. Assuming a certain degree of stability under acidic reaction conditions, the method is also applicable for a number of related compounds, such as various amino alcohols and the thiol-functional amino acid cysteine. While the basic methodology underlying this approach has been known for decades, it has evolved through recent developments connected to amino acid-derived chiral organocatalysts to become a more widely recognized procedure for large-scale preparation of many useful side-chain derivatives of hydroxyamino acids and related compounds. Such derivatives are useful in peptide chemistry and drug development, as amino acid amphiphiles for asymmetric catalysis, and as amino acid acrylic precursors for preparation of

  2. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  3. From Living under Attap to Residing in the Sky: Imagination and Empathy in Source-Based History Education in Singapore

    Science.gov (United States)

    Seng, Loh Kah; Wei, Lee Si

    2010-01-01

    To cultivate imagination and empathy among school students is a basic challenge for history teachers. This paper examines the relative roles of the teacher and student in nurturing imagination and empathy in the Singapore history classroom, specifically, through source-based studies. Both imagination and empathy are ways for students to think…

  4. Natural history of Ctenus medius Keyserling, 1891 (Aranae, Ctenidae II: life cycle and aspects of reproductive behavior under laboratory conditions

    Directory of Open Access Journals (Sweden)

    FOLLY-RAMOS E.

    2002-01-01

    Full Text Available Ctenus medius Keyserling, 1891 is a wandering spider common in the Brazilian Atlantic Forest. It has been the subject of few studies. Thus, this work aims to elucidate aspects of its natural history, such as the life cycle and reproductive behavior of this species, through laboratory and field observations. Two females with egg sacs were observed in the laboratory and one was observed in field (Barra Mansa, 22º32'S and 44º10'W until the emergence of the spiderlings. For observation of the immature stage development, a portion of the spiderlings from the same hatch were taken to the laboratory and watched until sexual maturity. In the field, the period between the oviposition and the emergence of spiderlings was of 36 days. The female selects a site for egg sac deposition and stays there until the spiderlings emerge. Seven days after the emergence, the female abandoned the site where the egg sac was made, concomitant to the spiderlings dispersion from observation's place and until the moment that the spiderlings started to eat. For the spiderlings kept under laboratory conditions, cannibalism was not observed in the first instars (1-4th when sufficient food was offered. Sexual maturity happened in the 14th or 15th instars, with an average of 309.2 to 344.5 days until the last/sexual molt, respectively. Until the date of sexual maturity, there was a mortality rate of 85%. This species is very fragile in captivity. This hampered deductions concerning longevity. Both females and males collected in the field were induced to mate in the laboratory. Courtship movements of males were registered, but the females did not permit the mating. These data may assist in initial biological studies of Ctenus genus and offer comparative parameters for studies of other related species.

  5. Natural history of Ctenus medius Keyserling, 1891 (Aranae, Ctenidae II: life cycle and aspects of reproductive behavior under laboratory conditions

    Directory of Open Access Journals (Sweden)

    E. FOLLY-RAMOS

    Full Text Available Ctenus medius Keyserling, 1891 is a wandering spider common in the Brazilian Atlantic Forest. It has been the subject of few studies. Thus, this work aims to elucidate aspects of its natural history, such as the life cycle and reproductive behavior of this species, through laboratory and field observations. Two females with egg sacs were observed in the laboratory and one was observed in field (Barra Mansa, 22º32'S and 44º10'W until the emergence of the spiderlings. For observation of the immature stage development, a portion of the spiderlings from the same hatch were taken to the laboratory and watched until sexual maturity. In the field, the period between the oviposition and the emergence of spiderlings was of 36 days. The female selects a site for egg sac deposition and stays there until the spiderlings emerge. Seven days after the emergence, the female abandoned the site where the egg sac was made, concomitant to the spiderlings dispersion from observation's place and until the moment that the spiderlings started to eat. For the spiderlings kept under laboratory conditions, cannibalism was not observed in the first instars (1-4th when sufficient food was offered. Sexual maturity happened in the 14th or 15th instars, with an average of 309.2 to 344.5 days until the last/sexual molt, respectively. Until the date of sexual maturity, there was a mortality rate of 85%. This species is very fragile in captivity. This hampered deductions concerning longevity. Both females and males collected in the field were induced to mate in the laboratory. Courtship movements of males were registered, but the females did not permit the mating. These data may assist in initial biological studies of Ctenus genus and offer comparative parameters for studies of other related species.

  6. Effects of medium renewal and handling stress on life history traits in Daphnia

    NARCIS (Netherlands)

    Rousseaux, S.; Vanoverbeke, J.; Aerts, J.; Declerck, S.A.J.

    2010-01-01

    The zooplankton genus Daphnia is used as a model organism in ecological, ecotoxicological and evolutionary research. It is often used in experimental laboratory setups to examine life history traits under a variety of factors inducing stress. One type of stress, handling stress because of

  7. Evolutionary trees and the rise of modern primatology: the forgotten contribution of St. George Mivart.

    Science.gov (United States)

    Bigoni, Francesca; Barsanti, Giulio

    2011-01-01

    The modern concept of the tree of life originated as a popular, iconic synthesis of the Darwinian evolutionary theory of descent by modification even if Darwin's own trees were hypothetical and abstract. It is generally thought that Ernst Haeckel in 1866 was the first to publish a true evolutionary tree which showed actual taxa. It is apparently forgotten that St. George Mivart beginning in 1865 made significant contributions to the development of evolutionary based trees of life which dealt with primate evolution, including human phylogeny. His trees were built on the most extensive sets of original data published up to that time, and were clearly articulated as working hypotheses. Mivart's trees were surprisingly modern for appearance and for content. Not only are most taxonomic names still in use today, but also many of the issues he raised are still under discussion in current scientific literature. The history of biology and especially that of primatology in the 19th century can benefit from a more thorough knowledge of how the image of the tree was used in scientific writings, especially after Darwin in the context of the theory of evolution by descent from common ancestors. A reappraisal of Mivart's scientific achievements is necessary to better establish the origins and the development not only of evolutionary trees but of modern primatology. The history of primatology, a discipline that is fundamental for investigating the place of humans in nature, would also benefit from a reappraisal of Mivart's role in Victorian biology.

  8. The Australian Education Union's Response to Kevin Donnelly's "The Australian Education Union: A History of Opposing School Choice and School Autonomy Down-Under"

    Science.gov (United States)

    Hopgood, Susan

    2015-01-01

    This article is a response to Kevin Donnelly's article, "The Australian Education Union: A History of Opposing School Choice and School Autonomy Down-Under," and aims to correct specific errors and misrepresentations as found by Susan Hopgood, Federal Secretary of the Australian Education Union. She argues that the article is misleading…

  9. Recurrence risk and prediction of a delivery under 34 weeks of gestation after a history of a severe hypertensive disorder

    NARCIS (Netherlands)

    Langenveld, J.; Buttinger, A.; van der Post, J.; Wolf, H.; Mol, B. W.; Ganzevoort, W.

    2011-01-01

    Please cite this paper as: Langenveld J, Buttinger A, van der Post J, Wolf H, Mol B, Ganzevoort W. Recurrence risk and prediction of a delivery under 34 weeks of gestation after a history of a severe hypertensive disorder. BJOG 2011;118:589-595. Objective  The aim of this study was to report

  10. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General ... Using some examples of classical games, we show how evolutionary game theory can help understand behavioural decisions of animals.

  12. Methodological problems in evolutionary biology. XII. Against evolutionary ethics.

    NARCIS (Netherlands)

    vd Steen, W.J.

    1999-01-01

    Evolutionary ethics has recently become popular again. Some of its representatives elaborate new attempts to derive ethics from evolutionary biology. The attempts, like previous ones, fail because they commit the naturalistic fallacy. Premises from evolutionary biology together with normative

  13. Towards a richer evolutionary game theory.

    Science.gov (United States)

    McNamara, John M

    2013-11-06

    Most examples of the application of evolutionary game theory to problems in biology involve highly simplified models. I contend that it is time to move on and include much more richness in models. In particular, more thought needs to be given to the importance of (i) between-individual variation; (ii) the interaction between individuals, and hence the process by which decisions are reached; (iii) the ecological and life-history context of the situation; (iv) the traits that are under selection, and (v) the underlying psychological mechanisms that lead to behaviour. I give examples where including variation between individuals fundamentally changes predicted outcomes of a game. Variation also selects for real-time responses, again resulting in changed outcomes. Variation can select for other traits, such as choosiness and social sensitivity. More generally, many problems involve coevolution of more than one trait. I identify situations where a reductionist approach, in which a game is isolated from is ecological setting, can be misleading. I also highlight the need to consider flexibility of behaviour, mental states and other issues concerned with the evolution of mechanism.

  14. Entrepreneurs and Evolutionary Biology: The Relationship between Testosterone and New Venture Creation

    Science.gov (United States)

    White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth

    2006-01-01

    Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…

  15. Endogenous ROS levels in C. elegans under exogenous stress support revision of oxidative stress theory of life-history tradeoffs.

    Science.gov (United States)

    Smith, Samson W; Latta, Leigh C; Denver, Dee R; Estes, Suzanne

    2014-07-24

    The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments--consistent with the oxidative stress theory of aging. Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory.

  16. Evolutionary dynamics from a variational principle

    Science.gov (United States)

    Klimek, Peter; Thurner, Stefan; Hanel, Rudolf

    2010-07-01

    We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of some evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. These novel entities change the conditions for already existing species. Even Darwin’s Demon, a hypothetical entity with exact knowledge of the abundance of all species and their fitness functions at a given time, could not prestate the impact of these novelties on established populations. We argue that fitness is always a posteriori knowledge—it measures but does not explain why a species has reproductive success or not. To overcome these conceptual limitations, a variational principle is proposed in a spin-model-like setup of evolutionary systems. We derive a functional which is minimized under the most general evolutionary formulation of a dynamical system, i.e., evolutionary trajectories causally emerge as a minimization of a functional. This functional allows the derivation of analytic solutions of the asymptotic diversity for stochastic evolutionary systems within a mean-field approximation. We test these approximations by numerical simulations of the corresponding model and find good agreement in the position of phase transitions in diversity curves. The model is further able to reproduce stylized facts of timeseries from several man-made and natural evolutionary systems. Light will be thrown on how species and their fitness landscapes dynamically coevolve.

  17. Evolutionary psychology. Controversies, questions, prospects, and limitations.

    Science.gov (United States)

    Confer, Jaime C; Easton, Judith A; Fleischman, Diana S; Goetz, Cari D; Lewis, David M G; Perilloux, Carin; Buss, David M

    2010-01-01

    Evolutionary psychology has emerged over the past 15 years as a major theoretical perspective, generating an increasing volume of empirical studies and assuming a larger presence within psychological science. At the same time, it has generated critiques and remains controversial among some psychologists. Some of the controversy stems from hypotheses that go against traditional psychological theories; some from empirical findings that may have disturbing implications; some from misunderstandings about the logic of evolutionary psychology; and some from reasonable scientific concerns about its underlying framework. This article identifies some of the most common concerns and attempts to elucidate evolutionary psychology's stance pertaining to them. These include issues of testability and falsifiability; the domain specificity versus domain generality of psychological mechanisms; the role of novel environments as they interact with evolved psychological circuits; the role of genes in the conceptual structure of evolutionary psychology; the roles of learning, socialization, and culture in evolutionary psychology; and the practical value of applied evolutionary psychology. The article concludes with a discussion of the limitations of current evolutionary psychology. 2009 APA, all rights reserved.

  18. Microstructural research on hot strips of low carbon steel produced by a compact strip production line under different thermal histories

    International Nuclear Information System (INIS)

    Yu Hao; Chen Qixiang; Kang Yonglin; Sun Yi

    2005-01-01

    Coupons with the same composition and thickness (4.0 mm nominal gauge) obtained from hot strips of low carbon steel underwent a series of investigations to analyze the microstructural characteristics and mechanisms responsible for their differences in mechanical properties. Two different industrial technologies were adopted, although the strips used in this research were produced on the same Compact Strip Production (CSP) line. One of the strips was produced with a routine γ→α CSP thermal history, but the other with a γ→α→γ* conventional thermal history. The only difference between them was that one technology had a α→γ* thermal history. Different specimens of both types of strips were prepared for metallographic observation, tensile tests, electron back-scattered diffraction tests and positron annihilation technique tests. Experimental results showed that the differences in mechanical properties could be ascribed to dissimilarities not only in the grain size and textural components but also in dislocation density

  19. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  20. The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System

    OpenAIRE

    Fuchs, Adrian C.D.; Alva, Vikram; Maldoner, Lorena; Albrecht, Reinhard; Hartmann, Marcus D.; Martin, Jörg

    2017-01-01

    Summary Proteasomes are self-compartmentalizing proteases that function at the core of the cellular protein degradation machinery in eukaryotes, archaea, and some bacteria. Although their evolutionary history is under debate, it is thought to be linked to that of the bacterial protease HslV and the hypothetical bacterial protease Anbu (ancestral beta subunit). Here, together with an extensive bioinformatic analysis, we present the first biophysical characterization of Anbu. Anbu forms a dodec...

  1. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

    Directory of Open Access Journals (Sweden)

    Bram Vrancken

    2014-04-01

    Full Text Available Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1 evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level