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Sample records for rapid evolutionary divergence

  1. Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

    Science.gov (United States)

    Funk, W Chris; Murphy, Melanie A

    2010-02-01

    Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

  2. An Exponential Regulator for Rapidity Divergences

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ye [Fermilab; Neill, Duff [MIT, Cambridge, CTP; Zhu, Hua Xing [MIT, Cambridge, CTP

    2016-04-01

    Finding an efficient and compelling regularization of soft and collinear degrees of freedom at the same invariant mass scale, but separated in rapidity is a persistent problem in high-energy factorization. In the course of a calculation, one encounters divergences unregulated by dimensional regularization, often called rapidity divergences. Once regulated, a general framework exists for their renormalization, the rapidity renormalization group (RRG), leading to fully resummed calculations of transverse momentum (to the jet axis) sensitive quantities. We examine how this regularization can be implemented via a multi-differential factorization of the soft-collinear phase-space, leading to an (in principle) alternative non-perturbative regularization of rapidity divergences. As an example, we examine the fully-differential factorization of a color singlet's momentum spectrum in a hadron-hadron collision at threshold. We show how this factorization acts as a mother theory to both traditional threshold and transverse momentum resummation, recovering the classical results for both resummations. Examining the refactorization of the transverse momentum beam functions in the threshold region, we show that one can directly calculate the rapidity renormalized function, while shedding light on the structure of joint resummation. Finally, we show how using modern bootstrap techniques, the transverse momentum spectrum is determined by an expansion about the threshold factorization, leading to a viable higher loop scheme for calculating the relevant anomalous dimensions for the transverse momentum spectrum.

  3. Speciation in rapidly diverging systems: lessons from Lake Malawi.

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    Danley, P D; Kocher, T D

    2001-05-01

    Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.

  4. Divergent evolutionary processes associated with colonization of offshore islands.

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    Martínková, Natália; Barnett, Ross; Cucchi, Thomas; Struchen, Rahel; Pascal, Marine; Pascal, Michel; Fischer, Martin C; Higham, Thomas; Brace, Selina; Ho, Simon Y W; Quéré, Jean-Pierre; O'Higgins, Paul; Excoffier, Laurent; Heckel, Gerald; Hoelzel, A Rus; Dobney, Keith M; Searle, Jeremy B

    2013-10-01

    Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic 'ark'. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land-use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island. © 2013 John Wiley & Sons Ltd.

  5. Software testing for evolutionary iterative rapid prototyping

    OpenAIRE

    Davis, Edward V., Jr.

    1990-01-01

    Approved for public release; distribution unlimited. Rapid prototyping is emerging as a promising software development paradigm. It provides a systematic and automatable means of developing a software system under circumstances where initial requirements are not well known or where requirements change frequently during development. To provide high software quality assurance requires sufficient software testing. The unique nature of evolutionary iterative prototyping is not well-suited for ...

  6. Ecological divergence and evolutionary transition of resprouting types in Banksia attenuata.

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    He, Tianhua

    2014-08-01

    Resprouting is a key functional trait that allows plants to survive diverse disturbances. The fitness benefits associated with resprouting include a rapid return to adult growth, early flowering, and setting seed. The resprouting responses observed following fire are varied, as are the ecological outcomes. Understanding the ecological divergence and evolutionary pathways of different resprouting types and how the environment and genetics interact to drive such morphological evolution represents an important, but under-studied, topic. In the present study, microsatellite markers and microevolutionary approaches were used to better understand: (1) whether genetic differentiation is related to morphological divergence among resprouting types and if so, whether there are any specific genetic variations associated with morphological divergence and (2) the evolutionary pathway of the transitions between two resprouting types in Banksia attenuata (epicormic resprouting from aerial stems or branch; resprouting from a underground lignotuber). The results revealed an association between population genetic differentiation and the morphological divergence of postfire resprouting types in B. attenuata. A microsatellite allele has been shown to be associated with epicormic populations. Approximate Bayesian Computation analysis revealed a likely evolutionary transition from epicormic to lignotuberous resprouting in B. attenuata. It is concluded that the postfire resprouting type in B. attenuata is likely determined by the fire's characteristics. The differentiated expression of postfire resprouting types in different environments is likely a consequence of local genetic adaptation. The capacity to shift the postfire resprouting type to adapt to diverse fire regimes is most likely the key factor explaining why B. attenuata is the most widespread member of the Banksia genus.

  7. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

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    Furman, Benjamin L S; Evans, Ben J

    2018-01-01

    Abstract There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions. PMID:29608717

  8. Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

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    Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

    2016-09-01

    Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  9. Structure of rapidity divergences in multi-parton scattering soft factors

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    Vladimirov, Alexey

    2018-04-01

    We discuss the structure of rapidity divergences that are presented in the soft factors of transverse momentum dependent (TMD) factorization theorems. To provide the discussion on the most general level we consider soft factors for multi-parton scattering. We show that the rapidity divergences are result of the gluon exchanges with the distant transverse plane, and are structurally equivalent to the ultraviolet divergences. It allows to formulate and to prove the renormalization theorem for rapidity divergences. The proof is made with the help the conformal transformation which maps rapidity divergences to ultraviolet divergences. The theorem is the systematic form of the factorization of rapidity divergences, which is required for the definition of TMD parton distributions. In particular, the definition of multi parton distributions is presented. The equivalence of ultraviolet and rapidity divergences leads to the exact relation between soft and rapidity anomalous dimensions. Using this relation we derive the rapidity anomalous dimension at the three-loop order.

  10. Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

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    Xiaoli Jin

    2017-06-01

    Full Text Available NAC (NAM/ATAF/CUC proteins constitute one of the biggest plant-specific transcription factor (TF families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1 uneven constitution of Clusters of Orthologous Groups (COGs and contrasting birth/death rates among subfamilies, and (2 two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.

  11. Conductive solar wind models in rapidly diverging flow geometries

    International Nuclear Information System (INIS)

    Holzer, T.E.; Leer, E.

    1980-01-01

    A detailed parameter study of conductive models of the solar wind has been carried out, extending the previous similar studies of Durney (1972) and Durney and Hundhausen (1974) by considering collisionless inhibition of thermal conduction, rapidly diverging flow geometries, and the structure of solutions for the entire n 0 -T 0 plane (n 0 and T 0 are the coronal base density and temperature). Primary emphasis is placed on understanding the complex effects of the physical processes operative in conductive solar wind models. There are five points of particular interest that have arisen from the study: (1) neither collisionless inhibition of thermal conduction nor rapidly diverging flow geometries can significantly increase the solar wind speed at 1 AU; (2) there exists a firm upper limit on the coronal base temperature consistent with observed values of the coronal base pressure and solar wind mass flux density; (3) the principal effect of rapidly diverging flow geometries is a decrease in the solar wind mass flux density at 1 AU and an increase in the mass flux density at the coronal base; (4) collisionless inhibition of thermal conduction can lead to a solar wind flow speed that either increases or decreases with increasing coronal base density (n 0 ) and temperature (T 0 , depending on the region of the n 0 -T 0 plane considered; (5) there is a region of the n 0 -T/sub o/ plane at high coronal base densities where low-speed, high-mass-flux, transonic solar wind flows exist: a region not previously considered

  12. Evolutionary divergence in sexual signals: Insights from within and among barn swallow populations

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    Wilkins, Matthew Reed

    A wealth of studies across diverse animal groups indicate the importance of sexual selection in shaping phenotypes within and across breeding populations. In recent decades, much research has focused on how divergent sexual selection pressures among populations may lead to speciation. For my first dissertation chapter, I performed a literature review on the causes and consequences of evolutionary divergence in acoustic signals and developed the acoustic window conceptual framework for understanding the contributions of selection, genetic drift, and evolutionary constraint to signal divergence. Further, I found that sexual selection explains acoustic differences between recently diverged populations of the best-studied taxa. However, the relative contributions of ecological selection, sexual selection, and drift to acoustic divergence have not typically been considered within the same study systems. The remainder of my dissertation used the Northern Hemisphere-distributed barn swallow ( Hirundo rustica) species complex as a model system to study sender-receiver dynamics, intra- and intersexual selection pressures, and visual and acoustic signal interactions at the local scale, and signal divergence across populations at the global scale. From song recordings taken across 19 sampling sites, spanning five of six described subspecies, I demonstrated considerable conservation in song structure. However, temporal traits were highly divergent across subspecies, and in particular, the speed of the terminal trill of songs. In a detailed study of the multimodal communication system of the barn swallow (including visual and acoustic traits), I demonstrated that males and females use different types of signals to mediate competition and mate choice. One of the only exceptions to this rule was trill rate, which was also implicated in song divergence across populations. In order to test the function of trill rate in communication, I performed a two-year playback study within the

  13. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco.

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    Pau Aleixandre

    Full Text Available The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis, and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands

  14. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

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    Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

    2013-01-01

    The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

  15. Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures.

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    Upadhyay, Mohita; Vivekanandan, Perumal

    2015-01-01

    results highlight the existence of divergent evolutionary pressures leading to CpG dinucleotide depletion among small ds-DNA viruses infecting vertebrate hosts.

  16. Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

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    Michael H. Kohn

    2008-01-01

    Full Text Available While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d5’ were found to increase as a function of synonymous (dS, and to a lesser extend, amino-acid (dA site divergence between duplicates. The rate d5’/dS was found to rapidly decay from values > 1 in young duplicate pairs (dS 0.8. Such rapid rates of 5 prime evolution exceeding 1 (~neutral predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization or division of labor among duplicate genes (subfunctionalization. In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

  17. Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species.

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    Bowsher, Alan W; Ali, Rifhat; Harding, Scott A; Tsai, Chung-Jui; Donovan, Lisa A

    2016-01-01

    Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.

  18. Evolutionary origin and divergence of GnIH and its homologous peptides.

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    Tsutsui, Kazuyoshi; Osugi, Tomohiro

    2009-03-01

    Probing undiscovered hypothalamic neuropeptides that play important roles in the regulation of pituitary function in vertebrates is essential for the progress of neuroendocrinology. In 2000, we discovered a novel hypothalamic dodecapeptide inhibiting gonadotropin release in quail and termed it gonadotropin-inhibitory hormone (GnIH). GnIH acts on the pituitary and gonadotropin-releasing hormone (GnRH) neurons in the hypothalamus via a novel G protein-coupled receptor for GnIH to inhibit gonadal development and maintenance by decreasing gonadotropin release and synthesis. Similar findings were observed in other avian species. Thus, GnIH is a key factor controlling avian reproduction. To give our findings a broader perspective, we also found GnIH homologous peptides in the hypothalamus of other vertebrates, such as mammals, reptiles, amphibians and teleosts. GnIH and its homologs share a common C-terminal LPXRFamide (X=L or Q) motif. A mammalian GnIH homolog also inhibited gonadotropin release in mammals like the GnIH action in birds. In contrast to higher vertebrates, hypophysiotropic activities of GnIH homologs were different in lower vertebrates. To clarify the evolutionary origin of GnIH and its homologs, we further sought to identify novel LPXRFamide peptides from the brain of sea lamprey and hagfish, two extant groups of the oldest lineage of vertebrates, Agnatha. In these agnathans, LPXRFamide peptide and its cDNA were identified only from the brain of hagfish. Based on these findings over the past decade, this paper summarizes the evolutionary origin and divergence of GnIH and its homologous peptides.

  19. Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives.

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    Iriondo, J M; Milla, R; Volis, S; Rubio de Casas, R

    2018-01-01

    Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  20. Rapid divergence of mussel populations despite incomplete barriers to dispersal.

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    Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

    2018-04-01

    Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

  1. Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.

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    Bauernfeind, Amy L; Soderblom, Erik J; Turner, Meredith E; Moseley, M Arthur; Ely, John J; Hof, Patrick R; Sherwood, Chet C; Wray, Gregory A; Babbitt, Courtney C

    2015-07-10

    Although transcriptomic profiling has become the standard approach for exploring molecular differences in the primate brain, very little is known about how the expression levels of gene transcripts relate to downstream protein abundance. Moreover, it is unknown whether the relationship changes depending on the brain region or species under investigation. We performed high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses on two regions of the human and chimpanzee brain: The anterior cingulate cortex and caudate nucleus. In both brain regions, we found a lower correlation between mRNA and protein expression levels in humans and chimpanzees than has been reported for other tissues and cell types, suggesting that the brain may engage extensive tissue-specific regulation affecting protein abundance. In both species, only a few categories of biological function exhibited strong correlations between mRNA and protein expression levels. These categories included oxidative metabolism and protein synthesis and modification, indicating that the expression levels of mRNA transcripts supporting these biological functions are more predictive of protein expression compared with other functional categories. More generally, however, the two measures of molecular expression provided strikingly divergent perspectives into differential expression between human and chimpanzee brains: mRNA comparisons revealed significant differences in neuronal communication, ion transport, and regulatory processes, whereas protein comparisons indicated differences in perception and cognition, metabolic processes, and organization of the cytoskeleton. Our results highlight the importance of examining protein expression in evolutionary analyses and call for a more thorough understanding of tissue-specific protein expression levels. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular

  2. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

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    Hellberg, M E; Moy, G W; Vacquier, V D

    2000-03-01

    Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

  3. 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

    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...

  4. Along the speciation continuum: Quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers.

    Science.gov (United States)

    Christie, Kyle; Strauss, Sharon Y

    2018-05-01

    Understanding the relative roles of intrinsic and extrinsic reproductive barriers, and their interplay within the geographic context of diverging taxa, remains an outstanding challenge in the study of speciation. We conducted a comparative analysis of reproductive isolation in California Jewelflowers (Streptanthus, s.l., Brassicaceae) by quantifying potential barriers to gene flow at multiple life history stages in 39 species pairs spanning five million years of evolutionary divergence. We quantified nine potential pre- and postzygotic barriers and explored patterns of reproductive isolation in relation to genetic distance. Intrinsic postzygotic isolation was initially weak, increased at intermediate genetic distances, and reached a threshold characterized by complete genetic incompatibility. Climatic niche differences were strong at shallow genetic distances, and species pairs with overlapping ranges showed slight but appreciable phenological isolation, highlighting the potential for ecological barriers to contribute to speciation. Geographic analyses suggest that speciation is not regionally allopatric in the California Jewelflowers, as recently diverged taxa occur in relatively close proximity and display substantial range overlap. Young pairs are characterized by incomplete intrinsic postzygotic isolation, suggesting that extrinsic barriers or fine-scale spatial segregation are more important early in the divergence process than genetic incompatibilities. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

  5. Divergent plate motion drives rapid exhumation of (ultra)high pressure rocks

    Science.gov (United States)

    Liao, Jie; Malusà, Marco G.; Zhao, Liang; Baldwin, Suzanne L.; Fitzgerald, Paul G.; Gerya, Taras

    2018-06-01

    Exhumation of (ultra)high pressure [(U)HP] rocks by upper-plate divergent motion above an unbroken slab, first proposed in the Western Alps, has never been tested by numerical methods. We present 2D thermo-mechanical models incorporating subduction of a thinned continental margin beneath either a continental or oceanic upper plate, followed by upper-plate divergent motion away from the lower plate. Results demonstrate how divergent plate motion may trigger rapid exhumation of large volumes of (U)HP rocks directly to the Earth's surface, without the need for significant overburden removal by erosion. Model exhumation paths are fully consistent with natural examples for a wide range of upper-plate divergence rates. Exhumation rates are systematically higher than the divergent rate imposed to the upper plate, and the modeled size of exhumed (U)HP domes is invariant for different rates of upper-plate divergence. Major variations are instead predicted at depth for differing model scenarios, as larger amounts of divergent motion may allow mantle-wedge exhumation to shallow depth under the exhuming domes. The transient temperature increase, due to ascent of mantle-wedge material in the subduction channel, has a limited effect on exhumed continental (U)HP rocks already at the surface. We test two examples, the Cenozoic (U)HP terranes of the Western Alps (continental upper plate) and eastern Papua New Guinea (oceanic upper plate). The good fit between model predictions and the geologic record in these terranes encourages the application of these models globally to pre-Cenozoic (U)HP terranes where the geologic record of exhumation is only partly preserved.

  6. Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

    Science.gov (United States)

    García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto

    2010-05-01

    Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony

  7. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

    Science.gov (United States)

    Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

    2005-05-22

    The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

  8. The UDP glucuronosyltransferase gene superfamily: suggested nomenclature based on evolutionary divergence

    NARCIS (Netherlands)

    Burchell, B.; Nebert, D. W.; Nelson, D. R.; Bock, K. W.; Iyanagi, T.; Jansen, P. L.; Lancet, D.; Mulder, G. J.; Chowdhury, J. R.; Siest, G.

    1991-01-01

    A nomenclature system for the UDP glucuronosyltransferase superfamily is proposed, based on divergent evolution of the genes. A total of 26 distinct cDNAs in five mammalian species have been sequenced to date. Comparison of the deduced amino acid sequences leads to the definition of two families and

  9. Rapid male-specific regulatory divergence and down regulation of spermatogenesis genes in Drosophila species hybrids.

    Directory of Open Access Journals (Sweden)

    Jennifer Ferguson

    Full Text Available In most crosses between closely related species of Drosophila, the male hybrids are sterile and show postmeiotic abnormalities. A series of gene expression studies using genomic approaches have found significant down regulation of postmeiotic spermatogenesis genes in sterile male hybrids. These results have led some to suggest a direct relationship between down regulation in gene expression and hybrid sterility. An alternative explanation to a cause-and-effect relationship between misregulation of gene expression and male sterility is rapid divergence of male sex regulatory elements leading to incompatible interactions in an interspecies hybrid genome. To test the effect of regulatory divergence in spermatogenesis gene expression, we isolated 35 fertile D. simulans strains with D. mauritiana introgressions in either the X, second or third chromosome. We analyzed gene expression in these fertile hybrid strains for a subset of spermatogenesis genes previously reported as significantly under expressed in sterile hybrids relative to D. simulans. We found that fertile autosomal introgressions can cause levels of gene down regulation similar to that of sterile hybrids. We also found that X chromosome heterospecific introgressions cause significantly less gene down regulation than autosomal introgressions. Our results provide evidence that rapid male sex gene regulatory divergence can explain misexpression of spermatogenesis genes in hybrids.

  10. Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications.

    Science.gov (United States)

    Bernardo, Pauline; Golden, Michael; Akram, Mohammad; Naimuddin; Nadarajan, Nagaswamy; Fernandez, Emmanuel; Granier, Martine; Rebelo, Anthony G; Peterschmitt, Michel; Martin, Darren P; Roumagnac, Philippe

    2013-10-01

    During a large scale "non a priori" survey in 2010 of South African plant-infecting single stranded DNA viruses, a highly divergent geminivirus genome was isolated from a wild spurge, Euphorbia caput-medusae. In addition to being infectious in E. caput-medusae, the cloned viral genome was also infectious in tomato and Nicotiana benthamiana. The virus, named Euphorbia caput-medusae latent virus (EcmLV) due to the absence of infection symptoms displayed by its natural host, caused severe symptoms in both tomato and N. benthamiana. The genome organisation of EcmLV is unique amongst geminiviruses and it likely expresses at least two proteins without any detectable homologues within public sequence databases. Although clearly a geminivirus, EcmLV is so divergent that we propose its placement within a new genus that we have tentatively named Capulavirus. Using a set of highly divergent geminiviruses genomes, it is apparent that recombination has likely been a primary process in the genus-level diversification of geminiviruses. It is also demonstrated how this insight, taken together with phylogenetic analyses of predicted coat protein and replication associated protein (Rep) amino acid sequences indicate that the most recent common ancestor of the geminiviruses was likely a dicot-infecting virus that, like modern day mastreviruses and becurtoviruses, expressed its Rep from a spliced complementary strand transcript. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  11. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    KAUST Repository

    Kuo, Dwight; Tan, Kai; Zinman, Guy; Ravasi, Timothy; Bar-Joseph, Ziv; Ideker, Trey

    2010-01-01

    Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

  12. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    KAUST Repository

    Kuo, Dwight

    2010-07-23

    Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

  13. The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates.

    Science.gov (United States)

    Sohn, Jae-Cheon; Labandeira, Conrad C; Davis, Donald R

    2015-02-04

    It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts. We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages. Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates.

  14. Pre- versus post-mass extinction divergence of Mesozoic marine reptiles dictated by time-scale dependence of evolutionary rates.

    Science.gov (United States)

    Motani, Ryosuke; Jiang, Da-Yong; Tintori, Andrea; Ji, Cheng; Huang, Jian-Dong

    2017-05-17

    The fossil record of a major clade often starts after a mass extinction even though evolutionary rates, molecular or morphological, suggest its pre-extinction emergence (e.g. squamates, placentals and teleosts). The discrepancy is larger for older clades, and the presence of a time-scale-dependent methodological bias has been suggested, yet it has been difficult to avoid the bias using Bayesian phylogenetic methods. This paradox raises the question of whether ecological vacancies, such as those after mass extinctions, prompt the radiations. We addressed this problem by using a unique temporal characteristic of the morphological data and a high-resolution stratigraphic record, for the oldest clade of Mesozoic marine reptiles, Ichthyosauromorpha. The evolutionary rate was fastest during the first few million years of ichthyosauromorph evolution and became progressively slower over time, eventually becoming six times slower. Using the later slower rates, estimates of divergence time become excessively older. The fast, initial rate suggests the emergence of ichthyosauromorphs after the end-Permian mass extinction, matching an independent result from high-resolution stratigraphic confidence intervals. These reptiles probably invaded the sea as a new ecosystem was formed after the end-Permian mass extinction. Lack of information on early evolution biased Bayesian clock rates. © 2017 The Author(s).

  15. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data

    Science.gov (United States)

    Xu, Kuipeng; Tang, Xianghai; Wang, Lu; Yu, Xinzi; Sun, Peipei; Mao, Yunxiang

    2017-08-01

    Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology ((( Bangia, Porphyra ) Pyropia ) Wildemania ). Molecular dating indicates that Bangiales diversified approximately 246.40 million years ago (95% highest posterior density (HPD)= 194.78u2013318.24 Ma, posterior probability (PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland (currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversification in Bangiales relative to Florideophyceae. Compared with Viridiplantae (green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome (ptDNA) and 15-fold for mitochondrial genome (mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.

  16. Pleiades rapid rotators - evidence for an evolutionary sequence

    International Nuclear Information System (INIS)

    Butler, R.P.; Marcy, G.W.; Cohen, R.D.; Duncan, D.K.; California Univ., La Jolla; Space Telescope Science Institute, Baltimore, MD)

    1987-01-01

    Four rapidly rotating early-K dwarfs in the Pleiades are shown to contain an order of magnitude more Li than four slow rotators of the same spectral type, as would be expected if they were systematically younger. This supports the idea that late-type stars first arrive on the main sequence with V(rot) greater than about 100 km/s, that they spin down to V(rot) less than about 10 km/s in 10 to the 7th to 10 to the 8th yr, and that the Pleiades lower main sequence shows such an age spread. 14 references

  17. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.

    Directory of Open Access Journals (Sweden)

    Katarzyna Bozek

    2014-05-01

    Full Text Available Metabolite concentrations reflect the physiological states of tissues and cells. However, the role of metabolic changes in species evolution is currently unknown. Here, we present a study of metabolome evolution conducted in three brain regions and two non-neural tissues from humans, chimpanzees, macaque monkeys, and mice based on over 10,000 hydrophilic compounds. While chimpanzee, macaque, and mouse metabolomes diverge following the genetic distances among species, we detect remarkable acceleration of metabolome evolution in human prefrontal cortex and skeletal muscle affecting neural and energy metabolism pathways. These metabolic changes could not be attributed to environmental conditions and were confirmed against the expression of their corresponding enzymes. We further conducted muscle strength tests in humans, chimpanzees, and macaques. The results suggest that, while humans are characterized by superior cognition, their muscular performance might be markedly inferior to that of chimpanzees and macaque monkeys.

  18. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

    Science.gov (United States)

    FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

    2016-01-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

  19. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

    Science.gov (United States)

    Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

    2016-05-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

  20. Evolutionary history of a dispersal-associated locus across sympatric and allopatric divergent populations of a wing-polymorphic beetle across Atlantic Europe

    NARCIS (Netherlands)

    van Belleghem, S.M.; Roelofs, D.; Hendrickx, F.

    2015-01-01

    Studying the evolutionary history of trait divergence, in particular those related to dispersal capacity, is of major interest for the process of local adaptation and metapopulation dynamics. Here, we reconstruct the evolution of different alleles at the nuclear-encoded mitochondrial NADP

  1. Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M. M.

    2017-01-01

    Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions....... Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether...... factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending...

  2. Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

    Science.gov (United States)

    Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

    2012-03-01

    Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

  3. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

    Directory of Open Access Journals (Sweden)

    Sebastian Pita

    2013-05-01

    Full Text Available In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae. The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome or both sex chromosomes (X and Y chromosomes. This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences.

  4. Micro-evolutionary divergence patterns of mandible shapes in wild house mouse (Mus musculus populations

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2011-10-01

    Full Text Available Abstract Background Insights into the micro-evolutionary patterns of morphological traits require an assessment of the natural variation of the trait within and between populations and closely related species. The mouse mandible is a particularly suitable morphological trait for such an analysis, since it has long been used as a model to study the quantitative genetics of shape. In addition, many distinct populations, sub-species and closely related species are known for the house mouse. However, morphological comparisons among wild caught animals require an assessment in how far environmental and technical factors could interfere with the shape change measurements. Results Using geometric morphometrics, we have surveyed mandible shapes in 15 natural populations of the genus Mus, with a focus on the subspecies Mus musculus domesticus. In parallel we have carefully assessed possibly confounding technical and biological factors. We find that there are distinct differences on average between populations, subspecies and species, but these differences are smaller than differences between individuals within populations. Populations from summer-dry regions, although more ancestral, are less distinct from each other than are populations from the more recently colonized northern areas. Populations with especially distinct shapes occur in an area of sympatry of M. m. domesticus and M. spretus and on recently colonized sub-antarctic islands. We have also studied a number of inbred strains to assess in how far their mandible shapes resemble those from the wild. We find that they fall indeed into the shape space of natural variation between individuals in populations. Conclusions Although mandible shapes in natural populations can be influenced by environmental variables, these influences are insufficient to explain the average extent of shape differences between populations, such that evolutionary processes must be invoked to explain this level of diversity

  5. Phylogenetic comparison of F-Box (FBX gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift.

    Directory of Open Access Journals (Sweden)

    Zhihua Hua

    Full Text Available The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of F-Box (FBX genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811 FBX loci from 18 plant species, ranging from the alga Chlamydomonas reinhardtii to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of FBX loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for Carica papaya to as many as 1350 predicted for Arabidopsis lyrata. This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of FBX genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous FBX loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of FBX genes in each species. Taken together, it appears that the FBX superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid

  6. Three human alcohol dehydrogenase subunits: cDNA structure and molecular and evolutionary divergence

    International Nuclear Information System (INIS)

    Ikuta, T.; Szeto, S.; Yoshida, A.

    1986-01-01

    Class I human alcohol dehydrogenase (ADH; alcohol:NAD + oxidoreductase, EC 1.1.1.1) consists of several homo- and heterodimers of α, β, and γ subunits that are governed by the ADH1, ADH2, and ADH3 loci. The authors previously cloned a full length of cDNA for the β subunit, and the complete sequence of 374 amino acid residues was established. cDNAs for the α and γ subunits were cloned and characterized. A human liver cDNA library, constructed in phage λgt11, was screened by using a synthetic oligonucleotide probe that was matched to the γ but not to the β sequence. Clone pUCADHγ21 and clone pUCADHα15L differed from β cDNA with respect to restriction sites and hybridization with the nucleotide probe. Clone pUCADHγ21 contained an insertion of 1.5 kilobase pairs (kbp) and encodes 374 amino acid residues compatible with the reported amino acid sequence of the γ subunit. Clone pUCADHα15L contained an insertion of 2.4 kbp and included nucleotide sequences that encode 374 amino acid residues for another subunit, the γ subunit. In addition, this clone contained the sequences that encode the COOH-terminal part of the β subunit at its extended 5' region. The amino acid sequences and coding regions of the cDNAs of the three subunits are very similar. A high degree of resemblance is observed also in their 3' noncoding regions. However, distinctive differences exist in the vicinity of the Zn-binding cysteine residue at position 46. Based on the cDNA sequences and the deduced amino acid sequences of the three subunits, their structural and evolutionary relationships are discussed

  7. Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

    Science.gov (United States)

    Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

    2000-01-01

    This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

  8. Morphological and genetic divergence between Agave inaequidens, A. cupreata and the domesticated A. hookeri. Analysis of their evolutionary relationships.

    Directory of Open Access Journals (Sweden)

    Carmen J Figueredo-Urbina

    Full Text Available Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733, than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510 and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567, a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other

  9. Morphological and genetic divergence between Agave inaequidens, A. cupreata and the domesticated A. hookeri. Analysis of their evolutionary relationships.

    Science.gov (United States)

    Figueredo-Urbina, Carmen J; Casas, Alejandro; Torres-García, Ignacio

    2017-01-01

    Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI) in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733), than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510) and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567), a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other member of the

  10. Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins

    Directory of Open Access Journals (Sweden)

    Rachel T. Wragg

    2017-05-01

    Full Text Available Complexin is a critical presynaptic protein that regulates both spontaneous and calcium-triggered neurotransmitter release in all synapses. Although the SNARE-binding central helix of complexin is highly conserved and required for all known complexin functions, the remainder of the protein has profoundly diverged across the animal kingdom. Striking disparities in complexin inhibitory activity are observed between vertebrate and invertebrate complexins but little is known about the source of these differences or their relevance to the underlying mechanism of complexin regulation. We found that mouse complexin 1 (mCpx1 failed to inhibit neurotransmitter secretion in Caenorhabditis elegans neuromuscular junctions lacking the worm complexin 1 (CPX-1. This lack of inhibition stemmed from differences in the C-terminal domain (CTD of mCpx1. Previous studies revealed that the CTD selectively binds to highly curved membranes and directs complexin to synaptic vesicles. Although mouse and worm complexin have similar lipid binding affinity, their last few amino acids differ in both hydrophobicity and in lipid binding conformation, and these differences strongly impacted CPX-1 inhibitory function. Moreover, function was not maintained if a critical amphipathic helix in the worm CPX-1 CTD was replaced with the corresponding mCpx1 amphipathic helix. Invertebrate complexins generally shared more C-terminal similarity with vertebrate complexin 3 and 4 isoforms, and the amphipathic region of mouse complexin 3 significantly restored inhibitory function to worm CPX-1. We hypothesize that the CTD of complexin is essential in conferring an inhibitory function to complexin, and that this inhibitory activity has been attenuated in the vertebrate complexin 1 and 2 isoforms. Thus, evolutionary changes in the complexin CTD differentially shape its synaptic role across phylogeny.

  11. 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.

  12. Evolutionary history of a dispersal-associated locus across sympatric and allopatric divergent populations of a wing-polymorphic beetle across Atlantic Europe.

    Science.gov (United States)

    Van Belleghem, Steven M; Roelofs, Dick; Hendrickx, Frederik

    2015-02-01

    Studying the evolutionary history of trait divergence, in particular those related to dispersal capacity, is of major interest for the process of local adaptation and metapopulation dynamics. Here, we reconstruct the evolution of different alleles at the nuclear-encoded mitochondrial NADP(+)-dependent isocitrate dehydrogenase (mtIdh) locus of the ground beetle Pogonus chalceus that are differentially and repeatedly selected in short- and long-winged populations in response to different hydrological regimes at both allopatric and sympatric scales along the Atlantic European coasts. We sequenced 2788 bp of the mtIdh locus spanning a ~7-kb genome region and compared its variation with that of two supposedly neutral genes. mtIdh sequences show (i) monophyletic clustering of the short-winged associated mtIDH-DE haplotypes within the long-winged associated mtIDH-AB haplotypes, (ii) a more than tenfold lower haplotype diversity associated with the mtIDH-DE alleles compared to the mtIDH-AB alleles and (iii) a high number of fixed nucleotide differences between both mtIDH haplotype clusters. Coalescent simulations suggest that this observed sequence variation in the mtIdh locus is most consistent with a singular origin in a partially isolated subpopulation, followed by a relatively recent spread of the mtIDH-DE allele in short-winged populations along the Atlantic coast. These results demonstrate that even traits associated with decreased dispersal capacity can rapidly spread and that reuse of adaptive alleles plays an important role in the adaptive potential within this sympatric mosaic of P. chalceus populations. © 2014 John Wiley & Sons Ltd.

  13. Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species

    Directory of Open Access Journals (Sweden)

    Hornett Emily A

    2012-08-01

    Full Text Available Abstract Background How well does RNA-Seq data perform for quantitative whole gene expression analysis in the absence of a genome? This is one unanswered question facing the rapidly growing number of researchers studying non-model species. Using Homo sapiens data and resources, we compared the direct mapping of sequencing reads to predicted genes from the genome with mapping to de novo transcriptomes assembled from RNA-Seq data. Gene coverage and expression analysis was further investigated in the non-model context by using increasingly divergent genomic reference species to group assembled contigs by unique genes. Results Eight transcriptome sets, composed of varying amounts of Illumina and 454 data, were assembled and assessed. Hybrid 454/Illumina assemblies had the highest transcriptome and individual gene coverage. Quantitative whole gene expression levels were highly similar between using a de novo hybrid assembly and the predicted genes as a scaffold, although mapping to the de novo transcriptome assembly provided data on fewer genes. Using non-target species as reference scaffolds does result in some loss of sequence and expression data, and bias and error increase with evolutionary distance. However, within a 100 million year window these effect sizes are relatively small. Conclusions Predicted gene sets from sequenced genomes of related species can provide a powerful method for grouping RNA-Seq reads and annotating contigs. Gene expression results can be produced that are similar to results obtained using gene models derived from a high quality genome, though biased towards conserved genes. Our results demonstrate the power and limitations of conducting RNA-Seq in non-model species.

  14. Evolutionary divergence of plant borate exporters and critical amino acid residues for the polar localization and boron-dependent vacuolar sorting of AtBOR1

    KAUST Repository

    Wakuta, Shinji

    2015-01-24

    Boron (B) is an essential micronutrient for plants but is toxic when accumulated in excess. The plant BOR family encodes plasma membrane-localized borate exporters (BORs) that control translocation and homeostasis of B under a wide range of conditions. In this study, we examined the evolutionary divergence of BORs among terrestrial plants and showed that the lycophyte Selaginella moellendorffii and angiosperms have evolved two types of BOR (clades I and II). Clade I includes AtBOR1 and homologs previously shown to be involved in efficient transport of B under conditions of limited B availability. AtBOR1 shows polar localization in the plasma membrane and high-B-induced vacuolar sorting, important features for efficient B transport under low-B conditions, and rapid down-regulation to avoid B toxicity. Clade II includes AtBOR4 and barley Bot1 involved in B exclusion for high-B tolerance. We showed, using yeast complementation and B transport assays, that three genes in S. moellendorffii, SmBOR1 in clade I and SmBOR3 and SmBOR4 in clade II, encode functional BORs. Furthermore, amino acid sequence alignments identified an acidic di-leucine motif unique in clade I BORs. Mutational analysis of AtBOR1 revealed that the acidic di-leucine motif is required for the polarity and high-B-induced vacuolar sorting of AtBOR1. Our data clearly indicated that the common ancestor of vascular plants had already acquired two types of BOR for low- and high-B tolerance, and that the BOR family evolved to establish B tolerance in each lineage by adapting to their environments. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

  15. Biotic response to late Quaternary rapid climate switches in Santa Barbara Basin: Ecological and evolutionary implications

    International Nuclear Information System (INIS)

    Cannariato, K.G.; Kennett, J.P.; Behl, R.J.

    1999-01-01

    Benthic foraminiferal assemblages from Santa Barbara Basin exhibit major faunal and ecological switches associated with late Quaternary millennial- to decadal-scale global climate oscillations. Repeated turnovers of entire faunas occurred rapidly (<40--400 yr) without extinction or speciation in conjunction with Dansgaard-Oeschger shifts in thermohaline circulation, ventilation, and climate, confirming evolutionary model predictions of Roy et al. Consistent faunal successions of dysoxic taxa during successive interstadials reflect the extreme sensitivity and adaptation of the benthic ecosystem to the rapid environmental changes that marked the late Quaternary and possibly other transitional intervals in the history of the Earth's ocean-atmosphere-cryosphere system. These data support the hypothesis that broad segments of the biosphere are well adapted to rapid climate change

  16. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

    Directory of Open Access Journals (Sweden)

    Stiassny Melanie LJ

    2010-05-01

    Full Text Available Abstract Background It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood. Results We examined genetic and morphological divergence among populations of two narrowly endemic cichlid species, Teleogramma depressum and Lamprologus tigripictilis, from a 100 km stretch of the lower Congo River using both nDNA microsatellites and mtDNA markers along with coordinate-based morphological techniques. In L. tigripictilis, the strongest genetic break was concordant with measurable phenotypic divergence but no morphological disjunction was detected for T. depressum despite significant differentiation at mtDNA and nDNA microsatellite markers. Conclusions The genetic markers revealed patterns of philopatry and estimates of genetic isolation that are among the highest reported for any African cichlid species over a comparable geographic scale. We hypothesize that the high levels of philopatry observed are generated and maintained by the extreme hydrology of the lower Congo River.

  17. Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean.

    Science.gov (United States)

    Deli, Temim; Kalkan, Evrim; Karhan, Selahattin Ünsal; Uzunova, Sonya; Keikhosravi, Alireza; Bilgin, Raşit; Schubart, Christoph D

    2018-04-11

    Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187). Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes

  18. Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories.

    Science.gov (United States)

    Avigdor, Bracha Erlanger; Cimino-Mathews, Ashley; DeMarzo, Angelo M; Hicks, Jessica L; Shin, James; Sukumar, Saraswati; Fetting, John; Argani, Pedram; Park, Ben H; Wheelan, Sarah J

    2017-12-21

    Heterogeneity within and among tumors in a metastatic cancer patient is a well-established phenomenon that may confound treatment and accurate prognosis. Here, we used whole-exome sequencing to survey metastatic breast cancer tumors from 5 patients in a rapid autopsy program to construct the origin and genetic development of metastases. Metastases were obtained from 5 breast cancer patients using a rapid autopsy protocol and subjected to whole-exome sequencing. Metastases were evaluated for sharing of somatic mutations, correlation of copy number variation and loss of heterozygosity, and genetic similarity scores. Pathological features of the patients' disease were assessed by immunohistochemical analyses. Our data support a monoclonal origin of metastasis in 3 cases, but in 2 cases, metastases arose from at least 2 distinct subclones in the primary tumor. In the latter 2 cases, the primary tumor presented with mixed histologic and pathologic features, suggesting early divergent evolution within the primary tumor with maintenance of metastatic capability in multiple lineages. We used genetic and histopathological evidence to demonstrate that metastases can be derived from a single or multiple independent clones within a primary tumor. This underscores the complexity of breast cancer clonal evolution and has implications for how best to determine and implement therapies for early- and late-stage disease.

  19. Divergent Cumulative Cultural Evolution

    OpenAIRE

    Marriott, Chris; Chebib, Jobran

    2016-01-01

    Divergent cumulative cultural evolution occurs when the cultural evolutionary trajectory diverges from the biological evolutionary trajectory. We consider the conditions under which divergent cumulative cultural evolution can occur. We hypothesize that two conditions are necessary. First that genetic and cultural information are stored separately in the agent. Second cultural information must be transferred horizontally between agents of different generations. We implement a model with these ...

  20. Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.

    Science.gov (United States)

    Yu, Jingyin; Tehrim, Sadia; Wang, Linhai; Dossa, Komivi; Zhang, Xiurong; Ke, Tao; Liao, Boshou

    2017-09-18

    The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana-B. rapa and A. thaliana-B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450

  1. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae

    OpenAIRE

    Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

    2005-01-01

    The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to t...

  2. More rapid climate change promotes evolutionary rescue through selection for increased dispersal distance.

    Science.gov (United States)

    Boeye, Jeroen; Travis, Justin M J; Stoks, Robby; Bonte, Dries

    2013-02-01

    Species can either adapt to new conditions induced by climate change or shift their range in an attempt to track optimal environmental conditions. During current range shifts, species are simultaneously confronted with a second major anthropogenic disturbance, landscape fragmentation. Using individual-based models with a shifting climate window, we examine the effect of different rates of climate change on the evolution of dispersal distances through changes in the genetically determined dispersal kernel. Our results demonstrate that the rate of climate change is positively correlated to the evolved dispersal distances although too fast climate change causes the population to crash. When faced with realistic rates of climate change, greater dispersal distances evolve than those required for the population to keep track of the climate, thereby maximizing population size. Importantly, the greater dispersal distances that evolve when climate change is more rapid, induce evolutionary rescue by facilitating the population in crossing large gaps in the landscape. This could ensure population persistence in case of range shifting in fragmented landscapes. Furthermore, we highlight problems in using invasion speed as a proxy for potential range shifting abilities under climate change.

  3. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Directory of Open Access Journals (Sweden)

    Kathleen Semple Delaney

    2010-09-01

    Full Text Available Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  4. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

    Science.gov (United States)

    Davies, Kalina T J; Tsagkogeorga, Georgia; Rossiter, Stephen J

    2014-12-19

    The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise

  5. Evolutionary divergence of the plant elicitor peptides (Peps) and their receptors: interfamily incompatibility of perception but compatibility of downstream signalling

    KAUST Repository

    Lori, M.

    2015-05-22

    Plant elicitor peptides (Peps) are potent inducers of pattern-triggered immunity and amplify the immune response against diverse pathogens. Peps have been discovered and studied extensively in Arabidopsis and only recently orthologs in maize were also identified and characterized in more detail. Here, the presence of PROPEPs, the Pep precursors, and PEPRs, the Pep receptors, was investigated within the plant kingdom. PROPEPs and PEPRs were identified in most sequenced species of the angiosperms. The conservation and compatibility of the Pep-PEPR-system was analysed by using plants of two distantly related dicot families, Brassicaceae and Solanaceae, and a representative family of monocot plants, the Poaceae. All three plant families contain important crop plants, including maize, rice, tomato, potato, and canola. Peps were not recognized by species outside of their plant family of origin, apparently because of a divergence of the Pep sequences. Three family-specific Pep motifs were defined and the integration of such a motif into the Pep sequence of an unrelated Pep enabled its perception. Transient transformation of Nicotiana benthamiana with the coding sequences of the AtPEPR1 and ZmPEPR1a led to the recognition of Pep peptides of Brassicaceae or Poaceae origin, respectively, and to the proper activation of downstream signalling. It was concluded that signalling machinery downstream of the PEPRs is highly conserved whereas the leucine-rich repeat domains of the PEPRs co-evolved with the Peps, leading to distinct motifs and, with it, interfamily incompatibility.

  6. Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts

    Science.gov (United States)

    Vea, Isabelle M.; Grimaldi, David A.

    2016-01-01

    The radiation of flowering plants in the mid-Cretaceous transformed landscapes and is widely believed to have fuelled the radiations of major groups of phytophagous insects. An excellent group to test this assertion is the scale insects (Coccomorpha: Hemiptera), with some 8,000 described Recent species and probably the most diverse fossil record of any phytophagous insect group preserved in amber. We used here a total-evidence approach (by tip-dating) employing 174 morphological characters of 73 Recent and 43 fossil taxa (48 families) and DNA sequences of three gene regions, to obtain divergence time estimates and compare the chronology of the most diverse lineage of scale insects, the neococcoid families, with the timing of the main angiosperm radiation. An estimated origin of the Coccomorpha occurred at the beginning of the Triassic, about 245 Ma [228–273], and of the neococcoids 60 million years later [210–165 Ma]. A total-evidence approach allows the integration of extinct scale insects into a phylogenetic framework, resulting in slightly younger median estimates than analyses using Recent taxa, calibrated with fossil ages only. From these estimates, we hypothesise that most major lineages of coccoids shifted from gymnosperms onto angiosperms when the latter became diverse and abundant in the mid- to Late Cretaceous. PMID:27000526

  7. Evolutionary History of a Desert Shrub Ephedra przewalskii (Ephedraceae): Allopatric Divergence and Range Shifts in Northwestern China.

    Science.gov (United States)

    Su, Zhi-Hao; Zhang, Ming-Li

    2016-01-01

    Based on two chloroplast DNA sequences, psbA-trnH and trnT-trnF, phylogeographical patterns of a desert shrub, Ephedra przewalskii, were examined across most of its geographic range in northwestern China. A total of sixteen haplotypes were detected. There was a common haplotype in each basin, that was haplotype A in Tarim Basin, haplotype G in Junggar Basin, and haplotype M in Qaidam Basin. Genetic variance mainly occurred among populations, geographic regions, and eleven geographic groups subdivided by SAMOVA analysis. E. przewalskii likely had a smaller and more fragmented geographic range during the Last Glacial Maximum, which was determined based on ecological niche modelling. Three groups of E. przewalskii populations were detected to have experience range expansion, and this was based on significant values of Fu's FS, Tajima's D, and unimodel mismatch distributions. The cold and dry climate during the glacial period of the Quaternary is postulated to have been a driver for significant genetic isolation and divergence among populations or groups in E. przewalskii, whereas the warmer and wetter climate during the interglacial period is speculated to have provided favourable conditions for range expansion of the species.

  8. Evolutionary divergence in the catalytic activity of the CAM-1, ROR1 and ROR2 kinase domains.

    Directory of Open Access Journals (Sweden)

    Travis W Bainbridge

    Full Text Available Receptor tyrosine kinase-like orphan receptors (ROR 1 and 2 are atypical members of the receptor tyrosine kinase (RTK family and have been associated with several human diseases. The vertebrate RORs contain an ATP binding domain that deviates from the consensus amino acid sequence, although the impact of this deviation on catalytic activity is not known and the kinase function of these receptors remains controversial. Recently, ROR2 was shown to signal through a Wnt responsive, β-catenin independent pathway and suppress a canonical Wnt/β-catenin signal. In this work we demonstrate that both ROR1 and ROR2 kinase domains are catalytically deficient while CAM-1, the C. elegans homolog of ROR, has an active tyrosine kinase domain, suggesting a divergence in the signaling processes of the ROR family during evolution. In addition, we show that substitution of the non-consensus residues from ROR1 or ROR2 into CAM-1 and MuSK markedly reduce kinase activity, while restoration of the consensus residues in ROR does not restore robust kinase function. We further demonstrate that the membrane-bound extracellular domain alone of either ROR1 or ROR2 is sufficient for suppression of canonical Wnt3a signaling, and that this domain can also enhance Wnt5a suppression of Wnt3a signaling. Based on these data, we conclude that human ROR1 and ROR2 are RTK-like pseudokinases.

  9. '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.

  10. Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus).

    Science.gov (United States)

    Vieira, Jorge; Ferreira, Pedro G; Aguiar, Bruno; Fonseca, Nuno A; Vieira, Cristina P

    2010-06-28

    Within Rosaceae, the RNase based gametophytic self-incompatibility (GSI) system has been studied at the molecular level in Maloideae and Prunus species that have been diverging for, at least, 32 million years. In order to understand RNase based GSI evolution within this family, comparative studies must be performed, using similar methodologies. It is here shown that many features are shared between the two species groups such as levels of recombination at the S-RNase (the S-pistil component) gene, and the rate at which new specificities arise. Nevertheless, important differences are found regarding the number of ancestral lineages and the degree of specificity sharing between closely related species. In Maloideae, about 17% of the amino acid positions at the S-RNase protein are found to be positively selected, and they occupy about 30% of the exposed protein surface. Positively selected amino acid sites are shown to be located on either side of the active site cleft, an observation that is compatible with current models of specificity determination. At positively selected amino acid sites, non-conservative changes are almost as frequent as conservative changes. There is no evidence that at these sites the most drastic amino acid changes may be more strongly selected. Many similarities are found between the GSI system of Prunus and Maloideae that are compatible with the single origin hypothesis for RNase based GSI. The presence of common features such as the location of positively selected amino acid sites and lysine residues that may be important for ubiquitylation, raise a number of issues that, in principle, can be experimentally addressed in Maloideae. Nevertheless, there are also many important differences between the two Rosaceae GSI systems. How such features changed during evolution remains a puzzling issue.

  11. Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus

    Directory of Open Access Journals (Sweden)

    Fonseca Nuno A

    2010-06-01

    Full Text Available Abstract Background Within Rosaceae, the RNase based gametophytic self-incompatibility (GSI system has been studied at the molecular level in Maloideae and Prunus species that have been diverging for, at least, 32 million years. In order to understand RNase based GSI evolution within this family, comparative studies must be performed, using similar methodologies. Result It is here shown that many features are shared between the two species groups such as levels of recombination at the S-RNase (the S-pistil component gene, and the rate at which new specificities arise. Nevertheless, important differences are found regarding the number of ancestral lineages and the degree of specificity sharing between closely related species. In Maloideae, about 17% of the amino acid positions at the S-RNase protein are found to be positively selected, and they occupy about 30% of the exposed protein surface. Positively selected amino acid sites are shown to be located on either side of the active site cleft, an observation that is compatible with current models of specificity determination. At positively selected amino acid sites, non-conservative changes are almost as frequent as conservative changes. There is no evidence that at these sites the most drastic amino acid changes may be more strongly selected. Conclusions Many similarities are found between the GSI system of Prunus and Maloideae that are compatible with the single origin hypothesis for RNase based GSI. The presence of common features such as the location of positively selected amino acid sites and lysine residues that may be important for ubiquitylation, raise a number of issues that, in principle, can be experimentally addressed in Maloideae. Nevertheless, there are also many important differences between the two Rosaceae GSI systems. How such features changed during evolution remains a puzzling issue.

  12. Population Divergence in Venom Bioactivities of Elapid Snake Pseudonaja textilis: Role of Procoagulant Proteins in Rapid Rodent Prey Incapacitation

    Science.gov (United States)

    Skejić, Jure; Hodgson, Wayne C.

    2013-01-01

    This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD) venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality) and Queensland (Mackay locality) populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver. PMID:23691135

  13. Population divergence in venom bioactivities of elapid snake Pseudonaja textilis: role of procoagulant proteins in rapid rodent prey incapacitation.

    Directory of Open Access Journals (Sweden)

    Jure Skejić

    Full Text Available This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality and Queensland (Mackay locality populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver.

  14. Finite Divergence

    DEFF Research Database (Denmark)

    Hansen, Michael Edberg; Pandya, P. K.; Chaochen, Zhou

    1995-01-01

    the framework of duration calculus. Axioms and proof rules are given. Patterns of occurrence of divergence are classified into dense divergence, accumulative divergence and discrete divergence by appropriate axioms. Induction rules are given for reasoning about discrete divergence...

  15. 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...

  16. Decoupled leaf and root carbon economics is a key component in the ecological diversity and evolutionary divergence of deciduous and evergreen lineages of genus Rhododendron.

    Science.gov (United States)

    Medeiros, Juliana S; Burns, Jean H; Nicholson, Jaynell; Rogers, Louisa; Valverde-Barrantes, Oscar

    2017-06-01

    We explored trait-trait and trait-climate relationships for 27 Rhododendron species while accounting for phylogenetic relationships and within-species variation to investigate whether leaf and root traits are coordinated across environments and over evolutionary time, as part of a whole-plant economics spectrum. We examined specific leaf area (SLA) and four root traits: specific root length (SRL), specific root tip abundance (SRTA), first order diameter, and link average length, for plants growing in a cold, seasonal climate (Kirtland, Ohio) and a warmer, less seasonal climate (Federal Way, Washington) in the United States. We estimated a phylogeny and species' climate of origin, determined phylogenetic signal on mean traits and within-species variation, and used phylogenetically informed analysis to compare trait-trait and trait-climate relationships for deciduous and evergreen lineages. Mean SLA and within-species variation in SRL were more similar between close relatives than expected by chance. SLA and root traits differed according to climate of origin and across growth environments, though SLA differed within- and among-species less than roots. A negative SRL-SRTA correlation indicates investment in foraging scale vs. precision as a fundamental trade-off defining the root economic spectrum. Also, the deciduous clade exhibited a strong negative relationship between SLA and SRL, while evergreen clades showed a weaker positive or no relationship. Our work suggests that natural selection has shaped relationships between above- and belowground traits in genus Rhododendron and that leaf and root traits may evolve independently. Morphological decoupling may help explain habitat diversity among Rhododendron species, as well as the changes accompanying the divergence of deciduous and evergreen lineages. © 2017 Botanical Society of America.

  17. The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

    Science.gov (United States)

    Turcotte, Martin M; Reznick, David N; Hare, J Daniel

    2011-11-01

    Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

  18. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

    DEFF Research Database (Denmark)

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien

    2016-01-01

    to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies......Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out innatural field conditions. We examined the evolutionary response...... associated to changes in soil temperature and soil moisture. This shows an evolutionaryresponse to realistic climate change happening over short-time scale, and calls for incorporating evolution into modelspredicting future response of species to climate change. It also shows that designed climate change...

  19. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

    Science.gov (United States)

    Liu, Shiping; Lorenzen, Eline D; Fumagalli, Matteo; Li, Bo; Harris, Kelley; Xiong, Zijun; Zhou, Long; Korneliussen, Thorfinn Sand; Somel, Mehmet; Babbitt, Courtney; Wray, Greg; Li, Jianwen; He, Weiming; Wang, Zhuo; Fu, Wenjing; Xiang, Xueyan; Morgan, Claire C; Doherty, Aoife; O'Connell, Mary J; McInerney, James O; Born, Erik W; Dalén, Love; Dietz, Rune; Orlando, Ludovic; Sonne, Christian; Zhang, Guojie; Nielsen, Rasmus; Willerslev, Eske; Wang, Jun

    2014-05-08

    Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.

    Science.gov (United States)

    Newton, Matilda S; Arcus, Vickery L; Patrick, Wayne M

    2015-06-06

    The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  1. CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba.

    Science.gov (United States)

    Kouri, Vivian; Khouri, Ricardo; Alemán, Yoan; Abrahantes, Yeissel; Vercauteren, Jurgen; Pineda-Peña, Andrea-Clemencia; Theys, Kristof; Megens, Sarah; Moutschen, Michel; Pfeifer, Nico; Van Weyenbergh, Johan; Pérez, Ana B; Pérez, Jorge; Pérez, Lissette; Van Laethem, Kristel; Vandamme, Anne-Mieke

    2015-03-01

    Clinicians reported an increasing trend of rapid progression (RP) (AIDS within 3 years of infection) in Cuba. Recently infected patients were prospectively sampled, 52 RP at AIDS diagnosis (AIDS-RP) and 21 without AIDS in the same time frame (non-AIDS). 22 patients were sampled at AIDS diagnosis (chronic-AIDS) retrospectively assessed as > 3 years infected. Clinical, demographic, virological, epidemiological and immunological data were collected. Pol and env sequences were used for subtyping, transmission cluster analysis, and prediction of resistance, co-receptor use and evolutionary fitness. Host, immunological and viral predictors of RP were explored through data mining. Subtyping revealed 26 subtype B strains, 6 C, 6 CRF18_cpx, 9 CRF19_cpx, 29 BG-recombinants and other subtypes/URFs. All patients infected with CRF19 belonged to the AIDS-RP group. Data mining identified CRF19, oral candidiasis and RANTES levels as the strongest predictors of AIDS-RP. CRF19 was more frequently predicted to use the CXCR4 co-receptor, had higher fitness scores in the protease region, and patients had higher viral load at diagnosis. CRF19 is a recombinant of subtype D (C-part of Gag, PR, RT and nef), subtype A (N-part of Gag, Integrase, Env) and subtype G (Vif, Vpr, Vpu and C-part of Env). Since subtypes D and A have been associated with respectively faster and slower disease progression, our findings might indicate a fit PR driving high viral load, which in combination with co-infections may boost RANTES levels and thus CXCR4 use, potentially explaining the fast progression. We propose that CRF19 is evolutionary very fit and causing rapid progression to AIDS in many newly infected patients in Cuba.

  2. Rapid evolutionary change of common bean (Phaseolus vulgaris L plastome, and the genomic diversification of legume chloroplasts

    Directory of Open Access Journals (Sweden)

    Dávila Guillermo

    2007-07-01

    Full Text Available Abstract Background Fabaceae (legumes is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes for these crops is limited. Results We sequenced the complete genome of the common bean (Phaseolus vulgaris cv. Negro Jamapa chloroplast. The plastome of P. vulgaris is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, rpl33 and rps16. A distinct inversion occurred at the junction points of trnH-GUG/rpl14 and rps19/rps8, as in adzuki bean 1. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, P. vulgaris plastome had higher evolutionary rates of change on both genomic and gene levels than G. max, which could be the consequence of pressure from both mutation and natural selection. Conclusion Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The P. vulgaris plastome is a rapidly evolving genome.

  3. Phylogenetic influences on leaf trait integration in Pelargonium (Geraniaceae): convergence, divergence, and historical adaptation to a rapidly changing climate.

    Science.gov (United States)

    Jones, Cynthia S; Martínez-Cabrera, Hugo I; Nicotra, Adrienne B; Mocko, Kerri; Marais, Elizabeth M; Schlichting, Carl D

    2013-07-01

    Trait integration may improve prediction of species and lineage responses to future climate change more than individual traits alone, particularly when analyses incorporate effects of phylogenetic relationships. The South African genus Pelargonium contains divergent major clades that have radiated along the same seasonal aridity gradient, presenting the opportunity to ask whether patterns of evolution in mean leaf trait values are achieved through the same set of coordinated changes among traits in each clade. Seven leaf traits were measured on field-collected leaves from one-third of the species (98) of the genus. Trait relationships were examined using phylogenetic regression within major clades. Disparity analysis determined whether the course of trait evolution paralleled historical climate change events. Divergence in mean trait values between sister clades A1 and A2 was consistent with expectations for leaves differing in longevity, despite strong similarity between clades in trait interactions. No traits in either clade exhibited significant relationships with multivariate climate axes, with one exception. Species in clades C and A2 included in this study occupied similar environments. These clades had similar values of individual trait means, except for δ(13)C, but they exhibited distinctive patterns of trait integration. Differing present-day patterns of trait integration are consistent with interpretations of adaptive responses to the prevailing climate at the time of each clade's origin. These differing patterns of integration are likely to exert strong effects on clade-level responses to future climate change in the winter rainfall region of South Africa.

  4. Phylogeny of an Albugo sp. infecting Barbarea vulgaris in Denmark and its frequency of symptom development in natural populations of two evolutionary divergent plant types

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Heimes, Christine; Hauser, Thure Pavlo

    2014-01-01

    The oomycete Albugo candida has long been considered a broad spectrum generalist pathogen, but recent studies suggest that it is diverged into several more specialised species in addition to the generalist Albugo candida s.s.. Whereas these species cause the disease white blister rust in many cru...

  5. Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences

    OpenAIRE

    Grandien, Kaj; Sommer, Ralf J.

    2001-01-01

    Hox transcription factors have been implicated in playing a central role in the evolution of animal morphology. Many studies indicate the evolutionary importance of regulatory changes in Hox genes, but little is known about the role of functional changes in Hox proteins. In the nematodes Pristionchus pacificus and Caenorhabditis elegans, developmental processes can be compared at the cellular, genetic, and molecular levels and differences in gene function can be identified. The Hox gene lin-3...

  6. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Soo Rin Kim

    Full Text Available Economic bioconversion of plant cell wall hydrolysates into fuels and chemicals has been hampered mainly due to the inability of microorganisms to efficiently co-ferment pentose and hexose sugars, especially glucose and xylose, which are the most abundant sugars in cellulosic hydrolysates. Saccharomyces cerevisiae cannot metabolize xylose due to a lack of xylose-metabolizing enzymes. We developed a rapid and efficient xylose-fermenting S. cerevisiae through rational and inverse metabolic engineering strategies, comprising the optimization of a heterologous xylose-assimilating pathway and evolutionary engineering. Strong and balanced expression levels of the XYL1, XYL2, and XYL3 genes constituting the xylose-assimilating pathway increased ethanol yields and the xylose consumption rates from a mixture of glucose and xylose with little xylitol accumulation. The engineered strain, however, still exhibited a long lag time when metabolizing xylose above 10 g/l as a sole carbon source, defined here as xylose toxicity. Through serial-subcultures on xylose, we isolated evolved strains which exhibited a shorter lag time and improved xylose-fermenting capabilities than the parental strain. Genome sequencing of the evolved strains revealed that mutations in PHO13 causing loss of the Pho13p function are associated with the improved phenotypes of the evolved strains. Crude extracts of a PHO13-overexpressing strain showed a higher phosphatase activity on xylulose-5-phosphate (X-5-P, suggesting that the dephosphorylation of X-5-P by Pho13p might generate a futile cycle with xylulokinase overexpression. While xylose consumption rates by the evolved strains improved substantially as compared to the parental strain, xylose metabolism was interrupted by accumulated acetate. Deletion of ALD6 coding for acetaldehyde dehydrogenase not only prevented acetate accumulation, but also enabled complete and efficient fermentation of xylose as well as a mixture of glucose and

  7. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes.

    Science.gov (United States)

    Steppan, Scott; Adkins, Ronald; Anderson, Joel

    2004-08-01

    The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.

  8. Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences.

    Science.gov (United States)

    Grandien, K; Sommer, R J

    2001-08-15

    Hox transcription factors have been implicated in playing a central role in the evolution of animal morphology. Many studies indicate the evolutionary importance of regulatory changes in Hox genes, but little is known about the role of functional changes in Hox proteins. In the nematodes Pristionchus pacificus and Caenorhabditis elegans, developmental processes can be compared at the cellular, genetic, and molecular levels and differences in gene function can be identified. The Hox gene lin-39 is involved in the regulation of nematode vulva development. Comparison of known lin-39 mutations in P. pacificus and C. elegans revealed both conservation and changes of gene function. Here, we study evolutionary changes of lin-39 function using hybrid transgenes and site-directed mutagenesis in an in vivo assay using C. elegans lin-39 mutants. Our data show that despite the functional differences of LIN-39 between the two species, Ppa-LIN-39, when driven by Cel-lin-39 regulatory elements, can functionally replace Cel-lin-39. Furthermore, we show that the MAPK docking and phosphorylation motifs unique for Cel-LIN-39 are dispensable for Cel-lin-39 function. Therefore, the evolution of lin-39 function is driven by changes in regulatory elements rather than changes in the protein itself.

  9. Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2.

    Science.gov (United States)

    Logeman, Brandon L; Wood, L Kent; Lee, Jaekwon; Thiele, Dennis J

    2017-07-07

    Copper is an essential element for proper organismal development and is involved in a range of processes, including oxidative phosphorylation, neuropeptide biogenesis, and connective tissue maturation. The copper transporter (Ctr) family of integral membrane proteins is ubiquitously found in eukaryotes and mediates the high-affinity transport of Cu + across both the plasma membrane and endomembranes. Although mammalian Ctr1 functions as a Cu + transporter for Cu acquisition and is essential for embryonic development, a homologous protein, Ctr2, has been proposed to function as a low-affinity Cu transporter, a lysosomal Cu exporter, or a regulator of Ctr1 activity, but its functional and evolutionary relationship to Ctr1 is unclear. Here we report a biochemical, genetic, and phylogenetic comparison of metazoan Ctr1 and Ctr2, suggesting that Ctr2 arose over 550 million years ago as a result of a gene duplication event followed by loss of Cu + transport activity. Using a random mutagenesis and growth selection approach, we identified amino acid substitutions in human and mouse Ctr2 proteins that support copper-dependent growth in yeast and enhance copper accumulation in Ctr1 -/- mouse embryonic fibroblasts. These mutations revert Ctr2 to a more ancestral Ctr1-like state while maintaining endogenous functions, such as stimulating Ctr1 cleavage. We suggest key structural aspects of metazoan Ctr1 and Ctr2 that discriminate between their biological roles, providing mechanistic insights into the evolutionary, biochemical, and functional relationships between these two related proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra.

    Science.gov (United States)

    Reddy, Puli Chandramouli; Ubhe, Suyog; Sirwani, Neha; Lohokare, Rasika; Galande, Sanjeev

    2017-08-01

    Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra. Here, we report identification of the complete repertoire of histone-coding genes in the Hydra magnipapillata genome. Hydra histones were classified based on their copy numbers, gene structure and other characteristic features. Genomic organization of canonical histone genes revealed the presence of H2A-H2B and H3-H4 paired clusters in high frequency and also a cluster with all core histones along with H1. Phylogenetic analysis of identified members of H2A and H2B histones suggested rapid expansion of these groups in Hydrozoa resulting in the appearance of unique subtypes. Amino acid sequence level comparisons of H2A and H2B forms with bilaterian counterparts suggest the possibility of a highly mobile nature of nucleosomes in hydra. Absolute quantitation of transcripts confirmed the high copy number of histones and supported the canonical nature of H2A. Furthermore, functional characterization of H2A.X.1 and a unique variant H2A.X.2 in the gastric region suggest their role in the maintenance of genome integrity and differentiation processes. These findings provide insights into the evolution of histones and their variants in hydra. Copyright © 2017 Elsevier GmbH. All rights reserved.

  11. Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

    Science.gov (United States)

    Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

    2016-06-01

    Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

  12. Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

    Science.gov (United States)

    Häger, K P; Wind, C

    1997-06-15

    Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

  13. Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

    Science.gov (United States)

    Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

    2016-01-01

    nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. PMID:26560065

  14. Selectivity and evolutionary divergence of metabotropic glutamate receptors for endogenous ligands and G proteins coupled to phospholipase C or TRP channels.

    Science.gov (United States)

    Kang, Hye Jin; Menlove, Kit; Ma, Jianpeng; Wilkins, Angela; Lichtarge, Olivier; Wensel, Theodore G

    2014-10-24

    To define the upstream and downstream signaling specificities of metabotropic glutamate receptors (mGluR), we have examined the ability of representative mGluR of group I, II, and III to be activated by endogenous amino acids and catalyze activation of G proteins coupled to phospholipase C (PLC), or activation of G(i/o) proteins coupled to the ion channel TRPC4β. Fluorescence-based assays have allowed us to observe interactions not previously reported or clearly identified. We have found that the specificity for endogenous amino acids is remarkably stringent. Even at millimolar levels, structurally similar compounds do not elicit significant activation. As reported previously, the clear exception is L-serine-O-phosphate (L-SOP), which strongly activates group III mGluR, especially mGluR4,-6,-8 but not group I or II mGluR. Whereas L-SOP cannot activate mGluR1 or mGluR2, it acts as a weak antagonist for mGluR1 and a potent antagonist for mGluR2, suggesting that co-recognition of L-glutamate and L-SOP arose early in evolution, and was followed later by divergence of group I and group II mGluR versus group III in l-SOP responses. mGluR7 has low affinity and efficacy for activation by both L-glutamate and L-SOP. Molecular docking studies suggested that residue 74 corresponding to lysine in mGluR4 and asparagine in mGluR7 might play a key role, and, indeed, mutagenesis experiments demonstrated that mutating this residue to lysine in mGluR7 enhances the potency of L-SOP. Experiments with pertussis toxin and dominant-negative Gα(i/o) proteins revealed that mGluR1 couples strongly to TRPC4β through Gα(i/o), in addition to coupling to PLC through Gα(q/11). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Selectivity and Evolutionary Divergence of Metabotropic Glutamate Receptors for Endogenous Ligands and G Proteins Coupled to Phospholipase C or TRP Channels*

    Science.gov (United States)

    Kang, Hye Jin; Menlove, Kit; Ma, Jianpeng; Wilkins, Angela; Lichtarge, Olivier; Wensel, Theodore G.

    2014-01-01

    To define the upstream and downstream signaling specificities of metabotropic glutamate receptors (mGluR), we have examined the ability of representative mGluR of group I, II, and III to be activated by endogenous amino acids and catalyze activation of G proteins coupled to phospholipase C (PLC), or activation of Gi/o proteins coupled to the ion channel TRPC4β. Fluorescence-based assays have allowed us to observe interactions not previously reported or clearly identified. We have found that the specificity for endogenous amino acids is remarkably stringent. Even at millimolar levels, structurally similar compounds do not elicit significant activation. As reported previously, the clear exception is l-serine-O-phosphate (l-SOP), which strongly activates group III mGluR, especially mGluR4,-6,-8 but not group I or II mGluR. Whereas l-SOP cannot activate mGluR1 or mGluR2, it acts as a weak antagonist for mGluR1 and a potent antagonist for mGluR2, suggesting that co-recognition of l-glutamate and l-SOP arose early in evolution, and was followed later by divergence of group I and group II mGluR versus group III in l-SOP responses. mGluR7 has low affinity and efficacy for activation by both l-glutamate and l-SOP. Molecular docking studies suggested that residue 74 corresponding to lysine in mGluR4 and asparagine in mGluR7 might play a key role, and, indeed, mutagenesis experiments demonstrated that mutating this residue to lysine in mGluR7 enhances the potency of l-SOP. Experiments with pertussis toxin and dominant-negative Gαi/o proteins revealed that mGluR1 couples strongly to TRPC4β through Gαi/o, in addition to coupling to PLC through Gαq/11. PMID:25193666

  16. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

    Directory of Open Access Journals (Sweden)

    Katarzyna Marta Bocian-Ostrzycka

    2015-10-01

    Full Text Available Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595 with a -propeller structure. The aim of presented work was to assess relations between HP0231 structure and function.We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C, a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in E. coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (Escherichia coli DsbA protein were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.

  17. Expression and evolutionary divergence of the non-conventional olfactory receptor in four species of fig wasp associated with one species of fig

    Directory of Open Access Journals (Sweden)

    Xiao Jinhua

    2009-02-01

    the known primary olfactory tissues indicates the location of cryptic olfactory inputs. The specialized ecological niche of these wasps explains the unique habits and adaptive evolution of Or2 genes. The Or2 gene in C. solmsi is evolving very rapidly. Negative deviation from the neutral model of evolution reflects possible selection pressures acting on Or2 sequences of fig wasp, particularly on PFWs who are more host-specific to figs.

  18. Diverging Cohesion?

    DEFF Research Database (Denmark)

    Charron, Nicholas

    2016-01-01

    – which we define here as a combination of impartial bureaucratic practices, corruption and the rule of law – limits, and in some cases reverses the tendency towards greater divergence linked to trade. Countries with high levels of state capacity – that is, those that have greater government effectiveness......, stronger rule of law and lower corruption – experience lower levels of divergence, as they have the mechanisms to counterbalance the strong centripetal forces linked to openness. This claim is tested on countries that have experienced relatively high levels of increases in levels of economic and political......Why do increases in globalisation in the face of European expansion lead to sharp levels of regional divergences in wealth in some countries but not in others? The central crux of this paper is that convergence/divergence trends in European states are conditioned by ‘state capacity’. State capacity...

  19. 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

  20. Divergence in function and expression of the NOD26-like intrinsic proteins in plants

    Directory of Open Access Journals (Sweden)

    Feng Ying

    2009-07-01

    Full Text Available Abstract Background NOD26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out. Results The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss P. patens. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that NIPs should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct NIP groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of cis-acting regulatory elements in the promoter regions may partially explain their distinction in expression. Conclusion A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have

  1. Non-LTR R2 element evolutionary patterns: phylogenetic incongruences, rapid radiation and the maintenance of multiple lineages.

    Directory of Open Access Journals (Sweden)

    Andrea Luchetti

    Full Text Available Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850-600 Million years ago placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host's 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the "library" model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.

  2. Convergence from divergence

    Science.gov (United States)

    Costin, Ovidiu; Dunne, Gerald V.

    2018-01-01

    We show how to convert divergent series, which typically occur in many applications in physics, into rapidly convergent inverse factorial series. This can be interpreted physically as a novel resummation of perturbative series. Being convergent, these new series allow rigorous extrapolation from an asymptotic region with a large parameter, to the opposite region where the parameter is small. We illustrate the method with various physical examples, and discuss how these convergent series relate to standard methods such as Borel summation, and also how they incorporate the physical Stokes phenomenon. We comment on the relation of these results to Dyson’s physical argument for the divergence of perturbation theory. This approach also leads naturally to a wide class of relations between bosonic and fermionic partition functions, and Klein-Gordon and Dirac determinants.

  3. Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

    Science.gov (United States)

    Toju, Hirokazu; Sota, Teiji

    2009-09-01

    One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

  4. Evolutionary perspectives into placental biology and disease

    Directory of Open Access Journals (Sweden)

    Edward B. Chuong

    2013-12-01

    Full Text Available In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal–fetal conflict shapes both basic placental and reproductive biology – in all species – will provide key insights into diseases of pregnancy.

  5. Metabolic Rate and Climatic Fluctuations Shape Continental Wide Pattern of Genetic Divergence and Biodiversity in Fishes

    Science.gov (United States)

    April, Julien; Hanner, Robert H.; Mayden, Richard L.; Bernatchez, Louis

    2013-01-01

    Taxonomically exhaustive and continent wide patterns of genetic divergence within and between species have rarely been described and the underlying evolutionary causes shaping biodiversity distribution remain contentious. Here, we show that geographic patterns of intraspecific and interspecific genetic divergence among nearly all of the North American freshwater fish species (>750 species) support a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence and very likely influencing speciation rates. Results indicate that the recurrent glacial cycles caused global reduction in intraspecific diversity, interspecific genetic divergence, and species richness at higher latitudes. At the opposite, longer geographic isolation, higher metabolic rate increasing substitution rate and possibly the rapid accumulation of genetic incompatibilities, led to an increasing biodiversity towards lower latitudes. This indicates that both intrinsic and extrinsic factors similarly affect micro and macro evolutionary processes shaping global patterns of biodiversity distribution. These results also indicate that factors favouring allopatric speciation are the main drivers underlying the diversification of North American freshwater fishes. PMID:23922969

  6. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Directory of Open Access Journals (Sweden)

    George L Sutphin

    2016-11-01

    Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  7. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

    Science.gov (United States)

    Sutphin, George L.; Mahoney, J. Matthew; Sheppard, Keith; Walton, David O.; Korstanje, Ron

    2016-01-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species—humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/. PMID:27812085

  8. Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

    Science.gov (United States)

    Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

    2015-02-15

    WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    for the capacity to evolve. This hypothesis is tested through experiments in two evolutionary robotics domains. The results show that combining extinction events with divergent search increases evolvability, while combining them with convergent search offers no similar benefit. The conclusion is that extinction...

  10. Phenotypic divergence along geographic gradients reveals potential for rapid adaptation of the White-nose Syndrome pathogen, Pseudogymnoascus destructans, in North America.

    Science.gov (United States)

    Forsythe, Adrian; Giglio, Victoria; Asa, Jonathan; Xu, Jianping

    2018-06-18

    White-nose Syndrome (WNS) is an ongoing epizootic affecting multiple species of North American bats, caused by epidermal infections of the psychrophilic filamentous fungus, Pseudogymnoascus destructans Since its introduction from Europe, WNS has spread rapidly across eastern North America and resulted in high mortality rates in bats. At present, the mechanisms behind its spread and the extent of its adaptation to different geographic and ecological niches remain unknown. The objective of this study was to examine the geographic patterns of phenotypic variation and the potential evidence for adaptation among strains representing broad geographic locations in eastern North America. The morphological features of these strains were evaluated on artificial medium, and the viability of asexual arthroconidia of representative strains were investigated after storage at high (23°C), moderate (14°C), and low (4°C) temperatures at different lengths of times. Our analyses identified evidence for a geographic pattern of colony morphology changes among the clonal descendants of the fungus, with trait values correlated with increased distance from the epicenter of WNS. Our genomic comparisons of three representative isolates revealed novel genetic polymorphisms and suggested potential candidate mutations that might be related to some of the phenotypic changes. These results show that even though this pathogen arrived in North America only recently and reproduces asexually, there has been substantial evolution and phenotypic diversification during its rapid clonal expansion. Importance The causal agent of White-nose Syndrome in bats is Pseudogymnoascus destructans , a filamentous fungus recently introduced from its native range in Europe. Infections caused by P. destructans have progressed across the eastern parts of Canada and the United States over the last ten years. It is not clear how the disease is spread as the pathogen is unable to grow above 23°C and ambient

  11. 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.

  12. Applications of Evolutionary Computation

    NARCIS (Netherlands)

    Mora, Antonio M.; Squillero, Giovanni; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Smith, Stephen L; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Mora, Antonio M.; Squillero, Giovanni; Jan, Mathieu; Matthias, M; Di Chio, C; Agapitos, Alexandros; Cagnoni, Stefano; Cotta, Carlos; Fernández De Vega, F; Di Caro, G A; Drechsler, R.; Ekárt, A; Esparcia-Alcázar, Anna I.; Farooq, M; Langdon, W B; Merelo-Guervós, J.J.; Preuss, M; Richter, O.-M.H.; Silva, Sara; Sim$\\$~oes, A; Squillero, Giovanni; Tarantino, Ernesto; Tettamanzi, Andrea G B; Togelius, J; Urquhart, Neil; Uyar, A S; Yannakakis, G N; Caserta, Marco; Ramirez, Adriana; Voß, Stefan; Squillero, Giovanni; Burelli, Paolo; Esparcia-Alcazar, Anna I; Silva, Sara; Agapitos, Alexandros; Cotta, Carlos; De Falco, Ivanoe; Cioppa, Antonio Della; Diwold, Konrad; Ekart, Aniko; Tarantino, Ernesto; Vega, Francisco Fernandez De; Burelli, Paolo; Sim, Kevin; Cagnoni, Stefano; Simoes, Anabela; Merelo, J.J.; Urquhart, Neil; Haasdijk, Evert; Zhang, Mengjie; Squillero, Giovanni; Eiben, A E; Tettamanzi, Andrea G B; Glette, Kyrre; Rohlfshagen, Philipp; Schaefer, Robert; Caserta, Marco; Ramirez, Adriana; Voß, Stefan

    2015-01-01

    The application of genetic and evolutionary computation to problems in medicine has increased rapidly over the past five years, but there are specific issues and challenges that distinguish it from other real-world applications. Obtaining reliable and coherent patient data, establishing the clinical

  13. Evolutionary insights into scleractinian corals using comparative genomic hybridizations.

    Science.gov (United States)

    Aranda, Manuel; DeSalvo, Michael K; Bayer, Till; Medina, Monica; Voolstra, Christian R

    2012-09-21

    Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this

  14. Evolutionary insights into scleractinian corals using comparative genomic hybridizations

    Directory of Open Access Journals (Sweden)

    Aranda Manuel

    2012-09-01

    Full Text Available Abstract Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization. Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than

  15. Divergence, recombination and retention of functionality during protein evolution

    Directory of Open Access Journals (Sweden)

    Xu Yanlong O

    2005-09-01

    Full Text Available Abstract We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates. These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality -- even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

  16. Divergence and adaptive evolution of the gibberellin oxidase genes in plants.

    Science.gov (United States)

    Huang, Yuan; Wang, Xi; Ge, Song; Rao, Guang-Yuan

    2015-09-29

    The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood. This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection. GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

  17. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

    Full Text Available 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 from 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 (which 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 the 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.

  18. Morphological divergence and flow-induced phenotypic plasticity in a native fish from anthropogenically altered stream habitats.

    Science.gov (United States)

    Franssen, Nathan R; Stewart, Laura K; Schaefer, Jacob F

    2013-11-01

    Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently diverged in reservoir habitats compared with streams; individuals from reservoirs were shallower bodied with smaller heads compared with individuals from streams. Significant population-level differences in morphology persisted in offspring but morphological variation compared with field-collected individuals was limited to the head region. Populations demonstrated dissimilar flow-induced phenotypic plasticity when reared under flow, but phenotypic plasticity in response to flow variation was an unlikely explanation for observed phenotypic divergence in the field. Our results, together with previous investigations, suggest the environmental conditions currently thought to drive morphological change in reservoirs (i.e., predation and flow regimes) may not be the sole drivers of phenotypic change.

  19. 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

  20. 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......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...

  1. String perturbation theory diverges

    International Nuclear Information System (INIS)

    Gross, D.J.; Periwal, V.

    1988-01-01

    We prove that perturbation theory for the bosonic string diverges for arbitrary values of the coupling constant and is not Borel summable. This divergence is independent of the existence of the infinities that occur in the theory due to the presence of tachyons and dilaton tadpoles. We discuss the physical implications of such a divergence

  2. 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

  3. 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...... 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......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...

  4. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

    Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

  5. 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.

  6. Core principles of evolutionary medicine

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

  7. Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae.

    Science.gov (United States)

    Lim, K Yoong; Kovarik, Ales; Matyasek, Roman; Chase, Mark W; Knapp, Sandra; McCarthy, Elizabeth; Clarkson, James J; Leitch, Andrew R

    2006-12-01

    Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploid Nicotiana section Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containing N. alata, N. langsdorffii, N. forgetiana and N. bonariensis (called the n = 9 group) and another containing N. plumbaginifolia and N. longiflora (called the n = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescent in situ hybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids of Nicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub-telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub-telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.

  8. Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.

    Science.gov (United States)

    Pereira, Ricardo J; Monahan, William B; Wake, David B

    2011-07-06

    Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI. By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI. These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

  9. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  10. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Directory of Open Access Journals (Sweden)

    Linbin Zhang

    2015-03-01

    Full Text Available Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  11. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Science.gov (United States)

    Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

    2015-03-01

    Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  12. 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 ...

  13. Transcriptome-wide patterns of divergence during allopatric evolution.

    Science.gov (United States)

    Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

    2016-04-01

    Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level. © 2016 John Wiley & Sons Ltd.

  14. The Patchwork Divergence Theorem

    OpenAIRE

    Dray, Tevian; Hellaby, Charles

    1994-01-01

    The divergence theorem in its usual form applies only to suitably smooth vector fields. For vector fields which are merely piecewise smooth, as is natural at a boundary between regions with different physical properties, one must patch together the divergence theorem applied separately in each region. We give an elegant derivation of the resulting "patchwork divergence theorem" which is independent of the metric signature in either region, and which is thus valid if the signature changes. (PA...

  15. On infrared divergences

    International Nuclear Information System (INIS)

    Parisi, G.

    1979-01-01

    The structure of infrared divergences is studied in superrenormalizable interactions. It is conjectured that there is an extension of the Bogoliubov-Parasiuk-Hepp theorem which copes also with infrared divergences. The consequences of this conjecture on the singularities of the Borel transform in a massless asymptotic free field theory are discussed. The application of these ideas to gauge theories is briefly discussed. (Auth.)

  16. 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.

  17. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae

    Directory of Open Access Journals (Sweden)

    Ober Karen A

    2010-08-01

    Full Text Available Abstract Background Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. Results According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Conclusions Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  18. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae).

    Science.gov (United States)

    Ober, Karen A; Heider, Thomas N

    2010-08-27

    Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

  19. Niche evolution and adaptive radiation: Testing the order of trait divergence

    Science.gov (United States)

    Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

    2006-01-01

    In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

  20. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Logue Kyle

    2013-02-01

    Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

  1. Regulatory divergence of X-linked genes and hybrid male sterility in mice.

    Science.gov (United States)

    Oka, Ayako; Shiroishi, Toshihiko

    2014-01-01

    Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

  2. Quantum skew divergence

    Energy Technology Data Exchange (ETDEWEB)

    Audenaert, Koenraad M. R., E-mail: koenraad.audenaert@rhul.ac.uk [Department of Mathematics, Royal Holloway University of London, Egham TW20 0EX, United Kingdom and Department of Physics and Astronomy, University of Ghent, S9, Krijgslaan 281, B-9000 Ghent (Belgium)

    2014-11-15

    In this paper, we study the quantum generalisation of the skew divergence, which is a dissimilarity measure between distributions introduced by Lee in the context of natural language processing. We provide an in-depth study of the quantum skew divergence, including its relation to other state distinguishability measures. Finally, we present a number of important applications: new continuity inequalities for the quantum Jensen-Shannon divergence and the Holevo information, and a new and short proof of Bravyi's Small Incremental Mixing conjecture.

  3. Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea).

    Science.gov (United States)

    Jue, Nathaniel K; Batta-Lona, Paola G; Trusiak, Sarah; Obergfell, Craig; Bucklin, Ann; O'Neill, Michael J; O'Neill, Rachel J

    2016-10-30

    A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering >50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni Using a nonredundant set of predicted proteins, >50% (16,823) of sequences showed significant homology to known proteins and ∼38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these

  4. Selection is stronger in early-versus-late stages of divergence in a Neotropical livebearing fish.

    Science.gov (United States)

    Ingley, Spencer J; Johnson, Jerald B

    2016-03-01

    How selection acts to drive trait evolution at different stages of divergence is of fundamental importance in our understanding of the origins of biodiversity. Yet, most studies have focused on a single point along an evolutionary trajectory. Here, we provide a case study evaluating the strength of divergent selection acting on life-history traits at early-versus-late stages of divergence in Brachyrhaphis fishes. We find that the difference in selection is stronger in the early-diverged population than the late-diverged population, and that trait differences acquired early are maintained over time. © 2016 The Author(s).

  5. When can stress facilitate divergence by altering time to flowering?

    OpenAIRE

    Jordan, Crispin Y.; Ally, Dilara; Hodgins, Kathryn A.

    2015-01-01

    Abstract Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce ...

  6. Divergent Geophysical Evolution of Vesta and Ceres

    Science.gov (United States)

    Raymond, C. A.; Ermakov, A.; Castillo, J. C.; Fu, R. R.; McSween, H. Y., Jr.; McCord, T. B.; Park, R. S.; Russell, C. T.; De Sanctis, M. C.; Jaumann, R.; Konopliv, A. S.

    2017-12-01

    The Dawn mission explored two massive protoplanets in the main asteroid belt, Vesta and Ceres, that are fossils from the earliest epoch of solar system formation. Dawn's data provide evidence that these bodies formed very early, within the first few million years after CAIs, yet they followed divergent evolutionary paths. Vesta formed globally homogeneous distribution of minerals across the surface indicates that Ceres' interior experienced pervasive alteration. Topography and morphology of the surface reveals smoother, apparently resurfaced areas, generally at lower elevation, and rougher areas with greater relief. Local morphology such as crater floor deposits, isolated mountains, and enigmatic bright areas indicate recently active processes on Ceres, likely driven by brine cryovolcanism. Causes of the divergent evolution of these bodies include their accretionary environment, timing of accretion and size. Acknowledgements: Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

  7. Divergent evolutionary processes associated with colonization of offshore islands

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália; Barnett, R.; Cucchi, T.; Struchen, R.; Pascal, M.; Pascal, M.; Fischer, M. C.; Higham, T.; Brace, S.; Ho, S. Y. W.; Quéré, J.-P.; O'Higgins, P.; Excoffier, L.; Heckel, G.; Hoelzel, A. R.; Dobney, K. M.; Searle, J. B.

    2013-01-01

    Roč. 22, č. 20 (2013), s. 5205-5220 ISSN 0962-1083 Grant - others:European Commission(XE) Marie Curie Intra European Fellowship Institutional support: RVO:68081766 Keywords : demographic analysis * genetic replacement * island colonization * Microtus arvalis * phylogeography Subject RIV: EG - Zoology Impact factor: 5.840, year: 2013

  8. Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone.

    Science.gov (United States)

    Cooke, Georgina M; Landguth, Erin L; Beheregaray, Luciano B

    2014-07-01

    Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  9. Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

    Science.gov (United States)

    Herrera, James P; Dávalos, Liliana M

    2016-09-01

    Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. 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.

  11. Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

    Science.gov (United States)

    Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

    2016-01-01

    An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

  12. Converging or Diverging Lens?

    Science.gov (United States)

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  13. Rapid changes in genetic architecture of behavioural syndromes following colonization of a novel environment.

    Science.gov (United States)

    Karlsson Green, K; Eroukhmanoff, F; Harris, S; Pettersson, L B; Svensson, E I

    2016-01-01

    Behavioural syndromes, that is correlated behaviours, may be a result from adaptive correlational selection, but in a new environmental setting, the trait correlation might act as an evolutionary constraint. However, knowledge about the quantitative genetic basis of behavioural syndromes, and the stability and evolvability of genetic correlations under different ecological conditions, is limited. We investigated the quantitative genetic basis of correlated behaviours in the freshwater isopod Asellus aquaticus. In some Swedish lakes, A. aquaticus has recently colonized a novel habitat and diverged into two ecotypes, presumably due to habitat-specific selection from predation. Using a common garden approach and animal model analyses, we estimated quantitative genetic parameters for behavioural traits and compared the genetic architecture between the ecotypes. We report that the genetic covariance structure of the behavioural traits has been altered in the novel ecotype, demonstrating divergence in behavioural correlations. Thus, our study confirms that genetic correlations behind behaviours can change rapidly in response to novel selective environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  14. Local divergence and curvature divergence in first order optics

    Science.gov (United States)

    Mafusire, Cosmas; Krüger, Tjaart P. J.

    2018-06-01

    The far-field divergence of a light beam propagating through a first order optical system is presented as a square root of the sum of the squares of the local divergence and the curvature divergence. The local divergence is defined as the ratio of the beam parameter product to the beam width whilst the curvature divergence is a ratio of the space-angular moment also to the beam width. It is established that the beam’s focusing parameter can be defined as a ratio of the local divergence to the curvature divergence. The relationships between the two divergences and other second moment-based beam parameters are presented. Their various mathematical properties are presented such as their evolution through first order systems. The efficacy of the model in the analysis of high power continuous wave laser-based welding systems is briefly discussed.

  15. A climate for speciation: rapid spatial diversification within the Sorex cinereus complex of shrews

    Science.gov (United States)

    Hope, Andrew G.; Speer, Kelly A.; Demboski, John R.; Talbot, Sandra L.; Cook, Joseph A.

    2012-01-01

    The cyclic climate regime of the late Quaternary caused dramatic environmental change at high latitudes. Although these events may have been brief in periodicity from an evolutionary standpoint, multiple episodes of allopatry and divergence have been implicated in rapid radiations of a number of organisms. Shrews of the Sorex cinereus complex have long challenged taxonomists due to similar morphology and parapatric geographic ranges. Here, multi-locus phylogenetic and demographic assessments using a coalescent framework were combined to investigate spatiotemporal evolution of 13 nominal species with a widespread distribution throughout North America and across Beringia into Siberia. For these species, we first test a hypothesis of recent differentiation in response to Pleistocene climate versus more ancient divergence that would coincide with pre-Pleistocene perturbations. We then investigate the processes driving diversification over multiple continents. Our genetic analyses highlight novel diversity within these morphologically conserved mammals and clarify relationships between geographic distribution and evolutionary history. Demography within and among species indicates both regional stability and rapid expansion. Ancestral ecological differentiation coincident with early cladogenesis within the complex enabled alternating and repeated episodes of allopatry and expansion where successive glacial and interglacial phases each promoted divergence. The Sorex cinereus complex constitutes a valuable model for future comparative assessments of evolution in response to cyclic environmental change.

  16. Evolutionary hotspots in the Mojave Desert

    Science.gov (United States)

    Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

    2013-01-01

    Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  17. Altitudinal divergence in maternal thermoregulatory behaviour may be driven by differences in selection on offspring survival in a viviparous lizard

    NARCIS (Netherlands)

    Uller, Tobias; While, Geoffrey M.; Cadby, Chloe D.; Harts, Anna; O'Connor, Katherine; Pen, Ido; Wapstra, Erik

    Plastic responses to temperature during embryonic development are common in ectotherms, but their evolutionary relevance is poorly understood. Using a combination of field and laboratory approaches, we demonstrate altitudinal divergence in the strength of effects of maternal thermal opportunity on

  18. Regularization of divergent integrals

    OpenAIRE

    Felder, Giovanni; Kazhdan, David

    2016-01-01

    We study the Hadamard finite part of divergent integrals of differential forms with singularities on submanifolds. We give formulae for the dependence of the finite part on the choice of regularization and express them in terms of a suitable local residue map. The cases where the submanifold is a complex hypersurface in a complex manifold and where it is a boundary component of a manifold with boundary, arising in string perturbation theory, are treated in more detail.

  19. The estimation of genetic divergence

    Science.gov (United States)

    Holmquist, R.; Conroy, T.

    1981-01-01

    Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

  20. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.

    Science.gov (United States)

    Gimmler, Anna; Stoeck, Thorsten

    2015-08-01

    Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  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. Anthropogenic habitat disturbance and ecological divergence between incipient species of the malaria mosquito Anopheles gambiae.

    Science.gov (United States)

    Kamdem, Colince; Tene Fossog, Billy; Simard, Frédéric; Etouna, Joachim; Ndo, Cyrille; Kengne, Pierre; Boussès, Philippe; Etoa, François-Xavier; Awono-Ambene, Parfait; Fontenille, Didier; Antonio-Nkondjio, Christophe; Besansky, Nora J; Costantini, Carlo

    2012-01-01

    Anthropogenic habitat disturbance is a prime cause in the current trend of the Earth's reduction in biodiversity. Here we show that the human footprint on the Central African rainforest, which is resulting in deforestation and growth of densely populated urban agglomerates, is associated to ecological divergence and cryptic speciation leading to adaptive radiation within the major malaria mosquito Anopheles gambiae. In southern Cameroon, the frequency of two molecular forms--M and S--among which reproductive isolation is strong but still incomplete, was correlated to an index of urbanisation extracted from remotely sensed data, expressed as the proportion of built-up surface in each sampling unit. The two forms markedly segregated along an urbanisation gradient forming a bimodal cline of ∼6-km width: the S form was exclusive to the rural habitat, whereas only the M form was present in the core of densely urbanised settings, co-occurring at times in the same polluted larval habitats of the southern house mosquito Culex quinquefasciatus--a species association that was not historically recorded before. Our results indicate that when humans create novel habitats and ecological heterogeneities, they can provide evolutionary opportunities for rapid adaptive niche shifts associated with lineage divergence, whose consequences upon malaria transmission might be significant.

  3. Ecological niche dimensionality and the evolutionary diversification of stick insects.

    Directory of Open Access Journals (Sweden)

    Patrik Nosil

    Full Text Available The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse ('speciation in reverse'. Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this 'niche dimensionality' hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation, physiology (to detoxify plant chemicals, or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of

  4. Behavioural divergence, interfertility and speciation: a review.

    Science.gov (United States)

    Pillay, Neville; Rymer, Tasmin L

    2012-11-01

    Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. 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

  6. Divergent Perturbation Series

    International Nuclear Information System (INIS)

    Suslov, I.M.

    2005-01-01

    Various perturbation series are factorially divergent. The behavior of their high-order terms can be determined by Lipatov's method, which involves the use of instanton configurations of appropriate functional integrals. When the Lipatov asymptotic form is known and several lowest order terms of the perturbation series are found by direct calculation of diagrams, one can gain insight into the behavior of the remaining terms of the series, which can be resummed to solve various strong-coupling problems in a certain approximation. This approach is demonstrated by determining the Gell-Mann-Low functions in φ 4 theory, QED, and QCD with arbitrary coupling constants. An overview of the mathematical theory of divergent series is presented, and interpretation of perturbation series is discussed. Explicit derivations of the Lipatov asymptotic form are presented for some basic problems in theoretical physics. A solution is proposed to the problem of renormalon contributions, which hampered progress in this field in the late 1970s. Practical perturbation-series summation schemes are described both for a coupling constant of order unity and in the strong-coupling limit. An interpretation of the Borel integral is given for 'non-Borel-summable' series. Higher order corrections to the Lipatov asymptotic form are discussed

  7. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General Article Volume 21 Issue 9 September 2016 pp 803- ... Keywords. Evolutionary game theory, evolutionary stable state, conflict, cooperation, biological games.

  8. When can stress facilitate divergence by altering time to flowering?

    Science.gov (United States)

    Jordan, Crispin Y; Ally, Dilara; Hodgins, Kathryn A

    2015-12-01

    Stressors and heterogeneity are ubiquitous features of natural environments, and theory suggests that when environmental qualities alter flowering schedules through phenotypic plasticity, assortative mating can result that promotes evolutionary divergence. Therefore, it is important to determine whether common ecological stressors induce similar changes in flowering time. We review previous studies to determine whether two important stressors, water restriction and herbivory, induce consistent flowering time responses among species; for example, how often do water restriction and herbivory both delay flowering? We focus on the direction of change in flowering time, which affects the potential for divergence in heterogeneous environments. We also tested whether these stressors influenced time to flowering and nonphenology traits using Mimulus guttatus. The literature review suggests that water restriction has variable effects on flowering time, whereas herbivory delays flowering with exceptional consistency. In the Mimulus experiment, low water and herbivory advanced and delayed flowering, respectively. Overall, our results temper theoretical predictions for evolutionary divergence due to habitat-induced changes in flowering time; in particular, we discuss how accounting for variation in the direction of change in flowering time can either increase or decrease the potential for divergence. In addition, we caution against adaptive interpretations of stress-induced phenology shifts.

  9. Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae.

    Science.gov (United States)

    Wang, Sibao; Leclerque, Andreas; Pava-Ripoll, Monica; Fang, Weiguo; St Leger, Raymond J

    2009-06-01

    Many strains of Metarhizium anisopliae have broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.

  10. Mutational and Evolutionary Analyses of Bovine Reprimo Gene ...

    African Journals Online (AJOL)

    It can therefore be concluded that bovine RPRM gene contained 4 transition mutations and 5 indels that can be used in marker assisted selection. Evolutionary findings also demonstrated the existence of a divergent evolution between bovine RPRM gene and RPRM gene of fishes and frog. Keywords: Identity, phylogeny ...

  11. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  12. Insect herbivores drive real-time ecological and evolutionary change in plant populations.

    Science.gov (United States)

    Agrawal, Anurag A; Hastings, Amy P; Johnson, Marc T J; Maron, John L; Salminen, Juha-Pekka

    2012-10-05

    Insect herbivores are hypothesized to be major factors affecting the ecology and evolution of plants. We tested this prediction by suppressing insects in replicated field populations of a native plant, Oenothera biennis, which reduced seed predation, altered interspecific competitive dynamics, and resulted in rapid evolutionary divergence. Comparative genotyping and phenotyping of nearly 12,000 O. biennis individuals revealed that in plots protected from insects, resistance to herbivores declined through time owing to changes in flowering time and lower defensive ellagitannins in fruits, whereas plant competitive ability increased. This independent real-time evolution of plant resistance and competitive ability in the field resulted from the relaxation of direct selective effects of insects on plant defense and through indirect effects due to reduced herbivory on plant competitors.

  13. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    Directory of Open Access Journals (Sweden)

    Annalise B. Paaby

    2016-06-01

    Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

  14. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    Science.gov (United States)

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

  15. Quadratic divergences and dimensional regularisation

    International Nuclear Information System (INIS)

    Jack, I.; Jones, D.R.T.

    1990-01-01

    We present a detailed analysis of quadratic and quartic divergences in dimensionally regulated renormalisable theories. We perform explicit three-loop calculations for a general theory of scalars and fermions. We find that the higher-order quartic divergences are related to the lower-order ones by the renormalisation group β-functions. (orig.)

  16. Core principles of evolutionary medicine: A Delphi study.

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

  17. On the Critical Role of Divergent Selection in Evolvability

    Directory of Open Access Journals (Sweden)

    Joel Lehman

    2016-08-01

    Full Text Available An ambitious goal in evolutionary robotics is to evolve increasingly complex robotic behaviors with minimal human design effort. Reaching this goal requires evolutionary algorithms that can unlock from genetic encodings their latent potential for evolvability. One issue clouding this goal is conceptual confusion about evolvability, which often obscures the aspects of evolvability that are important or desirable. The danger from such confusion is that it may establish unrealistic goals for evolvability that prove unproductive in practice. An important issue separate from conceptual confusion is the common misalignment between selection and evolvability in evolutionary robotics. While more expressive encodings can represent higher-level adaptations (e.g. sexual reproduction or developmental systems that increase long-term evolutionary potential (i.e. evolvability, realizing such potential requires gradients of fitness and evolvability to align. In other words, selection is often a critical factor limiting increasing evolvability. Thus, drawing from a series of recent papers, this article seeks to both (1 clarify and focus the ways in which the term evolvability is used within artificial evolution, and (2 argue for the importance of one type of selection, i.e. divergent selection, for enabling evolvability. The main argument is that there is a fundamental connection between divergent selection and evolvability (on both the individual and population level that does not hold for typical goal-oriented selection. The conclusion is that selection pressure plays a critical role in realizing the potential for evolvability, and that divergent selection in particular provides a principled mechanism for encouraging evolvability in artificial evolution.

  18. An empirical test of evolutionary theories for reproductive senescence and reproductive effort in the garter snake Thamnophis elegans.

    Science.gov (United States)

    Sparkman, Amanda M; Arnold, Stevan J; Bronikowski, Anne M

    2007-04-07

    Evolutionary theory predicts that differential reproductive effort and rate of reproductive senescence will evolve under different rates of external mortality. We examine the evolutionary divergence of age-specific reproduction in two life-history ecotypes of the western terrestrial garter snake, Thamnophis elegans. We test for the signature of reproductive senescence (decreasing fecundity with age) and increasing reproductive effort with age (increasing reproductive productivity per gram female) in replicate populations of two life-history ecotypes: snakes that grow fast, mature young and have shorter lifespans, and snakes that grow slow, mature late and have long lives. The difference between life-history ecotypes is due to genetic divergence in growth rate. We find (i) reproductive success (live litter mass) increases with age in both ecotypes, but does so more rapidly in the fast-growth ecotype, (ii) reproductive failure increases with age in both ecotypes, but the proportion of reproductive failure to total reproductive output remains invariant, and (iii) reproductive effort remains constant in fast-growth individuals with age, but declines in slow-growth individuals. This illustration of increasing fecundity with age, even at the latest ages, deviates from standard expectations for reproductive senescence, as does the lack of increases in reproductive effort. We discuss our findings in light of recent theories regarding the phenomenon of increased reproduction throughout life in organisms with indeterminate growth and its potential to offset theoretical expectations for the ubiquity of senescence.

  19. divergence, pseudogenes, and

    Indian Academy of Sciences (India)

    Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats ...

  20. Are hotspots of evolutionary potential adequately protected in southern California?

    Science.gov (United States)

    Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

    2008-01-01

    Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

  1. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models.

    Science.gov (United States)

    McCormack, John E; Zellmer, Amanda J; Knowles, L Lacey

    2010-05-01

    The role of ecology in the origin of species has been the subject of long-standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large-scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological-niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution--the Aphelocoma jays--we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.

  2. Evolutionary change in continuous reaction norms

    DEFF Research Database (Denmark)

    Murren, Courtney J; Maclean, Heidi J; Diamond, Sarah E

    2014-01-01

    Understanding the evolution of reaction norms remains a major challenge in ecology and evolution. Investigating evolutionary divergence in reaction norm shapes between populations and closely related species is one approach to providing insights. Here we use a meta-analytic approach to compare...... divergence in reaction norms of closely related species or populations of animals and plants across types of traits and environments. We quantified mean-standardized differences in overall trait means (Offset) and reaction norm shape (including both Slope and Curvature). These analyses revealed...... contributed to the best-fitting models, especially for Offset, Curvature, and the total differences (Total) between reaction norms. Congeneric species had greater differences in reaction norms than populations, and novel environmental conditions increased the differences in reaction norms between populations...

  3. Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

    Directory of Open Access Journals (Sweden)

    Runemark Anna

    2010-09-01

    Full Text Available Abstract Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s ST for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that

  4. 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.

  5. Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns

    Science.gov (United States)

    Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E.

    2016-01-01

    Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this ‘ancient’ fern lineage across the tropics. PMID:27412279

  6. Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns.

    Science.gov (United States)

    Ramírez-Barahona, Santiago; Barrera-Redondo, Josué; Eguiarte, Luis E

    2016-07-13

    Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics. © 2016 The Author(s).

  7. Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.

    Science.gov (United States)

    Prisilla, A; Prathiviraj, R; Chellapandi, P

    2017-04-01

    Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.

  8. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations.

    Science.gov (United States)

    Tobler, M; Plath, M; Riesch, R; Schlupp, I; Grasse, A; Munimanda, G K; Setzer, C; Penn, D J; Moodley, Y

    2014-05-01

    The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  9. Dike-induced contraction along oceanic and continental divergent plate boundaries

    KAUST Repository

    Trippanera, D.

    2014-10-28

    The axis of divergent plate boundaries shows extension fractures and normal faults at the surface. Here we present evidence of contraction along the axis of the oceanic ridge of Iceland and the continental Main Ethiopian Rift. Contraction is found at the base of the tilted hanging wall of dilational normal faults, balancing part of their extension. Our experiments suggest that these structures result from dike emplacement. Multiple dike injection induces subsidence above and uplift to the sides of the dikes; the transition in between is accommodated by reverse faults and subsequent peripheral inward dipping normal faults. Our results suggest that contraction is a direct product of magma emplacement along divergent plate boundaries, at various scales, marking a precise evolutionary stage and initiating part of the extensional structures (extension fractures and normal faults). Key Points Contraction along divergent plate boundaries results from dike emplacementContraction generates extensional structures along divergent plate boundariesSurface deformation along divergent plate boundaries may be magma induced

  10. Dike-induced contraction along oceanic and continental divergent plate boundaries

    KAUST Repository

    Trippanera, D.; Acocella, V.; Ruch, Joel

    2014-01-01

    The axis of divergent plate boundaries shows extension fractures and normal faults at the surface. Here we present evidence of contraction along the axis of the oceanic ridge of Iceland and the continental Main Ethiopian Rift. Contraction is found at the base of the tilted hanging wall of dilational normal faults, balancing part of their extension. Our experiments suggest that these structures result from dike emplacement. Multiple dike injection induces subsidence above and uplift to the sides of the dikes; the transition in between is accommodated by reverse faults and subsequent peripheral inward dipping normal faults. Our results suggest that contraction is a direct product of magma emplacement along divergent plate boundaries, at various scales, marking a precise evolutionary stage and initiating part of the extensional structures (extension fractures and normal faults). Key Points Contraction along divergent plate boundaries results from dike emplacementContraction generates extensional structures along divergent plate boundariesSurface deformation along divergent plate boundaries may be magma induced

  11. Neocortical development as an evolutionary platform for intragenomic conflict

    Directory of Open Access Journals (Sweden)

    Eric eLewitus

    2013-04-01

    Full Text Available Embryonic development in mammals has evolved a platform for genomic conflict between mothers and embryos and, by extension, between maternal and paternal genomes. The evolutionary interests of the mother and embryo may be maximized through the promotion of sex-chromosome genes and imprinted alleles, resulting in the rapid evolution of postzygotic phenotypes preferential to either the maternal or paternal genome. In eutherian mammals, extraordinary in utero maternal investment in the brain, and neocortex especially, suggests that convergent evolution of an expanded mammalian neocortex along divergent lineages may be explained, in part, by parent-of-origin-linked gene expression arising from parent-offspring conflict. The influence of this conflict on neocortical development and evolution, however, has not been investigated at the genomic level. In this hypothesis and theory article, we provide preliminary evidence for positive selection in humans in the regions of two platforms of intragenomic conflict – chromosomes 15q11-q13 and X – and explore the potential relevance of cis-regulated imprinted domains to neocortical expansion in mammalian evolution. We present the hypothesis that maternal- and paternal-specific pressures on the developing neocortex compete intragenomically to influence neocortical expansion in mammalian evolution.

  12. Rapid diversification of Tragopogon and ecological associates in Eurasia.

    Science.gov (United States)

    Bell, C D; Mavrodiev, E V; Soltis, P S; Calaminus, A K; Albach, D C; Cellinese, N; Garcia-Jacas, N; Soltis, D E

    2012-12-01

    Tragopogon comprises approximately 150 described species distributed throughout Eurasia from Ireland and the UK to India and China with a few species in North Africa. Most of the species diversity is found in Eastern Europe to Western Asia. Previous phylogenetic analyses identified several major clades, generally corresponding to recognized taxonomic sections, although relationships both among these clades and among species within clades remain largely unresolved. These patterns are consistent with rapid diversification following the origin of Tragopogon, and this study addresses the timing and rate of diversification in Tragopogon. Using BEAST to simultaneously estimate a phylogeny and divergence times, we estimate the age of a major split and subsequent rapid divergence within Tragopogon to be ~2.6 Ma (and 1.7-5.4 Ma using various clock estimates). Based on the age estimates obtained with BEAST (HPD 1.7-5.4 Ma) for the origin of crown group Tragopogon and 200 estimated species (to accommodate a large number of cryptic species), the diversification rate of Tragopogon is approximately 0.84-2.71 species/Myr for the crown group, assuming low levels of extinction. This estimate is comparable in rate to a rapid Eurasian radiation in Dianthus (0.66-3.89 species/Myr), which occurs in the same or similar habitats. Using available data, we show that subclades of various plant taxa that occur in the same semi-arid habitats of Eurasia also represent rapid radiations occurring during roughly the same window of time (1.7-5.4 Ma), suggesting similar causal events. However, not all species-rich plant genera from the same habitats diverged at the same time, or at the same tempo. Radiations of several other clades in this same habitat (e.g. Campanula, Knautia, Scabiosa) occurred at earlier dates (45-4.28 Ma). Existing phylogenetic data and diversification estimates therefore indicate that, although some elements of these semi-arid communities radiated during the Plio

  13. Evolutionary history of anglerfishes (Teleostei: Lophiiformes: a mitogenomic perspective

    Directory of Open Access Journals (Sweden)

    Shimazaki Mitsuomi

    2010-02-01

    Full Text Available Abstract Background The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome sequences from 39 lophiiforms (33 newly determined during this study representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation. Results Partitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae. The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep

  14. Segmenting the human genome based on states of neutral genetic divergence.

    Science.gov (United States)

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-03

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  15. Linear energy divergences in Coulomb gauge QCD

    OpenAIRE

    Andrasi, A.

    2011-01-01

    The structure of linear energy divergences is analysed on the example of one graph to 3-loop order. Such dangerous divergences do cancel when all graphs are added, but next to leading divergences do not cancel out.

  16. Attractive evolutionary equilibria

    OpenAIRE

    Roorda, Berend; Joosten, Reinoud

    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 dynamics. For instance, each attractive evolutionarily stable strategy is an attractive evolutionarily stable equilibrium for certain barycentric ray-projection dynamics, and vice versa.

  17. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-07

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Divergent synthesis and optoelectronic properties of oligodiacetylene building blocks

    NARCIS (Netherlands)

    Pilzak, G.S.; Lagen, van B.; Sudhölter, E.J.R.; Zuilhof, H.

    2008-01-01

    A new and divergent synthetic route to oligodiacetylene (ODA) building blocks has been developed via Sonogashira reactions under a reductive atmosphere. These central building blocks provide a new way for rapid preparation of long ODAs. In addition, we report on their optoelectronic properties which

  19. Boiling flow through diverging microchannel

    Indian Academy of Sciences (India)

    such systems, for small pressure drop penalty and with good flow stability. .... ied the effect of divergence angle on mean and transient pressure/temperature distribution and .... supplying a fixed voltage and current using a power source meter.

  20. Atmospheric horizontal divergence and diffusion

    International Nuclear Information System (INIS)

    Castans, M.

    1981-01-01

    The action of horizontal divergence on diffusion near the ground is established through.a very simple flow model. The shape of the well-known Pasquill-Gifford-Turner curves, that apparently take account in some way of divergence, is justified. The possibility of explaining the discre--pancies between the conventional straight line model and experimental results, mainly under low-wind-speed satable conditions, is considered. Some hints for further research are made. (auth.)

  1. Divergence of gene body DNA methylation and evolution of plant duplicate genes.

    Directory of Open Access Journals (Sweden)

    Jun Wang

    Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

  2. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

    Science.gov (United States)

    Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

    2014-11-01

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Evolutionary Turnover of Kinetochore Proteins: A Ship of Theseus?

    Science.gov (United States)

    Drinnenberg, Ines A; Henikoff, Steven; Malik, Harmit S

    2016-07-01

    The kinetochore is a multiprotein complex that mediates the attachment of a eukaryotic chromosome to the mitotic spindle. The protein composition of kinetochores is similar across species as divergent as yeast and human. However, recent findings have revealed an unexpected degree of compositional diversity in kinetochores. For example, kinetochore proteins that are essential in some species have been lost in others, whereas new kinetochore proteins have emerged in other lineages. Even in lineages with similar kinetochore composition, individual kinetochore proteins have functionally diverged to acquire either essential or redundant roles. Thus, despite functional conservation, the repertoire of kinetochore proteins has undergone recurrent evolutionary turnover. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids.

    Science.gov (United States)

    Breitkopf, Hendrik; Onstein, Renske E; Cafasso, Donata; Schlüter, Philipp M; Cozzolino, Salvatore

    2015-07-01

    Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  5. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... ... of events: 'Entities that were capable of independent replication ... There have been many major evolutionary events that this definition of .... selection at level x to exclusive selection at x – will probably require a multiplicity ...

  6. Evolutionary relationships among Astroviridae

    NARCIS (Netherlands)

    Lukashov, Vladimir V.; Goudsmit, Jaap

    2002-01-01

    To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other

  7. String loop divergences and effective lagrangians

    International Nuclear Information System (INIS)

    Fischler, W.; Klebanov, I.; Susskind, L.

    1988-01-01

    We isolate logarithmic divergences from bosonic string amplitudes on a disc. These divergences are compared with 'tadpole' divergences in the effective field theory, with a covariant cosmological term implied by the counting of string coupling constants. We find an inconsistency between the two. This might be a problem in eliminating divergences from the bosonic string. (orig.)

  8. Semantic search during divergent thinking.

    Science.gov (United States)

    Hass, Richard W

    2017-09-01

    Divergent thinking, as a method of examining creative cognition, has not been adequately analyzed in the context of modern cognitive theories. This article casts divergent thinking responding in the context of theories of memory search. First, it was argued that divergent thinking tasks are similar to semantic fluency tasks, but are more constrained, and less well structured. Next, response time distributions from 54 participants were analyzed for temporal and semantic clustering. Participants responded to two prompts from the alternative uses test: uses for a brick and uses for a bottle, for two minutes each. Participants' cumulative response curves were negatively accelerating, in line with theories of search of associative memory. However, results of analyses of semantic and temporal clustering suggested that clustering is less evident in alternative uses responding compared to semantic fluency tasks. This suggests either that divergent thinking responding does not involve an exhaustive search through a clustered memory trace, but rather that the process is more exploratory, yielding fewer overall responses that tend to drift away from close associates of the divergent thinking prompt. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Phylogeography of Rhodiola kirilowii (Crassulaceae: a story of Miocene divergence and quaternary expansion.

    Directory of Open Access Journals (Sweden)

    Jian-Qiang Zhang

    Full Text Available The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP, and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima's D and Fu's FS values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour

  10. Divergence of recently duplicated M{gamma}-type MADS-box genes in Petunia.

    Science.gov (United States)

    Bemer, Marian; Gordon, Jonathan; Weterings, Koen; Angenent, Gerco C

    2010-02-01

    The MADS-box transcription factor family has expanded considerably in plants via gene and genome duplications and can be subdivided into type I and MIKC-type genes. The two gene classes show a different evolutionary history. Whereas the MIKC-type genes originated during ancient genome duplications, as well as during more recent events, the type I loci appear to experience high turnover with many recent duplications. This different mode of origin also suggests a different fate for the type I duplicates, which are thought to have a higher chance to become silenced or lost from the genome. To get more insight into the evolution of the type I MADS-box genes, we isolated nine type I genes from Petunia, which belong to the Mgamma subclass, and investigated the divergence of their coding and regulatory regions. The isolated genes could be subdivided into two categories: two genes were highly similar to Arabidopsis Mgamma-type genes, whereas the other seven genes showed less similarity to Arabidopsis genes and originated more recently. Two of the recently duplicated genes were found to contain deleterious mutations in their coding regions, and expression analysis revealed that a third paralog was silenced by mutations in its regulatory region. However, in addition to the three genes that were subjected to nonfunctionalization, we also found evidence for neofunctionalization of one of the Petunia Mgamma-type genes. Our study shows a rapid divergence of recently duplicated Mgamma-type MADS-box genes and suggests that redundancy among type I paralogs may be less common than expected.

  11. Evolutionary Multiplayer Games

    OpenAIRE

    Gokhale, Chaitanya S.; Traulsen, Arne

    2014-01-01

    Evolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g.\\ increase less than linear wi...

  12. Infrastructure system restoration planning using evolutionary algorithms

    Science.gov (United States)

    Corns, Steven; Long, Suzanna K.; Shoberg, Thomas G.

    2016-01-01

    This paper presents an evolutionary algorithm to address restoration issues for supply chain interdependent critical infrastructure. Rapid restoration of infrastructure after a large-scale disaster is necessary to sustaining a nation's economy and security, but such long-term restoration has not been investigated as thoroughly as initial rescue and recovery efforts. A model of the Greater Saint Louis Missouri area was created and a disaster scenario simulated. An evolutionary algorithm is used to determine the order in which the bridges should be repaired based on indirect costs. Solutions were evaluated based on the reduction of indirect costs and the restoration of transportation capacity. When compared to a greedy algorithm, the evolutionary algorithm solution reduced indirect costs by approximately 12.4% by restoring automotive travel routes for workers and re-establishing the flow of commodities across the three rivers in the Saint Louis area.

  13. Hyperreal Numbers for Infinite Divergent Series

    OpenAIRE

    Bartlett, Jonathan

    2018-01-01

    Treating divergent series properly has been an ongoing issue in mathematics. However, many of the problems in divergent series stem from the fact that divergent series were discovered prior to having a number system which could handle them. The infinities that resulted from divergent series led to contradictions within the real number system, but these contradictions are largely alleviated with the hyperreal number system. Hyperreal numbers provide a framework for dealing with divergent serie...

  14. 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.

  15. Chained Kullback-Leibler Divergences

    Science.gov (United States)

    Pavlichin, Dmitri S.; Weissman, Tsachy

    2017-01-01

    We define and characterize the “chained” Kullback-Leibler divergence minw D(p‖w) + D(w‖q) minimized over all intermediate distributions w and the analogous k-fold chained K-L divergence min D(p‖wk−1) + … + D(w2‖w1) + D(w1‖q) minimized over the entire path (w1,…,wk−1). This quantity arises in a large deviations analysis of a Markov chain on the set of types – the Wright-Fisher model of neutral genetic drift: a population with allele distribution q produces offspring with allele distribution w, which then produce offspring with allele distribution p, and so on. The chained divergences enjoy some of the same properties as the K-L divergence (like joint convexity in the arguments) and appear in k-step versions of some of the same settings as the K-L divergence (like information projections and a conditional limit theorem). We further characterize the optimal k-step “path” of distributions appearing in the definition and apply our findings in a large deviations analysis of the Wright-Fisher process. We make a connection to information geometry via the previously studied continuum limit, where the number of steps tends to infinity, and the limiting path is a geodesic in the Fisher information metric. Finally, we offer a thermodynamic interpretation of the chained divergence (as the rate of operation of an appropriately defined Maxwell’s demon) and we state some natural extensions and applications (a k-step mutual information and k-step maximum likelihood inference). We release code for computing the objects we study. PMID:29130024

  16. Remarkable ancient divergences amongst neglected lorisiform primates

    Science.gov (United States)

    Nekaris, K. Anne‐Isola; Perkin, Andrew; Bearder, Simon K.; Pimley, Elizabeth R.; Schulze, Helga; Streicher, Ulrike; Nadler, Tilo; Kitchener, Andrew; Zischler, Hans; Zinner, Dietmar; Roos, Christian

    2015-01-01

    Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub‐Saharan Africa and South/South‐East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. © 2015 The Linnean Society of London PMID:26900177

  17. Evolutionary public health: introducing the concept.

    Science.gov (United States)

    Wells, Jonathan C K; Nesse, Randolph M; Sear, Rebecca; Johnstone, Rufus A; Stearns, Stephen C

    2017-07-29

    The emerging discipline of evolutionary medicine is breaking new ground in understanding why people become ill. However, the value of evolutionary analyses of human physiology and behaviour is only beginning to be recognised in the field of public health. Core principles come from life history theory, which analyses the allocation of finite amounts of energy between four competing functions-maintenance, growth, reproduction, and defence. A central tenet of evolutionary theory is that organisms are selected to allocate energy and time to maximise reproductive success, rather than health or longevity. Ecological interactions that influence mortality risk, nutrient availability, and pathogen burden shape energy allocation strategies throughout the life course, thereby affecting diverse health outcomes. Public health interventions could improve their own effectiveness by incorporating an evolutionary perspective. In particular, evolutionary approaches offer new opportunities to address the complex challenges of global health, in which populations are differentially exposed to the metabolic consequences of poverty, high fertility, infectious diseases, and rapid changes in nutrition and lifestyle. The effect of specific interventions is predicted to depend on broader factors shaping life expectancy. Among the important tools in this approach are mathematical models, which can explore probable benefits and limitations of interventions in silico, before their implementation in human populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. 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.

  19. Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion.

    Science.gov (United States)

    Sotiras, Aristeidis; Toledo, Jon B; Gur, Raquel E; Gur, Ruben C; Satterthwaite, Theodore D; Davatzikos, Christos

    2017-03-28

    During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8-20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization.

  20. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

  1. Applying Evolutionary Anthropology

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  2. EDEN: evolutionary dynamics within environments

    Science.gov (United States)

    Münch, Philipp C.; Stecher, Bärbel; McHardy, Alice C.

    2017-01-01

    Abstract Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact alice.mchardy@helmholtz-hzi.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637301

  3. Archaeogenetics in evolutionary medicine.

    Science.gov (United States)

    Bouwman, Abigail; Rühli, Frank

    2016-09-01

    Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.

  4. 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...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...

  5. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

    Science.gov (United States)

    Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

    2016-08-01

    A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

  6. Divergence with gene flow across a speciation continuum of Heliconius butterflies.

    Science.gov (United States)

    Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

    2015-09-24

    A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

  7. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  8. Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

    Science.gov (United States)

    Ravinet, Mark; Harrod, Chris; Eizaguirre, Christophe; Prodöhl, Paulo A

    2014-06-01

    Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.

  9. Demography and genome divergence of lake and stream populations of an East African cichlid fish.

    Science.gov (United States)

    Egger, Bernd; Roesti, Marius; Böhne, Astrid; Roth, Olivia; Salzburger, Walter

    2017-10-01

    Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site-associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome-wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re-evaluate the independence of replicate lake-stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake-stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake-stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations. © 2017 John Wiley & Sons Ltd.

  10. Divergence time estimates and the evolution of major lineages in the florideophyte red algae

    Science.gov (United States)

    Yang, Eun Chan; Boo, Sung Min; Bhattacharya, Debashish; Saunders, Gary W.; Knoll, Andrew H.; Fredericq, Suzanne; Graf, Louis; Yoon, Hwan Su

    2016-01-01

    The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817–1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681–879) Ma], Nemaliophycidae [ca. 661 (597–736) Ma], Corallinophycidae [ca. 579 (543–617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442–580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae. PMID:26892537

  11. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    Science.gov (United States)

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  12. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group-level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic

  13. Differential divergences of obligately insect-pathogenic Entomophthora species from fly and aphid hosts.

    Science.gov (United States)

    Jensen, Annette Bruun; Eilenberg, Jørgen; López Lastra, Claudia

    2009-11-01

    Three DNA regions (ITS 1, LSU rRNA and GPD) of isolates from the insect-pathogenic fungus genus Entomophthora originating from different fly (Diptera) and aphid (Hemiptera) host taxa were sequenced. The results documented a large genetic diversity among the fly-pathogenic Entomophthora and only minor differences among aphid-pathogenic Entomophthora. The evolutionary time of divergence of the fly and the aphid host taxa included cannot account for this difference. The host-driven divergence of Entomophthora, therefore, has been much greater in flies than in aphids. Host-range differences or a recent host shift to aphid are possible explanations.

  14. A study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast.

    Science.gov (United States)

    Hagman, Arne; Piškur, Jure

    2015-01-01

    Baker's yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anaerobic and aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125-150 million years ago in the Saccharomyces lineage. The "invention" of overflow metabolism was the first step in the evolution of aerobic fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The "invention" of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to "starve" competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently "invented" as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that were semi-anaerobic.

  15. A study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast.

    Directory of Open Access Journals (Sweden)

    Arne Hagman

    Full Text Available Baker's yeast Saccharomyces cerevisiae rapidly converts sugars to ethanol and carbon dioxide at both anaerobic and aerobic conditions. The later phenomenon is called Crabtree effect and has been described in two forms, long-term and short-term effect. We have previously studied under fully controlled aerobic conditions forty yeast species for their central carbon metabolism and the presence of long-term Crabtree effect. We have also studied ten steady-state yeast cultures, pulsed them with glucose, and followed the central carbon metabolism and the appearance of ethanol at dynamic conditions. In this paper we analyzed those wet laboratory data to elucidate possible mechanisms that determine the fate of glucose in different yeast species that cover approximately 250 million years of evolutionary history. We determine overflow metabolism to be the fundamental mechanism behind both long- and short-term Crabtree effect, which originated approximately 125-150 million years ago in the Saccharomyces lineage. The "invention" of overflow metabolism was the first step in the evolution of aerobic fermentation in yeast. It provides a general strategy to increase energy production rates, which we show is positively correlated to growth. The "invention" of overflow has also simultaneously enabled rapid glucose consumption in yeast, which is a trait that could have been selected for, to "starve" competitors in nature. We also show that glucose repression of respiration is confined mainly among S. cerevisiae and closely related species that diverged after the whole genome duplication event, less than 100 million years ago. Thus, glucose repression of respiration was apparently "invented" as a second step to further increase overflow and ethanol production, to inhibit growth of other microbes. The driving force behind the initial evolutionary steps was most likely competition with other microbes to faster consume and convert sugar into biomass, in niches that

  16. On Hölder Projective Divergences

    KAUST Repository

    Nielsen, Frank

    2017-03-16

    We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

  17. On Hölder Projective Divergences

    KAUST Repository

    Nielsen, Frank; Sun, Ke; Marchand-Maillet, Stephane

    2017-01-01

    We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

  18. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  19. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these

  20. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-10-01

    From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Editorial overview: Evolutionary psychology

    NARCIS (Netherlands)

    Gangestad, S.W.; Tybur, J.M.

    2016-01-01

    Functional approaches in psychology - which ask what behavior is good for - are almost as old as scientific psychology itself. Yet sophisticated, generative functional theories were not possible until developments in evolutionary biology in the mid-20th century. Arising in the last three decades,

  2. Biochemistry and evolutionary biology

    Indian Academy of Sciences (India)

    Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the ...

  3. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Hindi and English. Port 1. Resonance, Vo1.7 ... they use. Of course, many evolutionary biologists do work with fossils or DNA, or both, but there are also large numbers of ... The first major division that I like to make is between studies focussed ...

  4. Learning: An Evolutionary Analysis

    Science.gov (United States)

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  5. Complex systems, evolutionary planning?

    NARCIS (Netherlands)

    Bertolini, L.; de Roo, G.; Silva, E.A.

    2010-01-01

    Coping with uncertainty is a defining challenge for spatial planners. Accordingly, most spatial planning theories and methods are aimed at reducing uncertainty. However, the question is what should be done when this seems impossible? This chapter proposes an evolutionary interpretation of spatial

  6. 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...

  7. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  8. Computer recognition of divergences in Feynman graphs

    Energy Technology Data Exchange (ETDEWEB)

    Calmet, J

    1973-05-01

    The program described recognizes whether or not a graph is divergent. It determines the kind of the divergences found: vacuum polarizations, electron self energies and vertices. it does not consider infrared divergences. The programming language used is REDUCE. A LISP version is also available. The nature of the divergences and their counter terms was extensively used to write down this program, therefore it is limited to the case of quantum electrodynamics. (auth)

  9. Genetic divergence of tomato subsamples

    Directory of Open Access Journals (Sweden)

    André Pugnal Mattedi

    2014-02-01

    Full Text Available Understanding the genetic variability of a species is crucial for the progress of a genetic breeding program and requires characterization and evaluation of germplasm. This study aimed to characterize and evaluate 101 tomato subsamples of the Salad group (fresh market and two commercial controls, one of the Salad group (cv. Fanny and another of the Santa Cruz group (cv. Santa Clara. Four experiments were conducted in a randomized block design with three replications and five plants per plot. The joint analysis of variance was performed and characteristics with significant complex interaction between control and experiment were excluded. Subsequently, the multicollinearity diagnostic test was carried out and characteristics that contributed to severe multicollinearity were excluded. The relative importance of each characteristics for genetic divergence was calculated by the Singh's method (Singh, 1981, and the less important ones were excluded according to Garcia (1998. Results showed large genetic divergence among the subsamples for morphological, agronomic and organoleptic characteristics, indicating potential for genetic improvement. The characteristics total soluble solids, mean number of good fruits per plant, endocarp thickness, mean mass of marketable fruit per plant, total acidity, mean number of unmarketable fruit per plant, internode diameter, internode length, main stem thickness and leaf width contributed little to the genetic divergence between the subsamples and may be excluded in future studies.

  10. Genome-wide detection of selection and other evolutionary forces

    DEFF Research Database (Denmark)

    Xu, Zhuofei; Zhou, Rui

    2015-01-01

    As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed...... to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome...

  11. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B.; Andersen, E.S.; Damgaard, C.

    2004-01-01

    Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

  12. Genetic and evolutionary analysis of the Drosophila larval neuromuscular junction

    Science.gov (United States)

    Campbell, Megan

    Although evolution of brains and behaviors is of fundamental biological importance, we lack comprehensive understanding of the general principles governing these processes or the specific mechanisms and molecules through which the evolutionary changes are effected. Because synapses are the basic structural and functional units of nervous systems, one way to address these problems is to dissect the genetic and molecular pathways responsible for morphological evolution of a defined synapse. I have undertaken such an analysis by examining morphology of the larval neuromuscular junction (NMJ) in wild caught D. melanogaster as well as in over 20 other species of Drosophila. Whereas variation in NMJ morphology within a species is limited, I discovered a surprisingly extensive variation among different species. Compared with evolution of other morphological traits, NMJ morphology appears to be evolving very rapidly. Moreover, my data indicate that natural selection rather than genetic drift is primarily responsible for evolution of NMJ morphology. To dissect underlying molecular mechanisms that may govern NMJ growth and evolutionary divergence, I focused on a naturally occurring variant in D. melanogaster that causes NMJ overgrowth. I discovered that the variant mapped to Mob2, a gene encoding a kinase adapter protein originally described in yeast as a member of the Mitotic Exit Network (MEN). I have subsequently examined mutations in the Drosophila orthologs of all the core components of the yeast MEN and found that all of them function as part of a common pathway that acts presynaptically to negatively regulate NMJ growth. As in the regulation of yeast cytokinesis, these components of the MEN appear to act ultimately by regulating actin dynamics during the process of bouton growth and division. These studies have thus led to the discovery of an entirely new role for the MEN---regulation of synaptic growth---that is separate from its function in cell division. This work

  13. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts

    Science.gov (United States)

    Wood, Dustin A.; Vandergast, Amy G.; Barr, Kelly R.; Inman, Richard D.; Esque, Todd C.; Nussear, Kenneth E.; Fisher, Robert N.

    2013-01-01

    Aim: We explored lineage diversification within desert-dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre-Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location: Mojave, Colorado, and Sonoran Deserts, USA. Methods: We analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra-population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results: In seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions: Most of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long-term preservation of species-level biodiversity would

  14. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

    Science.gov (United States)

    Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A

    2016-07-01

    Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

  15. Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

    Science.gov (United States)

    Ciofi, C.; Beaumont, M. A.; Swingland, I. R.; Bruford, M. W.

    1999-01-01

    In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world's largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.

  16. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  17. Statistical inference based on divergence measures

    CERN Document Server

    Pardo, Leandro

    2005-01-01

    The idea of using functionals of Information Theory, such as entropies or divergences, in statistical inference is not new. However, in spite of the fact that divergence statistics have become a very good alternative to the classical likelihood ratio test and the Pearson-type statistic in discrete models, many statisticians remain unaware of this powerful approach.Statistical Inference Based on Divergence Measures explores classical problems of statistical inference, such as estimation and hypothesis testing, on the basis of measures of entropy and divergence. The first two chapters form an overview, from a statistical perspective, of the most important measures of entropy and divergence and study their properties. The author then examines the statistical analysis of discrete multivariate data with emphasis is on problems in contingency tables and loglinear models using phi-divergence test statistics as well as minimum phi-divergence estimators. The final chapter looks at testing in general populations, prese...

  18. Introduction to Evolutionary Algorithms

    CERN Document Server

    Yu, Xinjie

    2010-01-01

    Evolutionary algorithms (EAs) are becoming increasingly attractive for researchers from various disciplines, such as operations research, computer science, industrial engineering, electrical engineering, social science, economics, etc. This book presents an insightful, comprehensive, and up-to-date treatment of EAs, such as genetic algorithms, differential evolution, evolution strategy, constraint optimization, multimodal optimization, multiobjective optimization, combinatorial optimization, evolvable hardware, estimation of distribution algorithms, ant colony optimization, particle swarm opti

  19. Evolutionary games on graphs

    Science.gov (United States)

    Szabó, György; Fáth, Gábor

    2007-07-01

    Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

  20. Evolutionary mysteries in meiosis.

    Science.gov (United States)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

  1. Asymmetric Evolutionary Games

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

  2. Ultraviolet divergences and supersymmetric theories

    International Nuclear Information System (INIS)

    Sagnotti, A.

    1984-09-01

    This article is closely related to the one by Ferrara in these same Proceedings. It deals with what is perhaps the most fascinating property of supersymmetric theories, their improved ultraviolet behavior. My aim here is to present a survey of the state of the art as of August, 1984, and a somewhat more detailed discussion of the breakdown of the superspace power-counting beyond N = 2 superfields. A method is also described for simplifying divergence calculations that uses the locality of subtracted Feynman integrals. 74 references

  3. Ultraviolet divergences of Einstein gravity

    International Nuclear Information System (INIS)

    Goroff, M.H.

    1986-01-01

    The author discuss a two-loop calculation showing that the S matrix of Einstein's theory of gravity contains nonrenormalizable ultraviolet divergences in four dimension. The author discusses the calculation in both background field and normal field theory. The author describes a new method for dealing with ghost fields in gauge theories by combining them with suitable extensions of the gauge fields in higher dimensions. The author shows how using subtracted integrals in the calculation of higher loop graphs simplifies the calculation in the background field method by eliminating the need for mixed counterterms. Finally, the author makes some remarks about the implications of the result for supergravity theories

  4. Ground state energies from converging and diverging power series expansions

    International Nuclear Information System (INIS)

    Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E.; Su, Q.; Grobe, R.

    2016-01-01

    It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

  5. Ground state energies from converging and diverging power series expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E., E-mail: eugene-stefanovich@usa.net; Su, Q.; Grobe, R.

    2016-10-15

    It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

  6. Species divergence and phylogenetic variation of ecophysiological traits in lianas and trees.

    Science.gov (United States)

    Rios, Rodrigo S; Salgado-Luarte, Cristian; Gianoli, Ernesto

    2014-01-01

    The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [A(max)], dark respiration rate [R(d)], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that R(d) evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for R(d), while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. R(d) followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for A(max). R(d) may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades.

  7. The four cornerstones of Evolutionary Toxicology.

    Science.gov (United States)

    Bickham, John W

    2011-05-01

    Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © Springer Science+Business Media, LLC 2011

  8. Differential Survival between Visual Environments Supports a Role of Divergent Sensory Drive in Cichlid Fish Speciation.

    Science.gov (United States)

    Maan, Martine E; Seehausen, Ole; Groothuis, Ton G G

    2017-01-01

    Identifying the selective forces that initiate ecological speciation is a major challenge in evolutionary biology. Sensory drive has been implicated in speciation in various taxa, largely based on phenotype-environment correlations and signatures of selection in sensory genes. Here, we present a reciprocal transplant experiment revealing species differences in performance in alternative visual environments, consistent with speciation by divergent sensory drive. The closely related cichlids Pundamilia pundamilia and Pundamilia nyererei inhabit different visual environments in Lake Victoria and show associated differences in visual system properties. Mimicking the two light environments in the laboratory, we find a substantial reduction in survival of both species when reared in the other species' visual environment. This implies that the observed differences in Pundamilia color vision are indeed adaptive and substantiates the implicit assumption in sensory drive speciation models that divergent environmental selection is strong enough to drive divergence in sensory properties.

  9. The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

    Directory of Open Access Journals (Sweden)

    Eichler Evan E

    2008-08-01

    Full Text Available Abstract Background It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs. This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements. Results Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

  10. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

    Science.gov (United States)

    Sachdeva, Himani; Barton, Nicholas H

    2017-06-01

    Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  11. Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish.

    Science.gov (United States)

    Brauer, Chris J; Unmack, Peter J; Beheregaray, Luciano B

    2017-12-01

    Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations. © 2017 John Wiley & Sons Ltd.

  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. 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

  14. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    of population performance will increase in frequency. Yield, one of the fundamental agronomic variables, is not an individual, but a population characteristic. A farmer wants a high yield per hectare; he is not interested in the performance of individual plants. When individual selection and population...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  15. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  16. Divergent thinking and constructing episodic simulations.

    Science.gov (United States)

    Addis, Donna Rose; Pan, Ling; Musicaro, Regina; Schacter, Daniel L

    2016-01-01

    Divergent thinking likely plays an important role in simulating autobiographical events. We investigated whether divergent thinking is differentially associated with the ability to construct detailed imagined future and imagined past events as opposed to recalling past events. We also examined whether age differences in divergent thinking might underlie the reduced episodic detail generated by older adults. The richness of episodic detail comprising autobiographical events in young and older adults was assessed using the Autobiographical Interview. Divergent thinking abilities were measured using the Alternative Uses Task. Divergent thinking was significantly associated with the amount of episodic detail for imagined future events. Moreover, while age was significantly associated with imagined episodic detail, this effect was strongly related to age-related changes in episodic retrieval rather than divergent thinking.

  17. Molecular cloning, functional characterization, and evolutionary analysis of vitamin D receptors isolated from basal vertebrates.

    Directory of Open Access Journals (Sweden)

    Erin M Kollitz

    Full Text Available The vertebrate genome is a result of two rapid and successive rounds of whole genome duplication, referred to as 1R and 2R. Furthermore, teleost fish have undergone a third whole genome duplication (3R specific to their lineage, resulting in the retention of multiple gene paralogs. The more recent 3R event in teleosts provides a unique opportunity to gain insight into how genes evolve through specific evolutionary processes. In this study we compare molecular activities of vitamin D receptors (VDR from basal species that diverged at key points in vertebrate evolution in order to infer derived and ancestral VDR functions of teleost paralogs. Species include the sea lamprey (Petromyzon marinus, a 1R jawless fish; the little skate (Leucoraja erinacea, a cartilaginous fish that diverged after the 2R event; and the Senegal bichir (Polypterus senegalus, a primitive 2R ray-finned fish. Saturation binding assays and gel mobility shift assays demonstrate high affinity ligand binding and classic DNA binding characteristics of VDR has been conserved across vertebrate evolution. Concentration response curves in transient transfection assays reveal EC50 values in the low nanomolar range, however maximum transactivational efficacy varies significantly between receptor orthologs. Protein-protein interactions were investigated using co-transfection, mammalian 2-hybrid assays, and mutations of coregulator activation domains. We then combined these results with our previous study of VDR paralogs from 3R teleosts into a bioinformatics analysis. Our results suggest that 1, 25D3 acts as a partial agonist in basal species. Furthermore, our bioinformatics analysis suggests that functional differences between VDR orthologs and paralogs are influenced by differential protein interactions with essential coregulator proteins. We speculate that we may be observing a change in the pharmacodynamics relationship between VDR and 1, 25D3 throughout vertebrate evolution that may

  18. Divergent unprotected peptide macrocyclisation by palladium-mediated cysteine arylation.

    Science.gov (United States)

    Rojas, Anthony J; Zhang, Chi; Vinogradova, Ekaterina V; Buchwald, Nathan H; Reilly, John; Pentelute, Bradley L; Buchwald, Stephen L

    2017-06-01

    Macrocyclic peptides are important therapeutic candidates due to their improved physicochemical properties in comparison to their linear counterparts. Here we detail a method for a divergent macrocyclisation of unprotected peptides by crosslinking two cysteine residues with bis-palladium organometallic reagents. These synthetic intermediates are prepared in a single step from commercially available aryl bis-halides. Two bioactive linear peptides with cysteine residues at i , i + 4 and i , i + 7 positions, respectively, were cyclised to introduce a diverse array of aryl and bi-aryl linkers. These two series of macrocyclic peptides displayed similar linker-dependent lipophilicity, phospholipid affinity, and unique volume of distributions. Additionally, one of the bioactive peptides showed target binding affinity that was predominantly affected by the length of the linker. Collectively, this divergent strategy allowed rapid and convenient access to various aryl linkers, enabling the systematic evaluation of the effect of appending unit on the medicinal properties of macrocyclic peptides.

  19. Genetic divergence analysis in pumpkin

    International Nuclear Information System (INIS)

    Quamruzzaman, A.M.; Moniruzzaman, M.

    2013-01-01

    Genetic divergence among 18 punpkin genotypes was estimated using Mahalanohis's 1) statistic. Altogether lour clusters were formed where cluster I contained the highest number of genotypes (8) and cluster II contained the lowest (I). The highest intra-cluster distance was observed h.ir cluster I (0.83 I) and the lowest for clustcr IV (0.65 I). The highest inter-cluster distance was observed between cluster I and 11(24.346). Cluster II recorded the highest mean for fruit number/plant, TSS, fruit yield and niinitnuiii III cavity length and cavity diameter. Cluster III had the second highest mean for fruit diameter, fruit number/plant, individual unit weight, fruit yield and the fewest number of days to 1st Female flowering, earliness being a desirable trait. These crosses may produce new recombinants with desirable traits. (author)

  20. Divergence operator and related inequalities

    CERN Document Server

    Acosta, Gabriel

    2017-01-01

    This Brief is mainly devoted to two classical and related results: the existence of a right inverse of the divergence operator and the so-called Korn Inequalities. It is well known that both results are fundamental tools in the analysis of some classic differential equations, particularly in those arising in fluid dynamics and elasticity. Several connections between these two topics and improved Poincaré inequalities are extensively treated. From simple key ideas the book is growing smoothly in complexity. Beginning with the study of these problems on star-shaped domains the arguments are extended first to John domains and then to Hölder α domains where the need of weighted spaces arises naturally. In this fashion, the authors succeed in presenting in an unified and concise way several classic and recent developments in the field. These features certainly makes this Brief useful for students, post-graduate students, and researchers as well.

  1. Ramanujan summation of divergent series

    CERN Document Server

    Candelpergher, Bernard

    2017-01-01

    The aim of this monograph is to give a detailed exposition of the summation method that Ramanujan uses in Chapter VI of his second Notebook. This method, presented by Ramanujan as an application of the Euler-MacLaurin formula, is here extended using a difference equation in a space of analytic functions. This provides simple proofs of theorems on the summation of some divergent series. Several examples and applications are given. For numerical evaluation, a formula in terms of convergent series is provided by the use of Newton interpolation. The relation with other summation processes such as those of Borel and Euler is also studied. Finally, in the last chapter, a purely algebraic theory is developed that unifies all these summation processes. This monograph is aimed at graduate students and researchers who have a basic knowledge of analytic function theory.

  2. Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

    Science.gov (United States)

    Sato, Yukuto; Tsukamoto, Katsumi; Nishida, Mutsumi

    2015-01-01

    Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post–teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70–80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis. PMID:26578810

  3. Beam divergence scaling in neutral beam injectors

    International Nuclear Information System (INIS)

    Holmes, A.J.T.

    1976-01-01

    One of the main considerations in the design of neutral beam injectors is to monimize the divergence of the primary ion beam and hence maximize the beam transport and minimize the input of thermal gas. Experimental measurements of the divergence of a cylindrical ion beam are presented and these measurements are used to analyze the major components of ion beam divergence, namely: space charge expansion, gas-ion scattering, emittance and optical aberrations. The implication of these divergence components in the design of a neutral beam injector system is discussed and a method of maximizing the beam current is described for a given area of source plasma

  4. Guises and disguises of quadratic divergences

    Energy Technology Data Exchange (ETDEWEB)

    Cherchiglia, A.L., E-mail: adriano@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Vieira, A.R., E-mail: arvieira@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Hiller, Brigitte, E-mail: brigitte@teor.fis.uc.pt [Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra (Portugal); Baêta Scarpelli, A.P., E-mail: scarpelli.apbs@dpf.gov.br [Setor Técnico-Científico, Departamento de Polícia Federal, Rua Hugo D’Antola, 95 - Lapa, São Paulo (Brazil); Sampaio, Marcos, E-mail: marcos.sampaio@durham.ac.uk [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Centre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road Durham DH1 3LE (United Kingdom)

    2014-12-15

    In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.

  5. Divergence Palsy due to Divalproex and Oxcarbazepine.

    Science.gov (United States)

    Bouffard, Marc Albert; Caplan, Louis R; Torun, Nurhan

    This case series is the first to describe divergence palsy as an adverse effect of antiepileptic drug use. Diplopia is a common adverse effect of antiepileptic drugs, but no explanatory motility deficit has ever been reported. We present 2 patients, 1 on oxcarbazepine and 1 on divalproex, each with a normal examination result between spells and divergency palsy when symptomatic. Discontinuation of the antiepileptic medication led to resolution of the episodes in both cases. Rechallenge with the offending agent after washout in one patient resulted in recurrence of diplopia and divergence palsy, both resolving after subsequent withdrawal of the antiepileptic. Antiepileptic drugs may cause divergence palsy.

  6. Practical advantages of evolutionary computation

    Science.gov (United States)

    Fogel, David B.

    1997-10-01

    Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.

  7. Evolutionary patterns and processes in the radiation of phyllostomid bats

    Directory of Open Access Journals (Sweden)

    Monteiro Leandro R

    2011-05-01

    Full Text Available Abstract Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores or the relative size of tooth rows and mandibular processes (sanguivores and frugivores, which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya, larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory. Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the

  8. Evolutionary patterns and processes in the radiation of phyllostomid bats

    Science.gov (United States)

    2011-01-01

    Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were

  9. The evolutionary status of symbiotic stars

    International Nuclear Information System (INIS)

    Rudak, B.

    1982-01-01

    The evolutionary relations between symbiotic stars and cataclysmic variables are presented. The symbiotic stars are assumed to be long period detached binaries containing a carbon-oxygen degenerate primary and a red giant losing its mass through a spherically symmetric wind. Such systems can be obtained in Case C evolution, provided a common envelope during a rapid mass transfer phase was not formed. The same way recurrent novae containing a red giant as a secondary component may be produced. The factors influencing the differences between symbiotic stars and nova-type stars are discussed. (Auth.)

  10. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  11. 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.

  12. Ecological and evolutionary drivers of the elevational gradient of diversity.

    Science.gov (United States)

    Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

    2018-05-02

    Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

  13. The evolutionary turnover of recombination hot spots contributes to speciation in mice.

    Science.gov (United States)

    Smagulova, Fatima; Brick, Kevin; Pu, Yongmei; Camerini-Otero, R Daniel; Petukhova, Galina V

    2016-02-01

    Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation. Published by Cold Spring Harbor Laboratory Press.

  14. Evolutionary change in physiological phenotypes along the human lineage.

    Science.gov (United States)

    Vining, Alexander Q; Nunn, Charles L

    2016-01-01

    Research in evolutionary medicine provides many examples of how evolution has shaped human susceptibility to disease. Traits undergoing rapid evolutionary change may result in associated costs or reduce the energy available to other traits. We hypothesize that humans have experienced more such changes than other primates as a result of major evolutionary change along the human lineage. We investigated 41 physiological traits across 50 primate species to identify traits that have undergone marked evolutionary change along the human lineage. We analysed the data using two Bayesian phylogenetic comparative methods. One approach models trait covariation in non-human primates and predicts human phenotypes to identify whether humans are evolutionary outliers. The other approach models adaptive shifts under an Ornstein-Uhlenbeck model of evolution to assess whether inferred shifts are more common on the human branch than on other primate lineages. We identified four traits with strong evidence for an evolutionary increase on the human lineage (amylase, haematocrit, phosphorus and monocytes) and one trait with strong evidence for decrease (neutrophilic bands). Humans exhibited more cases of distinct evolutionary change than other primates. Human physiology has undergone increased evolutionary change compared to other primates. Long distance running may have contributed to increases in haematocrit and mean corpuscular haemoglobin concentration, while dietary changes are likely related to increases in amylase. In accordance with the pathogen load hypothesis, human monocyte levels were increased, but many other immune-related measures were not. Determining the mechanisms underlying conspicuous evolutionary change in these traits may provide new insights into human disease. The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

  15. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Science.gov (United States)

    Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

    2009-01-01

    Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials

  16. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2009-07-01

    Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

  17. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    Science.gov (United States)

    Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

    2016-01-01

    Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

  18. gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

    Directory of Open Access Journals (Sweden)

    Mirjana Domazet-Lošo

    Full Text Available Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure, a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos.

  19. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

    OpenAIRE

    Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V

    2007-01-01

    Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...

  20. k-Means Clustering with Hölder Divergences

    KAUST Repository

    Nielsen, Frank; Sun, Ke; Marchand-Maillet, Sté phane

    2017-01-01

    We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

  1. k-Means Clustering with Hölder Divergences

    KAUST Repository

    Nielsen, Frank

    2017-10-24

    We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

  2. Investigating intertemporal choice through experimental evolutionary robotics.

    Science.gov (United States)

    Paglieri, Fabio; Parisi, Domenico; Patacchiola, Massimiliano; Petrosino, Giancarlo

    2015-06-01

    In intertemporal choices, subjects face a trade-off between value and delay: achieving the most valuable outcome requires a longer time, whereas the immediately available option is objectively poorer. Intertemporal choices are ubiquitous, and comparative studies reveal commonalities and differences across species: all species devalue future rewards as a function of delay (delay aversion), yet there is a lot of inter-specific variance in how rapidly such devaluation occurs. These differences are often interpreted in terms of ecological rationality, as depending on environmental factors (e.g., feeding ecology) and the physiological and morphological constraints of different species (e.g., metabolic rate). Evolutionary hypotheses, however, are hard to verify in vivo, since it is difficult to observe precisely enough real environments, not to mention ancestral ones. In this paper, we discuss the viability of an approach based on evolutionary robotics: in Study 1, we evolve robots without a metabolism in five different ecologies; in Study 2, we evolve metabolic robots (i.e., robots that consume energy over time) in three different ecologies. The intertemporal choices of the robots are analyzed both in their ecology and under laboratory conditions. Results confirm the generality of delay aversion and the usefulness of studying intertemporal choice through experimental evolutionary robotics. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Ecological interactions drive evolutionary loss of traits.

    Science.gov (United States)

    Ellers, Jacintha; Kiers, E Toby; Currie, Cameron R; McDonald, Bradon R; Visser, Bertanne

    2012-10-01

    Loss of traits can dramatically alter the fate of species. Evidence is rapidly accumulating that the prevalence of trait loss is grossly underestimated. New findings demonstrate that traits can be lost without affecting the external phenotype, provided the lost function is compensated for by species interactions. This is important because trait loss can tighten the ecological relationship between partners, affecting the maintenance of species interactions. Here, we develop a new perspective on so-called `compensated trait loss' and how this type of trait loss may affect the evolutionary dynamics between interacting organisms. We argue that: (1) the frequency of compensated trait loss is currently underestimated because it can go unnoticed as long as ecological interactions are maintained; (2) by analysing known cases of trait loss, specific factors promoting compensated trait loss can be identified and (3) genomic sequencing is a key way forwards in detecting compensated trait loss. We present a comprehensive literature survey showing that compensated trait loss is taxonomically widespread, can involve essential traits, and often occurs as replicated evolutionary events. Despite its hidden nature, compensated trait loss is important in directing evolutionary dynamics of ecological relationships and has the potential to change facultative ecological interactions into obligatory ones. © 2012 Blackwell Publishing Ltd/CNRS.

  4. Diabetes and Obesity—An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Sylvia Kirchengast

    2017-01-01

    Full Text Available Obesity and type II diabetes belong to the most serious public health challenges of the 21st century. Initially both diseases were typical of affluent societies. Currently both conditions however are increasingly found in low and middle income countries. In future obesity and diabetes are expected to reach epidemic proportions and affect developing countries to a greater extent than developed ones. A globalization of obesity and diabetes is observable. Recently prevalence rates increased, especially in Asia, the Near and Middle East, the Western Pacific region and even in Sub-Saharan Africa. Evolutionary Anthropology tries to understand the evolutionary mechanisms promoting rising obesity and diabetes type II rates. Homo sapiens evolved in an environment quite different from our recent one. Profound changes in physical activity patterns and nutritional habits during the last 10,000 years and increasingly during the last 200 years increased the risk of obesity and diabetes type II. Consequently our recent environment is called “obesogenic”. This mismatch has been recently observable among societies experiencing rapid cultural changes characterized by Westernization and modernization. This review focuses on obesity and type II diabetes from the viewpoint of evolutionary anthropology.

  5. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

    Science.gov (United States)

    Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

    2017-12-02

    Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty

  6. Reduced larval feeding rate is a strong evolutionary correlate of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 85; Issue 3. Reduced larval feeding rate is a strong evolutionary correlate of rapid development in Drosophila melanogaster. M. Rajamani N. Raghavendra ... Keywords. life-history evolution; development time; larval feeding rate; competition; tradeoffs; Drosophila melanogaster.

  7. Does the evolutionary conservation of microsatellite loci imply function?

    Energy Technology Data Exchange (ETDEWEB)

    Shriver, M.D.; Deka, R.; Ferrell, R.E. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  8. Complexity in Evolutionary Processes

    International Nuclear Information System (INIS)

    Schuster, P.

    2010-01-01

    Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)

  9. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  10. 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.

  11. The fossilized birth–death process for coherent calibration of divergence-time estimates

    Science.gov (United States)

    Heath, Tracy A.; Huelsenbeck, John P.; Stadler, Tanja

    2014-01-01

    Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data—most commonly, fossil age estimates—are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the “fossilized birth–death” (FBD) process—a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene. PMID:25009181

  12. Differential paralog divergence modulates genome evolution across yeast species.

    Directory of Open Access Journals (Sweden)

    Monica R Sanchez

    2017-02-01

    Full Text Available Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200-500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution.

  13. Lexicographic presentation of grammatical divergence in Sesotho ...

    African Journals Online (AJOL)

    Relying on existing insights from the field of theoretical lexicography this article gives an innovative application to the relation of divergence by introducing the notion of grammatical divergence. In bilingual dictionaries with English and Sesotho sa Leboa as language pair lexicographers are confronted with a real challenge ...

  14. Divergent Thinking and Age-Related Changes

    Science.gov (United States)

    Palmiero, Massimiliano; Di Giacomo, Dina; Passafiume, Domenico

    2014-01-01

    Aging can affect cognition in different ways. The extent to which aging affects divergent thinking is unclear. In this study, younger and older adults were compared at the performance on the Torrance Test of Creative Thinking in visual and verbal form. Results showed that older adults can think divergently as younger participants, although they…

  15. A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice.

    Science.gov (United States)

    White, Michael A; Ikeda, Akihiro; Payseur, Bret A

    2012-08-01

    The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2-4 million years ago. In this study we used a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period.

  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. Evolutionary economics and industry location

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2003-01-01

    This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both

  18. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

  19. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...

  20. Fixation Time for Evolutionary Graphs

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

  1. Applications of evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx

    2008-01-01

    This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of

  2. Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.

    Science.gov (United States)

    Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

    2008-10-01

    Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.

  3. Remotely Sensed Predictions and In Situ Observations of Lower Congo River Dynamics in Support of Fish Evolutionary Biology

    Science.gov (United States)

    Gardiner, N.; Bjerklie, D. M.

    2011-12-01

    Ongoing research into the evolution of fishes in the lower Congo River suggests a close tie between diversity and hydraulic complexity of flow in the channel. For example, fish populations on each side of the rapids at the head of the lower Congo are within 1.5 km of one another, a distance normally allowing for interbreeding in river systems of comparable size, yet these fish populations show about 5% divergence in their mitochondrial DNA signatures. The proximal reason for this divergence is hydraulic complexity: the speed and turbulence of water moving through the thalweg is a barrier to dispersal for these fishes. Further examination of fish diversity suggests additional correlations of evolutionary divergence of fish clades in association with geomorphic and hydraulic features such as deep pools, extensive systems of rapids, alternating sections of fast and slow current, and recurring whirlpools. Due to prohibitive travel costs, limited field time, and the large geographic domain (approximately 400 river km) of the study area, we undertook a nested set of remote sensing analyses to extract habitat features, geomorphic descriptors, and hydraulic parameters including channel forming velocity, depth, channel roughness, slope, and shear stress. Each of these estimated parameters is mapped for each 1 km segment of the river from the rapids described above to below Inga Falls, a massive cataract where several endemic fish species have been identified. To validate remote sensing estimates, we collected depth and velocity data within the river using gps-enabled sonar measurements from a kayak and Doppler profiling from a motor-driven dugout canoe. Observations corroborate remote sensing estimates of geomorphic parameters. Remote sensing-based estimates of channel-forming velocity and depth were less than the observed maximum channel depth but correlated well with channel properties within 1 km reach segments. This correspondence is notable. The empirical models used

  4. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  5. Divergence of iron metabolism in wild Malaysian yeast.

    Science.gov (United States)

    Lee, Hana N; Mostovoy, Yulia; Hsu, Tiffany Y; Chang, Amanda H; Brem, Rachel B

    2013-12-09

    Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

  6. Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus.

    Science.gov (United States)

    Kindler, Eveline; Arlettaz, Raphaël; Heckel, Gerald

    2012-11-01

    The grasshopper Oedaleus decorus is a thermophilic insect with a large, mostly south-Palaearctic distribution range, stretching from the Mediterranean regions in Europe to Central-Asia and China. In this study, we analyzed the extent of phylogenetic divergence and the recent evolutionary history of the species based on 274 specimens from 26 localities across the distribution range in Europe. Phylogenetic relationships were determined using sequences of two mitochondrial loci (ctr, ND2) with neighbour-joining and Bayesian methods. Additionally, genetic differentiation was analyzed based on mitochondrial DNA and 11 microsatellite markers using F-statistics, model-free multivariate and model-based Bayesian clustering approaches. Phylogenetic analyses detected consistently two highly divergent, allopatrically distributed lineages within O. decorus. The divergence among these Western and Eastern lineages meeting in the region of the Alps was similar to the divergence of each lineage to the sister species O. asiaticus. Genetic differentiation for ctr was extremely high between Western and Eastern grasshopper populations (F(ct)=0.95). Microsatellite markers detected much lower but nevertheless very significant genetic structure among population samples. The nuclear data also demonstrated a case of cytonuclear discordance because the affiliation with mitochondrial lineages was incongruent in Northern Italy. Taken together these results provide evidence of an ancient separation within Oedaleus and either historical introgression of mtDNA among lineages and/or ongoing sex-specific gene flow in this grasshopper. Our study stresses the importance of multilocus approaches for unravelling the history and status of taxa of uncertain evolutionary divergence. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes.

    Science.gov (United States)

    Keogh, J Scott; Scott, Ian A W; Hayes, Christine

    2005-01-01

    It is a well-known phenomenon that islands can support populations of gigantic or dwarf forms of mainland conspecifics, but the variety of explanatory hypotheses for this phenomenon have been difficult to disentangle. The highly venomous Australian tiger snakes (genus Notechis) represent a well-known and extreme example of insular body size variation. They are of special interest because there are multiple populations of dwarfs and giants and the age of the islands and thus the age of the tiger snake populations are known from detailed sea level studies. Most are 5000-7000 years old and all are less than 10,000 years old. Here we discriminate between two competing hypotheses with a molecular phylogeography dataset comprising approximately 4800 bp of mtDNA and demonstrate that populations of island dwarfs and giants have evolved five times independently. In each case the closest relatives of the giant or dwarf populations are mainland tiger snakes, and in four of the five cases, the closest relatives are also the most geographically proximate mainland tiger snakes. Moreover, these body size shifts have evolved extremely rapidly and this is reflected in the genetic divergence between island body size variants and mainland snakes. Within south eastern Australia, where populations of island giants, populations of island dwarfs, and mainland tiger snakes all occur, the maximum genetic divergence is only 0.38%. Dwarf tiger snakes are restricted to prey items that are much smaller than the prey items of mainland tiger snakes and giant tiger snakes are restricted to seasonally available prey items that are up three times larger than the prey items of mainland tiger snakes. We support the hypotheses that these body size shifts are due to strong selection imposed by the size of available prey items, rather than shared evolutionary history, and our results are consistent with the notion that adaptive plasticity also has played an important role in body size shifts. We suggest

  8. Neurogenomics and the role of a large mutational target on rapid behavioral change.

    Science.gov (United States)

    Stanley, Craig E; Kulathinal, Rob J

    2016-11-08

    Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast

  9. Genetic divergence of common bean cultivars.

    Science.gov (United States)

    Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

    2015-09-22

    The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

  10. Verbal and visual divergent thinking in aging.

    Science.gov (United States)

    Palmiero, Massimiliano; Nori, Raffaella; Piccardi, Laura

    2017-04-01

    According to the peak and decline model divergent thinking declines at a specific age (in or after middle age). However, if divergent thinking declines steadily in aging still has to be clarified. In order to explore the age-related changes in verbal and visual divergent thinking, in the present study a sample of 159 participants was divided in five age groups: young adults (18-35 years), middle-aged adults (36-55), young old (56-74), old (75-85) and the oldest-old (86-98). Two divergent thinking tasks were administered: the alternative uses for cardboard boxes, aimed at assessing verbal ideational fluency, flexibility and originality; the completion drawing task, aimed at assessing visual ideational fluency, flexibility and originality. Results showed that after peaking in the young adult group (20-35 years) all components of verbal and visual divergent thinking stabilized in the middle-aged adult group (36-55 years) and then started declining in the young old group (56-75). Interestingly, all components were found to be preserved after declining. Yet, verbal and visual divergent thinking were found at the same extent across age groups, with the exception of visual ideational fluency, that was higher in the young old group, the old group and the oldest-old group than verbal ideational fluency. These results support the idea that divergent thinking does not decline steadily in the elderly. Given that older people can preserve to some extent verbal and visual divergent thinking, these findings have important implications for active aging, that is, divergent thinking might be fostered in aging in order to prevent the cognitive decline.

  11. Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

    Science.gov (United States)

    Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

    2010-03-01

    Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

  12. Chemical evolutionary games.

    Science.gov (United States)

    Aristotelous, Andreas C; Durrett, Richard

    2014-05-01

    Inspired by the use of hybrid cellular automata in modeling cancer, we introduce a generalization of evolutionary games in which cells produce and absorb chemicals, and the chemical concentrations dictate the death rates of cells and their fitnesses. Our long term aim is to understand how the details of the interactions in a system with n species and m chemicals translate into the qualitative behavior of the system. Here, we study two simple 2×2 games with two chemicals and revisit the two and three species versions of the one chemical colicin system studied earlier by Durrett and Levin (1997). We find that in the 2×2 examples, the behavior of our new spatial model can be predicted from that of the mean field differential equation using ideas of Durrett and Levin (1994). However, in the three species colicin model, the system with diffusion does not have the coexistence which occurs in the lattices model in which sites interact with only their nearest neighbors. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Evolutionary and developmental modules.

    Science.gov (United States)

    Lacquaniti, Francesco; Ivanenko, Yuri P; d'Avella, Andrea; Zelik, Karl E; Zago, Myrka

    2013-01-01

    The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates.

  14. Global similarity and local divergence in human and mouse gene co-expression networks

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2006-09-01

    Full Text Available Abstract Background A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species. Results At the global level, the topological properties of the human and mouse gene coexpression networks are, essentially, identical. For instance, both networks have topologies with small-world and scale-free properties as well as closely similar average node degrees, clustering coefficients, and path lengths. However, the human and mouse coexpression networks are highly divergent at the local level: only a small fraction ( Conclusion The dissonance between global versus local network divergence suggests that the interspecies similarity of the global network properties is of limited biological significance, at best, and that the biologically relevant aspects of the architectures of gene coexpression are specific and particular, rather than universal. Nevertheless, there is substantial evolutionary conservation of the local network structure which is compatible with the notion that gene coexpression networks are subject to purifying selection.

  15. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate.

    Science.gov (United States)

    Cutter, Asher D

    2008-04-01

    Accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. Molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. This underlies the notion of a molecular clock. Most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa with poor fossil records must rely on external, potentially inappropriate, calibration with distantly related species. The classic biological models Caenorhabditis and Drosophila are examples of such problem taxa. Here, I illustrate internal calibration in these groups with direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection on the assumption of neutrality of substitutions. Divergence times are inferred among 6 species each of Caenorhabditis and Drosophila, based on thousands of orthologous groups of genes. I propose that the 2 closest known species of Caenorhabditis shared a common ancestor <24 MYA (Caenorhabditis briggsae and Caenorhabditis sp. 5) and that Caenorhabditis elegans diverged from its closest known relatives <30 MYA, assuming that these species pass through at least 6 generations per year; these estimates are much more recent than reported previously with molecular clock calibrations from non-nematode phyla. Dates inferred for the common ancestor of Drosophila melanogaster and Drosophila simulans are roughly concordant with previous studies. These revised dates have important implications for rates of genome evolution and the origin of self-fertilization in Caenorhabditis.

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

    OpenAIRE

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

    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...

  17. Lifespan divergence between social insect castes : Challenges and opportunities for evolutionary theories of aging

    NARCIS (Netherlands)

    Kramer, Boris H; van Doorn, G Sander; Weissing, Franz J; Pen, Ido

    The extraordinarily long lifespans of queens (and kings) in eusocial insects and the strikingly large differences in life expectancy between workers and queens challenge our understanding of the evolution of aging and provide unique opportunities for studying the causes underlying adaptive variation

  18. Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): allopatric divergence and regional expansion

    Czech Academy of Sciences Publication Activity Database

    Jia, Dong-Rui; Liu, T.-L.; Wang, L -Y.; Zhou, D.-W.; Liu, J.-Q.

    2011-01-01

    Roč. 102, č. 1 (2011), s. 37-50 ISSN 0024-4066 Institutional research plan: CEZ:AV0Z60050516 Keywords : coalescent simulations * cpDNA * glacial refugia * orogenic processes * Quaternary glaciation Subject RIV: EF - Botanics Impact factor: 2.193, year: 2011

  19. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness

    DEFF Research Database (Denmark)

    Bozek, Katarzyna; Wei, Yuning; Yan, Zheng

    2014-01-01

    Metabolite concentrations reflect the physiological states of tissues and cells. However, the role of metabolic changes in species evolution is currently unknown. Here, we present a study of metabolome evolution conducted in three brain regions and two non-neural tissues from humans, chimpanzees,...

  20. Evidence of Possible Evolutionary Divergence in Plant Genera Based on Antioxidant Properties

    Science.gov (United States)

    Asai, Elizabeth; Cao, Sharon

    2009-01-01

    The purpose of this investigation was to determine if three Western species of the Panax, Lycium, and Astragalus genera had antibacterial and/or antioxidant properties, and how their properties compared to Eastern herbs in the same genera. The group hypothesized that when compared, the corresponding herbs would have identical antibacterial and…

  1. Two New Measures of Fuzzy Divergence and Their Properties

    Directory of Open Access Journals (Sweden)

    Om Parkash

    2006-06-01

    Full Text Available Several measures of directed divergence and their corresponding measures of fuzzy divergence are available in the exiting literature. Two new measures of fuzzy divergence have been developed and their desirable properties have been discussed.

  2. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  3. Evolutionary movement of centromeres in horse, donkey, and zebra.

    Science.gov (United States)

    Carbone, Lucia; Nergadze, Solomon G; Magnani, Elisa; Misceo, Doriana; Francesca Cardone, Maria; Roberto, Roberta; Bertoni, Livia; Attolini, Carmen; Francesca Piras, Maria; de Jong, Pieter; Raudsepp, Terje; Chowdhary, Bhanu P; Guérin, Gérard; Archidiacono, Nicoletta; Rocchi, Mariano; Giulotto, Elena

    2006-06-01

    Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing considerably, we investigated the role of CR in the karyotype evolution of the genus Equus. Using appropriate panels of BAC clones in FISH experiments, we compared the centromere position and marker order arrangement among orthologous chromosomes of Burchelli's zebra (Equus burchelli), donkey (Equus asinus), and horse (Equus caballus). Surprisingly, at least eight CRs took place during the evolution of this genus. Even more surprisingly, five cases of CR have occurred in the donkey after its divergence from zebra, that is, in a very short evolutionary time (approximately 1 million years). These findings suggest that in some species the CR phenomenon could have played an important role in karyotype shaping, with potential consequences on population dynamics and speciation.

  4. Treatment of divergent expansions in scattering theory

    International Nuclear Information System (INIS)

    Gersten, A.; Malin, S.

    1978-01-01

    One of the biggest obstacles in applying quantum field theory to realistic scattering problems are the divergencies of pertubation expansions for large coupling constants and the divergencies of partial wave expansions for massless particles exchanges. There exist, however, methods of summation of the divergent expansions which can lead to significant application in physics. In this paper we treat the problem of summing such expansions using three methods: (i) a generalization of the Pade approximation to the multivariable case. The suggested definition is unique and preserves unitarity. (ii) The summation of divergent partial waves for arbitrary spins. (iii) A successful application of a series inversion to the 3 P 1 nucleon-nucleon phase shift up to 200 MeV. (orig./WL) [de

  5. Divergence and convergence in nutrition science

    NARCIS (Netherlands)

    Penders, Bart; Spruit, Shannon L.; Sikkema, Jan; Maat, Jan; Schuurbiers, Daan

    2015-01-01

    Nutrigenomics diverged from mainstream nutrition science, ideologically, instrumentally and culturally, due to the establishment of a protective niche. That protection is fading. This article chronicles a case in which convergence between nutrigenomics and nutrition science is pursued. Here we

  6. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus).

    Science.gov (United States)

    Culumber, Zachary W; Tobler, Michael

    2016-02-19

    Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species' geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process.

  7. Phylogeny and evolutionary history of the silkworm.

    Science.gov (United States)

    Sun, Wei; Yu, Hongsong; Shen, Yihong; Banno, Yutaka; Xiang, Zhonghuai; Zhang, Ze

    2012-06-01

    The silkworm, Bombyx mori, played an important role in the old Silk Road that connected ancient Asia and Europe. However, to date, there have been few studies of the origins and domestication of this species using molecular methods. In this study, DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives. All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm. Domestication was estimated to have occurred about 4100 years ago (ya), and the radiation of the different geographic strains of B. mori about 2000 ya. The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya. These estimates are in good agreement with the fossil evidence and historical records. In addition, we show that the domesticated silkworm experienced a population expansion around 1000 ya. The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics, in the genetic analysis of domestic animals, and for understanding the spread of human civilizations.

  8. Utopianism in the British evolutionary synthesis.

    Science.gov (United States)

    Esposito, Maurizio

    2011-03-01

    In this paper I propose a new interpretation of the British evolutionary synthesis. The synthetic work of J. B. S. Haldane, R. A. Fisher and J. S. Huxley was characterized by both an integration of Mendelism and Darwinism and the unification of different biological subdisciplines within a coherent framework. But it must also be seen as a bold and synthetic Darwinian program in which the biosciences served as a utopian blueprint for the progress of civilization. Describing the futuristic visions of these three scientists in their synthetic heydays, I show that, despite a number of important divergences, their biopolitical ideals could be biased toward a controlled and regimented utopian society. Their common ideals entailed a social order where liberal and democratic principles were partially or totally suspended in favor of bioscientific control and planning for the future. Finally, I will argue that the original redefinition of Darwinism that modern synthesizers proposed is a significant historical example of how Darwinism has been used and adapted in different contexts. The lesson I draw from this account is a venerable one: that, whenever we wish to define Darwinism, we need to recognize not only its scientific content and achievements but expose the other traditions and ideologies it may have supported. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  10. Evolutionary disarmament in interspecific competition.

    Science.gov (United States)

    Kisdi, E; Geritz, S A

    2001-12-22

    Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

  11. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    Whiteson, S.; Wiering, M.; van Otterlo, M.

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces,

  12. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    Evolutionary genetics straddles the two fundamental processes of life, ... of the genus Drosophila have been used extensively as model systems in experimental ... issue will prove interesting, informative and thought-provoking for both estab-.

  13. Integrating genomics into evolutionary medicine.

    Science.gov (United States)

    Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

    2014-12-01

    The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Evolutionary robotics – A review

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    a need for a technique by which the robot is able to acquire new behaviours automatically .... Evolutionary robotics is a comparatively new field of robotics research, which seems to ..... Technical Report: PCIA-94-04, Institute of Psychology,.

  15. Decoding divergent series in nonparaxial optics.

    Science.gov (United States)

    Borghi, Riccardo; Gori, Franco; Guattari, Giorgio; Santarsiero, Massimo

    2011-03-15

    A theoretical analysis aimed at investigating the divergent character of perturbative series involved in the study of free-space nonparaxial propagation of vectorial optical beams is proposed. Our analysis predicts a factorial divergence for such series and provides a theoretical framework within which the results of recently published numerical experiments concerning nonparaxial propagation of vectorial Gaussian beams find a meaningful interpretation in terms of the decoding operated on such series by the Weniger transformation.

  16. Evolutionary Game Theory: A Renaissance

    Directory of Open Access Journals (Sweden)

    Jonathan Newton

    2018-05-01

    Full Text Available Economic agents are not always rational or farsighted and can make decisions according to simple behavioral rules that vary according to situation and can be studied using the tools of evolutionary game theory. Furthermore, such behavioral rules are themselves subject to evolutionary forces. Paying particular attention to the work of young researchers, this essay surveys the progress made over the last decade towards understanding these phenomena, and discusses open research topics of importance to economics and the broader social sciences.

  17. Freud: the first evolutionary psychologist?

    Science.gov (United States)

    LeCroy, D

    2000-04-01

    An evolutionary perspective on attachment theory and psychoanalytic theory brings these two fields together in interesting ways. Application of the evolutionary principle of parent-offspring conflict to attachment theory suggests that attachment styles represent context-sensitive, evolved (adaptive) behaviors. In addition, an emphasis on offspring counter-strategies to adult reproductive strategies leads to consideration of attachment styles as overt manifestations of psychodynamic mediating processes, including the defense mechanisms of repression and reaction formation.

  18. Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change

    Science.gov (United States)

    Egan, Ashley N; Crandall, Keith A

    2008-01-01

    Background Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC). We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1) testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2) investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification. Results NAm Psoraleeae represents a recent, rapid radiation with several genera originating during the Pleistocene, 1 to 2 million years ago. A shift in diversification rate is supported by both methods with a 2.67-fold increase suggested around 2 million years ago followed by a 8.73-fold decrease 440,000 years ago. The hypothesis that a climate regime shift from mesic to xeric habitats drove increased diversification in affected taxa was not supported. Timing of the diversification rate increase supports the hypothesis that glaciation-induced climate changes during the Quaternary influenced diversification of the group. Nonrandom spatial diversification also exists, with greater species richness in the American Southwest. Conclusion This study outlines NAm Psoraleeae as a model example of a recent, rapid

  19. Divergence and diversification in North American Psoraleeae (Fabaceae due to climate change

    Directory of Open Access Journals (Sweden)

    Crandall Keith A

    2008-12-01

    Full Text Available Abstract Background Past studies in the legume family (Fabaceae have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC. We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1 testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2 investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification. Results NAm Psoraleeae represents a recent, rapid radiation with several genera originating during the Pleistocene, 1 to 2 million years ago. A shift in diversification rate is supported by both methods with a 2.67-fold increase suggested around 2 million years ago followed by a 8.73-fold decrease 440,000 years ago. The hypothesis that a climate regime shift from mesic to xeric habitats drove increased diversification in affected taxa was not supported. Timing of the diversification rate increase supports the hypothesis that glaciation-induced climate changes during the Quaternary influenced diversification of the group. Nonrandom spatial diversification also exists, with greater species richness in the American Southwest. Conclusion This study outlines NAm Psoraleeae as a model example

  20. Collinearity, convergence and cancelling infrared divergences

    International Nuclear Information System (INIS)

    Lavelle, Martin; McMullan, David

    2006-01-01

    The Lee-Nauenberg theorem is a fundamental quantum mechanical result which provides the standard theoretical response to the problem of collinear and infrared divergences. Its argument, that the divergences due to massless charged particles can be removed by summing over degenerate states, has been successfully applied to systems with final state degeneracies such as LEP processes. If there are massless particles in both the initial and final states, as will be the case at the LHC, the theorem requires the incorporation of disconnected diagrams which produce connected interference effects at the level of the cross-section. However, this aspect of the theory has never been fully tested in the calculation of a cross-section. We show through explicit examples that in such cases the theorem introduces a divergent series of diagrams and hence fails to cancel the infrared divergences. It is also demonstrated that the widespread practice of treating soft infrared divergences by the Bloch-Nordsieck method and handling collinear divergences by the Lee-Nauenberg method is not consistent in such cases

  1. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

    Science.gov (United States)

    Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

    2015-11-01

    Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

  2. Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

    Directory of Open Access Journals (Sweden)

    Naoki Takata

    Full Text Available EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

  3. Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

    Science.gov (United States)

    Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

    2013-01-01

    EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

  4. Evolutionary growth process of highly conserved sequences in vertebrate genomes.

    Science.gov (United States)

    Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

    2012-08-01

    Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

    Science.gov (United States)

    Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

    2013-07-01

    Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

  6. Divergence and Conservative Evolution of XTNX Genes in Land Plants

    Directory of Open Access Journals (Sweden)

    Yan-Mei Zhang

    2017-10-01

    Full Text Available The Toll-interleukin-1 receptor (TIR and Nucleotide-binding site (NBS domains are two major components of the TIR-NBS-leucine-rich repeat family plant disease resistance genes. Extensive functional and evolutionary studies have been performed on these genes; however, the characterization of a small group of genes that are composed of atypical TIR and NBS domains, namely XTNX genes, is limited. The present study investigated this specific gene family by conducting genome-wide analyses of 59 green plant genomes. A total of 143 XTNX genes were identified in 51 of the 52 land plant genomes, whereas no XTNX gene was detected in any green algae genomes, which indicated that XTNX genes originated upon emergence of land plants. Phylogenetic analysis revealed that the ancestral XTNX gene underwent two rounds of ancient duplications in land plants, which resulted in the formation of clades I/II and clades IIa/IIb successively. Although clades I and IIb have evolved conservatively in angiosperms, the motif composition difference and sequence divergence at the amino acid level suggest that functional divergence may have occurred since the separation of the two clades. In contrast, several features of the clade IIa genes, including the absence in the majority of dicots, the long branches in the tree, the frequent loss of ancestral motifs, and the loss of expression in all detected tissues of Zea mays, all suggest that the genes in this lineage might have undergone pseudogenization. This study highlights that XTNX genes are a gene family originated anciently in land plants and underwent specific conservative pattern in evolution.

  7. A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice

    OpenAIRE

    White, Michael A.; Ikeda, Akihiro; Payseur, Bret A.

    2012-01-01

    The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located jus...

  8. Extrapolating Weak Selection in Evolutionary Games

    Science.gov (United States)

    Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

    2013-01-01

    In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

  9. Incorporating evolutionary insights to improve ecotoxicology for freshwater species

    Science.gov (United States)

    Brady, Steven P.; Richardson, Jonathan L.; Kunz, Bethany K.

    2017-01-01

    Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution. First, by mapping chloride toxicity values derived from the literature onto a phylogeny of macroinvertebrates, fish, and amphibians, we tested whether macroevolutionary relationships across species and taxa are predictive of chloride tolerance. Next, we conducted chloride exposure tests for two amphibian species to assess whether potential contemporary evolutionary change associated with environmental chloride contamination influences chloride tolerance across local populations. We show that explicitly evaluating both macroevolution and contemporary evolution can provide important and even qualitatively different insights from those obtained via traditional ecotoxicological studies. While macroevolutionary perspectives can help forecast toxicological end points for species with untested sensitivities, contemporary evolutionary perspectives demonstrate the need to consider the environmental context of exposed populations when measuring toxicity. Accounting for divergence among populations of interest can provide more accurate and relevant information related to the sensitivity of populations that may be evolving in response to selection from contaminant exposure. Our data show that approaches accounting for and specifically examining variation among natural populations should become standard practice in ecotoxicology.

  10. Rapid molecular evolution across amniotes of the IIS/TOR network.

    Science.gov (United States)

    McGaugh, Suzanne E; Bronikowski, Anne M; Kuo, Chih-Horng; Reding, Dawn M; Addis, Elizabeth A; Flagel, Lex E; Janzen, Fredric J; Schwartz, Tonia S

    2015-06-02

    The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

  11. The extended evolutionary synthesis: its structure, assumptions and predictions

    Science.gov (United States)

    Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

    2015-01-01

    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

  12. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Directory of Open Access Journals (Sweden)

    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  13. The evolutionary ecology of clonally propagated domesticated plants.

    Science.gov (United States)

    McKey, Doyle; Elias, Marianne; Pujol, Benoît; Duputié, Anne

    2010-04-01

    While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

  14. Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes.

    Science.gov (United States)

    Li, H; Liu, J; Xiong, L; Zhang, H; Zhou, H; Yin, H; Jing, W; Li, J; Shi, Q; Wang, Y; Liu, J; Nie, L

    2017-05-01

    provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  15. Optimizing a reconfigurable material via evolutionary computation

    Science.gov (United States)

    Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.

    2015-08-01

    Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

  16. Properties of classical and quantum Jensen-Shannon divergence

    NARCIS (Netherlands)

    J. Briët (Jop); P. Harremoës (Peter)

    2009-01-01

    htmlabstractJensen-Shannon divergence (JD) is a symmetrized and smoothed version of the most important divergence measure of information theory, Kullback divergence. As opposed to Kullback divergence it determines in a very direct way a metric; indeed, it is the square of a metric. We consider a

  17. Beam Angular Divergence Effects in Ion Implantation

    International Nuclear Information System (INIS)

    Horsky, T. N.; Hahto, S. K.; Bilbrough, D. G.; Jacobson, D. C.; Krull, W. A.; Goldberg, R. D.; Current, M. I.; Hamamoto, N.; Umisedo, S.

    2008-01-01

    An important difference between monomer ion beams and heavy molecular beams is a significant reduction in beam angular divergence and increased on-wafer angular accuracy for molecular beams. This advantage in beam quality stems from a reduction in space-charge effects within the beam. Such improved angular accuracy has been shown to have a significant impact on the quality and yield of transistor devices [1,12]. In this study, B 18 H x + beam current and angular divergence data collected on a hybrid scanned beam line that magnetically scans the beam across the wafer is presented. Angular divergence is kept below 0.5 deg from an effective boron energy of 200 eV to 3000 eV. Under these conditions, the beam current is shown analytically to be limited by space charge below about 1 keV, but by the matching of the beam emittance to the acceptance of the beam line above 1 keV. In addition, results of a beam transport model which includes variable space charge compensation are presented, in which a drift mode B 18 H x + beam is compared to an otherwise identical boron beam after deceleration. Deceleration is shown to introduce significant space-charge blow up resulting in a large on-wafer angular divergence. The divergence effects introduced by wafer charging are also discussed.

  18. Ion divergence in magnetically insulated diodes

    International Nuclear Information System (INIS)

    Slutz, S.A.; Lemke, R.W.; Pointon, T.D.; Desjarlais, M.P.; Johnson, D.J.; Mehlhorn, T.A.; Filuk, A.; Bailey, J.

    1995-01-01

    Magnetically insulated ion diodes are being developed to drive inertial confinement fusion. Ion beam microdivergence must be reduced to achieve the very high beam intensities required to achieve this goal. Three-dimensional particle-in-cell simulations indicate that instability induced fluctuations can produce significant ion divergence during acceleration. These simulations exhibit a fast growing mode early in time, which has been identified as the diocotron instability. The divergence generated by this mode is modest due to the relatively high frequency (>1GHz). Later, a low-frequency low-phase-velocity instability develops. This instability couples effectively to the ions, since the frequency is approximately the reciprocal of the ion transit time, and can generate unacceptably large ion divergences (>30 mrad). Linear stability theory reveals that this mode requires perturbations parallel to the applied magnetic field and is related to the modified two stream instability. Measurements of ion density fluctuations and energy-momentum correlations have confirmed that instabilities develop in ion diodes and contribute to the ion divergence. In addition, spectroscopic measurements indicate that the ions have a significant transverse temperature very close to the emission surface. Passive lithium fluoride (LiF) anodes have larger transverse beam temperatures than laser irradiated active sources. Calculations of source divergence expected from the roughness of LiF surfaces and the possible removal of this layer is presented

  19. 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.

  20. Differential evolution of members of the rhomboid gene family with conservative and divergent patterns.

    Science.gov (United States)

    Li, Qi; Zhang, Ning; Zhang, Liangsheng; Ma, Hong

    2015-04-01

    Rhomboid proteins are intramembrane serine proteases that are involved in a plethora of biological functions, but the evolutionary history of the rhomboid gene family is not clear. We performed a comprehensive molecular evolutionary analysis of the rhomboid gene family and also investigated the organization and sequence features of plant rhomboids in different subfamilies. Our results showed that eukaryotic rhomboids could be divided into five subfamilies (RhoA-RhoD and PARL). Most orthology groups appeared to be conserved only as single or low-copy genes in all lineages in RhoB-RhoD and PARL, whereas RhoA genes underwent several duplication events, resulting in multiple gene copies. These duplication events were due to whole genome duplications in plants and animals and the duplicates might have experienced functional divergence. We also identified a novel group of plant rhomboid (RhoB1) that might have lost their enzymatic activity; their existence suggests that they might have evolved new mechanisms. Plant and animal rhomboids have similar evolutionary patterns. In addition, there are mutations affecting key active sites in RBL8, RBL9 and one of the Brassicaceae PARL duplicates. This study delineates a possible evolutionary scheme for intramembrane proteins and illustrates distinct fates and a mechanism of evolution of gene duplicates. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  1. Next-generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis.

    Science.gov (United States)

    Webb, Kristen M; Rosenthal, Benjamin M

    2011-01-01

    The mitochondrial genome's non-recombinant mode of inheritance and relatively rapid rate of evolution has promoted its use as a marker for studying the biogeographic history and evolutionary interrelationships among many metazoan species. A modest portion of the mitochondrial genome has been defined for 12 species and genotypes of parasites in the genus Trichinella, but its adequacy in representing the mitochondrial genome as a whole remains unclear, as the complete coding sequence has been characterized only for Trichinella spiralis. Here, we sought to comprehensively describe the extent and nature of divergence between the mitochondrial genomes of T. spiralis (which poses the most appreciable zoonotic risk owing to its capacity to establish persistent infections in domestic pigs) and Trichinella murrelli (which is the most prevalent species in North American wildlife hosts, but which poses relatively little risk to the safety of pork). Next generation sequencing methodologies and scaffold and de novo assembly strategies were employed. The entire protein-coding region was sequenced (13,917 bp), along with a portion of the highly repetitive non-coding region (1524 bp) of the mitochondrial genome of T. murrelli with a combined average read depth of 250 reads. The accuracy of base calling, estimated from coding region sequence was found to exceed 99.3%. Genome content and gene order was not found to be significantly different from that of T. spiralis. An overall inter-species sequence divergence of 9.5% was estimated. Significant variation was identified when the amount of variation between species at each gene is compared to the average amount of variation between species across the coding region. Next generation sequencing is a highly effective means to obtain previously unknown mitochondrial genome sequence. Particular to parasites, the extremely deep coverage achieved through this method allows for the detection of sequence heterogeneity between the multiple

  2. The divergence theorem for divergence measure vectorfields on sets with fractal boundaries

    Czech Academy of Sciences Publication Activity Database

    Šilhavý, Miroslav

    2009-01-01

    Roč. 14, č. 5 (2009), s. 445-455 ISSN 1081-2865 Institutional research plan: CEZ:AV0Z10190503 Keywords : divergence measure vectorfields * fractal s * divergence theorem Subject RIV: BA - General Mathematics Impact factor: 1.065, year: 2009

  3. Rapid discrimination of visual scene content in the human brain

    Science.gov (United States)

    Anokhin, Andrey P.; Golosheykin, Simon; Sirevaag, Erik; Kristjansson, Sean; Rohrbaugh, John W.; Heath, Andrew C.

    2007-01-01

    The rapid evaluation of complex visual environments is critical for an organism's adaptation and survival. Previous studies have shown that emotionally significant visual scenes, both pleasant and unpleasant, elicit a larger late positive wave in the event-related brain potential (ERP) than emotionally neutral pictures. The purpose of the present study was to examine whether neuroelectric responses elicited by complex pictures discriminate between specific, biologically relevant contents of the visual scene and to determine how early in the picture processing this discrimination occurs. Subjects (n=264) viewed 55 color slides differing in both scene content and emotional significance. No categorical judgments or responses were required. Consistent with previous studies, we found that emotionally arousing pictures, regardless of their content, produce a larger late positive wave than neutral pictures. However, when pictures were further categorized by content, anterior ERP components in a time window between 200−600 ms following stimulus onset showed a high selectivity for pictures with erotic content compared to other pictures regardless of their emotional valence (pleasant, neutral, and unpleasant) or emotional arousal. The divergence of ERPs elicited by erotic and non-erotic contents started at 185 ms post-stimulus in the fronto-central midline regions, with a later onset in parietal regions. This rapid, selective, and content-specific processing of erotic materials and its dissociation from other pictures (including emotionally positive pictures) suggests the existence of a specialized neural network for prioritized processing of a distinct category of biologically relevant stimuli with high adaptive and evolutionary significance. PMID:16712815

  4. The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.

    Science.gov (United States)

    Brucker, Robert M; Bordenstein, Seth R

    2012-02-01

    The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  5. Vibhakti Divergence between Sanskrit and Hindi

    Science.gov (United States)

    Shukla, Preeti; Shukl, Devanand; Kulkarni, Amba

    Translation divergence at various levels between languages arises due to the different conventions followed by different languages for coding the information of grammatical relations. Though Sanskrit and Hindi belong to the same Indo-Aryan family and structurally as well as lexically Hindi inherits a lot from Sanskrit, yet divergences are observed at the level of function words such as vibhaktis. Pāṇini in his Aṣṭādhyāyī has assigned a default vibhakti to kārakas alongwith many scopes for exceptions. He handles these exceptions either by imposing a new kāraka role or by assigning a special vibhakti. However, these methods are not acceptable in Hindi in toto. Based on the nature of deviation, we propose seven cases of divergences in this paper.

  6. Evolutionary engineering for industrial microbiology.

    Science.gov (United States)

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  7. Sympatric and allopatric divergence of MHC genes in threespine stickleback.

    Directory of Open Access Journals (Sweden)

    Blake Matthews

    2010-06-01

    Full Text Available Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatibility Complex (MHC, can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus, as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.

  8. Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

    Science.gov (United States)

    Huang, Bing-Hong; Liao, Pei-Chun

    2015-07-01

    Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  9. Founder effects and the evolution of asymmetrical sexual isolation in a rapidly-speciating clade

    Directory of Open Access Journals (Sweden)

    Kevin P. OH, Gina L. CONTE, Kerry L. SHAW

    2013-04-01

    Full Text Available Sexual isolation resulting from differences in mate choice behaviors is a hallmark of rapidly-speciating lineages. When present, asymmetrical sexual isolation may provide insights into the mechanisms responsible for the evolutionary change in mate signaling traits. In particular, Kaneshiro’s hypothesis suggests that divergence in sexual characters between populations may arise in allopatry when ‘derived’ founding populations are subject to severe population bottlenecks, accompanied by a relaxation of sexual selection relative to ‘ancestral’ source populations. In the present study, we tested predictions of asymmetrical sexual isolation between two allopatric species of Hawaiian Laupala crickets, representing ‘ancestral’ (L. makaio and ‘derived’ (L. nigra taxa. While crickets in this genus are notable for rapid divergence of male courtship songs, these species share similar song types, thus suggesting that patterns of sexual isolation are likely due to other mating cues. Analysis of behavioral responses in conspecific and heterospecific ‘no-choice’ mating trials revealed pronounced asymmetrical isolation in the direction predicted by Kaneshiro’s hypothesis, wherein we observed a significant reduction in mating success for crosses involving ‘derived’ males paired with ‘ancestral’ females, compared to the reciprocal heterospecific and both conspecific pairings. Further dissection of courtship behaviors suggested this difference did not reflect male mate choice, but rather, marked reduced spermatophore acceptance rates by ‘ancestral’ females paired with ‘derived’ males. The results are discussed with respect to founder effect models of speciation and the potential role of chemosensory signals in mate choice in these species [Current Zoology 59 (2: 230-238, 2013].

  10. 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

  11. 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.

  12. Evolutionary programming as a platform for in silico metabolic engineering

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen

    2005-01-01

    , and it is therefore interesting to develop new faster algorithms. Results In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters...... of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span several different pathways and may be necessary for solving challenging metabolic engineering problems....

  13. 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.

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

    KAUST Repository

    Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

    2014-01-01

    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.

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

    Science.gov (United States)

    Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

    2014-01-01

    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. PMID:24799432

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

    Science.gov (United States)

    Jackson, Andrew P; Otto, Thomas D; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B; Moussa, Ehab; Nair, Mridul; Reid, Adam J; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A; Weir, William; Wastling, Jonathan M; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R; Pain, Arnab

    2014-06-01

    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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  18. The evolutionary psychology of hunger.

    Science.gov (United States)

    Al-Shawaf, Laith

    2016-10-01

    An evolutionary psychological perspective suggests that emotions can be understood as coordinating mechanisms whose job is to regulate various psychological and physiological programs in the service of solving an adaptive problem. This paper suggests that it may also be fruitful to approach hunger from this coordinating mechanism perspective. To this end, I put forward an evolutionary task analysis of hunger, generating novel a priori hypotheses about the coordinating effects of hunger on psychological processes such as perception, attention, categorization, and memory. This approach appears empirically fruitful in that it yields a bounty of testable new hypotheses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  20. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    Many firms assume that outsourcing partnerships may allow them to strengthen their overall competitiveness. Lured by its intuitive appeal, several enter into such partnerships, only to realize that they represent a marginal rather than a magical solution to their quest for increasing market...... performance. We explore the proposed impact of diverging relationship norms on relationship expectations using data from an ongoing field study of Danish buyers and Chinese suppliers. We link these diverging expectations to the business practices of Danish buyers and Chinese and their institutional contexts...

  1. Universal portfolios generated by the Bregman divergence

    Science.gov (United States)

    Tan, Choon Peng; Kuang, Kee Seng

    2017-04-01

    The Bregman divergence of two probability vectors is a stronger form of the f-divergence introduced by Csiszar. Two versions of the Bregman universal portfolio are presented by exploiting the mean-value theorem. The explicit form of the Bregman universal portfolio generated by a function of a convex polynomial is derived and studied empirically. This portfolio can be regarded as another generalized of the well-known Helmbold portfolio. By running the portfolios on selected stock-price data sets from the local stock exchange, it is shown that it is possible to increase the wealth of the investor by using the portfolios in investment.

  2. Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex

    Science.gov (United States)

    Daza-Vamenta, Riza; Glusman, Gustavo; Rowen, Lee; Guthrie, Brandon; Geraghty, Daniel E.

    2004-01-01

    The major histocompatibility complex (MHC) is comprised of the class I, class II, and class III regions, including the MHC class I and class II genes that play a primary role in the immune response and serve as an important model in studies of primate evolution. Although nonhuman primates contribute significantly to comparative human studies, relatively little is known about the genetic diversity and genomics underlying nonhuman primate immunity. To address this issue, we sequenced a complete rhesus macaque MHC spanning over 5.3 Mb, and obtained an additional 2.3 Mb from a second haplotype, including class II and portions of class I and class III. A major expansion of from six class I genes in humans to as many as 22 active MHC class I genes in rhesus and levels of sequence divergence some 10-fold higher than a similar human comparison were found, averaging from 2% to 6% throughout extended portions of class I and class II. These data pose new interpretations of the evolutionary constraints operating between MHC diversity and T-cell selection by contrasting with models predicting an optimal number of antigen presenting genes. For the clinical model, these data and derivative genetic tools can be implemented in ongoing genetic and disease studies that involve the rhesus macaque. PMID:15289473

  3. Anticipatory Mechanisms in Evolutionary Living Systems

    Science.gov (United States)

    Dubois, Daniel M.; Holmberg, Stig C.

    2010-11-01

    This paper deals firstly with a revisiting of Darwin's theory of Natural Selection. Darwin in his book never uses the word "evolution", but shows a clear position about mutability of species. Darwin's Natural Selection was mainly inspired by the anticipatory Artificial Selection by humans in domestication, and the Malthus struggle for existence. Darwin showed that the struggle for existence leads to the preservation of the most divergent offspring of any one species. He cited several times the canon of "Natura non facit saltum". He spoke about the origin of life from some one primordial form, into which life was first breathed. Finally, Darwin made anticipation about the future researches in psychology. This paper cites the work of Ernst Mayr who was the first, after 90 years of an intense scientific debate, to present a new and stable Darwinian paradigm as the "Evolutionary Synthesis" in 1942. To explain what is life, the Living Systems Theory (LST) by J. G. Miller is presented. It is showed that the Autopoietic Systems Theory of Varela et al is also a fundamental component of living systems. In agreement with Darwin, the natural selection is a necessary condition for transformation of biological systems, but is not a sufficient condition. Thus, in this paper we conjecture that an anticipatory evolutionary mechanism exists with the genetic code that is a self-replicating and self-modifying anticipatory program. As demonstrated by Nobel laureate McClintock, evolution in genomes is programmed. The word "program" comes from "pro-gram" meaning to write before, by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes of behavioural responses, that is part of an organism. For example, cell death may be programmed by what is called the apoptosis. This definitively is a great breakthrough in our understanding of biological evolution. Hence

  4. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

    Science.gov (United States)

    Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

    2017-07-18

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

  5. Design and testing of low-divergence elliptical-jet nozzles

    Energy Technology Data Exchange (ETDEWEB)

    Rouly, Etienne; Warkentin, Andrew; Bauer, Robert [Dalhousie University, Halifax (China)

    2015-05-15

    A novel approach was developed to design and fabricate nozzles to produce high-pressure low-divergence fluid jets. Rapid-prototype fabrication allowed for myriad experiments investigating effects of different geometric characteristics of nozzle internal geometry on jet divergence angle and fluid distribution. Nozzle apertures were elliptical in shape with aspect ratios between 1.00 and 2.45. The resulting nozzle designs were tested and the lowest elliptical jet divergence angle was 0.4 degrees. Nozzle pressures and flowrates ranged from 0.32 to 4.45 MPa and 13.6 to 37.9 LPM, respectively. CimCool CimTech 310 machining fluid was used in all experiments at a Brix concentration of 6.6 percent.

  6. The Hawaiian cave planthoppers (Homoptera: Fulgoroidea: Cixiidae - A model for rapid subterranean speciation?

    Directory of Open Access Journals (Sweden)

    Hannelore Hoch

    1997-01-01

    Full Text Available After the successful colonization of a single ancestral species in the Hawaiian Islands, planthoppers of the cixiid genus Oliarus underwent intensive adaptive radiation resulting in 80 described endemic species. Oliarus habitats range from montaneous rain forests to dry coastal biotopes and subterranean environments. At least 7 independant evolutionary lines represented by different species have adapted to lava tubes on Molokai (1, Maui (3, and Hawaii Island (3. Behavioral and morphological studies on one of these evolutionary lines on Hawaii Island, the blind, flight- and pigmentless Oliarus polyphentus have provided evidence for reproductive isolation between allopatric populations which may in fact be separate species. Significant differences in song parameters were observed even between populations from neighbouring lava tubes, although the planthoppers are capable of underground migration through the voids and cracks of the mesocavernous rock system which is extant in young basalt: after a little more than 20 years, lava tubes within the Mauna Ulu 1974 flow had been colonized by O. ‘polyphenius” individuals, most probably originating from a near-by forestkipuka. Amazingly, this species complex is found on the youngest of the Hawaiian Islands, with probably less than 0.5 m.y., which suggests rapid speciation processes. Field observations have led to the development of a hypothesis to match underground speciation with the dynamics of vegetational succession on the surface of active volcanoes. Planthopper range partitioning and geographic separation of populations by young lava flows, founder events and small population size may be important factors involved in rapid divergence.

  7. Radiating despite a Lack of Character: Ecological Divergence among Closely Related, Morphologically Similar Honeyeaters (Aves: Meliphagidae) Co-occurring in Arid Australian Environments.

    Science.gov (United States)

    Miller, Eliot T; Wagner, Sarah K; Harmon, Luke J; Ricklefs, Robert E

    2017-02-01

    Quantifying the relationship between form and function can inform use of morphology as a surrogate for ecology. How the strength of this relationship varies continentally can inform understanding of evolutionary radiations; for example, does the relationship break down when certain lineages invade and diversify in novel habitats? The 75 species of Australian honeyeaters (Meliphagidae) are morphologically and ecologically diverse, with species feeding on nectar, insects, fruit, and other resources. We investigated Meliphagidae ecomorphology and community structure by (1) quantifying the concordance between morphology and ecology (foraging behavior), (2) estimating rates of trait evolution in relation to the packing of ecological space, and (3) comparing phylogenetic and trait community structure across the broad environmental gradients of the continent. We found that morphology explained 37% of the variance in ecology (and 62% vice versa), and we uncovered well-known bivariate relationships among the multivariate ecomorphological data. Ecological trait diversity declined less rapidly than phylogenetic diversity along a gradient of decreasing precipitation. We employ a new method (trait fields) and extend another (phylogenetic fields) to show that while species in phylogenetically clustered, arid-environment assemblages are similar morphologically, they are as varied in foraging behavior as those from more diverse assemblages. Thus, although closely related and similar morphologically, these arid-adapted species have diverged in ecological space to a similar degree as their mesic counterparts.

  8. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae

    Directory of Open Access Journals (Sweden)

    Kingston Sarah E

    2009-10-01

    Full Text Available Abstract Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

  9. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

    Science.gov (United States)

    Schwartz, Tonia S; Bronikowski, Anne M

    2013-02-01

    The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

  10. Natural selection on MHC IIβ in parapatric lake and stream stickleback: Balancing, divergent, both or neither?

    Science.gov (United States)

    Stutz, William E; Bolnick, Daniel I

    2017-09-01

    Major histocompatibility complex (MHC) genes encode proteins that play a central role in vertebrates' adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates' genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations and divergence between populations. Leading hypotheses include balancing selection favouring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results. We suggest a novel strategy to distinguish balancing vs. divergent selection on MHC, taking advantage of natural admixture between parapatric populations. With divergent selection, individuals with immigrant alleles will be more infected and less fit because they are susceptible to novel parasites in their new habitat. With balancing selection, individuals with locally rare immigrant alleles will be more fit (less infected). We tested these contrasting predictions using three-spine stickleback from three replicate pairs of parapatric lake and stream habitats. We found numerous positive and negative associations between particular MHC IIβ alleles and particular parasite taxa. A few allele-parasite comparisons supported balancing selection, and others supported divergent selection between habitats. But, there was no overall tendency for fish with immigrant MHC alleles to be more or less heavily infected. Instead, locally rare MHC alleles (not necessarily immigrants) were associated with heavier infections. Our results illustrate the complex relationship between MHC IIβ allelic variation and spatially varying multispecies parasite communities: different hypotheses may be concurrently true for different allele-parasite combinations. © 2017 John Wiley & Sons Ltd.

  11. Divergence in Patterns of Leaf Growth Polarity Is Associated with the Expression Divergence of miR396.

    Science.gov (United States)

    Das Gupta, Mainak; Nath, Utpal

    2015-10-01

    Lateral appendages often show allometric growth with a specific growth polarity along the proximo-distal axis. Studies on leaf growth in model plants have identified a basipetal growth direction with the highest growth rate at the proximal end and progressively lower rates toward the distal end. Although the molecular mechanisms governing such a growth pattern have been studied recently, variation in leaf growth polarity and, therefore, its evolutionary origin remain unknown. By surveying 75 eudicot species, here we report that leaf growth polarity is divergent. Leaf growth in the proximo-distal axis is polar, with more growth arising from either the proximal or the distal end; dispersed with no apparent polarity; or bidirectional, with more growth contributed by the central region and less growth at either end. We further demonstrate that the expression gradient of the miR396-GROWTH-REGULATING FACTOR module strongly correlates with the polarity of leaf growth. Altering the endogenous pattern of miR396 expression in transgenic Arabidopsis thaliana leaves only partially modified the spatial pattern of cell expansion, suggesting that the diverse growth polarities might have evolved via concerted changes in multiple gene regulatory networks. © 2015 American Society of Plant Biologists. All rights reserved.

  12. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  13. Darwinian foundations for evolutionary economics

    NARCIS (Netherlands)

    Stoelhorst, J.W.

    2008-01-01

    This paper engages with the methodological debate on the contribution of Darwinism to Veblen's (1898) evolutionary research program for economics. I argue that ontological continuity, generalized Darwinism, and multi-level selection are necessary building blocks for an explanatory framework that can

  14. Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:

  15. Evolutionary Biology Research in India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 10. Evolutionary Biology Research in India. Information and Announcements Volume 5 Issue 10 October 2000 pp 102-104. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/005/10/0102-0104 ...

  16. Realism, Relativism, and Evolutionary Psychology

    NARCIS (Netherlands)

    Derksen, M.

    Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with

  17. Ancient Biomolecules and Evolutionary Inference

    DEFF Research Database (Denmark)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando

    2018-01-01

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleo...

  18. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  19. Evolutionary trends in directional hearing

    DEFF Research Database (Denmark)

    Carr, Catherine E; Christensen-Dalsgaard, Jakob

    2016-01-01

    Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds...

  20. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  1. Haldane and modern evolutionary genetics

    Indian Academy of Sciences (India)

    Brian Charlesworth

    2017-11-24

    Nov 24, 2017 ... q(t) of an allele at a locus among the gametes produced at time t, to its .... the importance of disease as an evolutionary factor, which is now a ..... VII. Selection intensity as a function of mortality rate. Proc. Camb. Philos. Soc.

  2. Genetic approaches in comparative and evolutionary physiology

    Science.gov (United States)

    Bridgham, Jamie T.; Kelly, Scott A.; Garland, Theodore

    2015-01-01

    Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

  3. Stora's fine notion of divergent amplitudes

    Directory of Open Access Journals (Sweden)

    Joseph C. Várilly

    2016-11-01

    Full Text Available Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  4. Taming infrared divergences in the effective potential

    Energy Technology Data Exchange (ETDEWEB)

    Elias-Miro, J. [IFAE, Univ. Autonoma de Barcelona (Spain); Universitat Autonoma de Barcelona (Spain). Dept. de Fisica; Espinosa, J.R. [IFAE, Univ. Autonoma de Barcelona (Spain); ICREA, Institucio Catalana de Recerca i Estudis Avancats, Barcelona (Spain); Konstandin, T. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2014-06-15

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective theory.

  5. Bounding the bias of contrastive divergence learning

    DEFF Research Database (Denmark)

    Fischer, Anja; Igel, Christian

    2011-01-01

    Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k...

  6. Hamiltonian representation of divergence-free fields

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1984-11-01

    Globally divergence-free fields, such as the magnetic field and the vorticity, can be described by a two degree of freedom Hamiltonian. The Hamiltonian function provides a complete topological description of the field lines. The formulation also separates the dissipative and inertial time scale evolution of the magnetic and the vorticity fields

  7. Viewpoint Environmental Slogans: Memes with Diverging ...

    African Journals Online (AJOL)

    Environmental slogans can be seen as memes, i.e. cultural constructs that, not unlike genes, replicate themselves from one generation to the next. Memes may, however, be divergently interpreted and some memes can even have unwanted side-effects. We wanted to find out how supporters of an environmental ...

  8. The divergence theorem for unbounded vector fields

    OpenAIRE

    De Pauw, Thierry; Pfeffer, Washek F.

    2007-01-01

    In the context of Lebesgue integration, we derive the divergence theorem for unbounded vector. elds that can have singularities at every point of a compact set whose Minkowski content of codimension greater than two is. nite. The resulting integration by parts theorem is applied to removable sets of holomorphic and harmonic functions.

  9. Divergent Priors and well Behaved Bayes Factors

    NARCIS (Netherlands)

    R.W. Strachan (Rodney); H.K. van Dijk (Herman)

    2011-01-01

    textabstractDivergent priors are improper when defined on unbounded supports. Bartlett's paradox has been taken to imply that using improper priors results in ill-defined Bayes factors, preventing model comparison by posterior probabilities. However many improper priors have attractive properties

  10. The Harmonic Series Diverges Again and Again

    Science.gov (United States)

    Kifowit, Steven J.; Stamps, Terra A.

    2006-01-01

    The harmonic series is one of the most celebrated infinite series of mathematics. A quick glance at a variety of modern calculus textbooks reveals that there are two very popular proofs of the divergence of the harmonic series. In this article, the authors survey these popular proofs along with many other proofs that are equally simple and…

  11. Design of a divergence and alignment indicator

    International Nuclear Information System (INIS)

    Brenizer, J.S. Jr.; Raine, D.A.; Gao, J.; Chen, J.

    1996-01-01

    The divergence and alignment indicator (DAI) is an extension of the ASTM E803 L/D thermal neutron radiography L/D device that allows the user to determine both the beam centerline and the beam divergence. The DAI was made using aluminium plate and rods, and incorporated cadmium wire for contrast. Circular symmetry was utilized to simplify manufacture. The DAI was placed with the five posts against the film cassette or radioscopic imaging device in the physical center of the beam. The DAI was perpendicular to the selected beam radius when the front and back center Cd wire images overlap. The degree of misalignment was indicated by their image positions. After the DAI was aligned, analysis of the cadmium wire ''+'' image spacing yielded the beam divergence. The DAI was tested in a neutron beam which has an L/D of 30 but a small degree of divergence. The DAI was also imaged using an X-ray source. The point source predictions of Cd wire image locations showed good agreement with those measured from the X-ray radiograph. The neutron radiographic locations could be predicted using the point source equations, even though the neutron beam was a complex distributed source. (orig.)

  12. Taming infrared divergences in the effective potential

    International Nuclear Information System (INIS)

    Elias-Miro, J.; Konstandin, T.

    2014-06-01

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective theory.

  13. A Rapid Aeroelasticity Optimization Method Based on the Stiffness characteristics

    OpenAIRE

    Yuan, Zhe; Huo, Shihui; Ren, Jianting

    2018-01-01

    A rapid aeroelasticity optimization method based on the stiffness characteristics was proposed in the present study. Large time expense in static aeroelasticity analysis based on traditional time domain aeroelasticity method is solved. Elastic axis location and torsional stiffness are discussed firstly. Both torsional stiffness and the distance between stiffness center and aerodynamic center have a direct impact on divergent velocity. The divergent velocity can be adjusted by changing the cor...

  14. Evolutionary history and stress regulation of the lectin superfamily in higher plants

    Directory of Open Access Journals (Sweden)

    Ramachandran Srinivasan

    2010-03-01

    Full Text Available Abstract Background Lectins are a class of carbohydrate-binding proteins. They play roles in various biological processes. However, little is known about their evolutionary history and their functions in plant stress regulation. The availability of full genome sequences from various plant species makes it possible to perform a whole-genome exploration for further understanding their biological functions. Results Higher plant genomes encode large numbers of lectin proteins. Based on their domain structures and phylogenetic analyses, a new classification system has been proposed. In this system, 12 different families have been classified and four of them consist of recently identified plant lectin members. Further analyses show that some of lectin families exhibit species-specific expansion and rapid birth-and-death evolution. Tandem and segmental duplications have been regarded as the major mechanisms to drive lectin expansion although retrogenes also significantly contributed to the birth of new lectin genes in soybean and rice. Evidence shows that lectin genes have been involved in biotic/abiotic stress regulations and tandem/segmental duplications may be regarded as drivers for plants to adapt various environmental stresses through duplication followed by expression divergence. Each member of this gene superfamily may play specialized roles in a specific stress condition and function as a regulator of various environmental factors such as cold, drought and high salinity as well as biotic stresses. Conclusions Our studies provide a new outline of the plant lectin gene superfamily and advance the understanding of plant lectin genes in lineage-specific expansion and their functions in biotic/abiotic stress-related developmental processes.

  15. Ecological explanations to island gigantism: dietary niche divergence, predation, and size in an endemic lizard.

    Science.gov (United States)

    Runemark, Anna; Sagonas, Kostas; Svensson, Erik I

    2015-08-01

    Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.

  16. Temperature niche shift observed in a Lepidoptera population under allochronic divergence.

    Science.gov (United States)

    Santos, H; Paiva, M R; Tavares, C; Kerdelhué, C; Branco, M

    2011-09-01

    A process of adaptive divergence for tolerance to high temperatures was identified using a rare model system, consisting of two sympatric populations of a Lepidoptera (Thaumetopoea pityocampa) with different life cycle timings, a 'mutant' population with summer larval development, Leiria SP, and the founder natural population, having winter larval development, Leiria WP. A third, allopatric population (Bordeaux WP) was also studied. First and second instar larvae were experimentally exposed to daily-cycles of heat treatment reaching maximum values of 36, 38, 40 and 42 °C; control groups placed at 25 °C. A lethal temperature effect was only significant at 42 °C, for Leiria SP, whereas all temperatures tested had a significant negative effect upon Leiria WP, thus indicating an upper threshold of survival c.a. 6 °C above that of the WP. Cox regression model, for pooled heat treatments, predicted mortality hazard to increase for Leiria WP (+108%) and Bordeaux WP (+78%) in contrast to Leiria SP; to increase by 24% for each additional °C; and to decrease by 53% from first to second instar larvae. High variability among individuals was observed, a population characteristic that may favour selection and consequent adaptation. Present findings provide an example of ecological differentiation, following a process of allochronic divergence. Results further contribute to a better understanding of the implications of climate change for ecological genetics. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  17. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

    Science.gov (United States)

    Leaché, Adam D; Banbury, Barbara L; Linkem, Charles W; de Oca, Adrián Nieto-Montes

    2016-03-22

    Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20-25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.

  18. Strengths and Weaknesses of McNamara's Evolutionary Psychological Model of Dreaming

    Directory of Open Access Journals (Sweden)

    Sandra Olliges

    2010-10-01

    Full Text Available This article includes a brief overview of McNamara's (2004 evolutionary model of dreaming. The strengths and weaknesses of this model are then evaluated in terms of its consonance with measurable neurological and biological properties of dreaming, its fit within the tenets of evolutionary theories of dreams, and its alignment with evolutionary concepts of cooperation and spirituality. McNamara's model focuses primarily on dreaming that occurs during rapid eye movement (REM sleep; therefore this article also focuses on REM dreaming.

  19. Thrust characteristics of a series of convergent-divergent exhaust nozzles at subsonic and supersonic flight speeds

    Science.gov (United States)

    Fradenburgh, Evan A; Gorton, Gerald C; Beke, Andrew

    1954-01-01

    An experimental investigation of a series of four convergent-divergent exhaust nozzles was conducted in the Lewis 8-by-6 foot supersonic wind tunnel at Mach numbers of 0.1, 0.6, 1.6, and 2.0 over a range of nozzle pressure ratios. The thrust characteristics of these nozzles were determined by a pressure-integration technique. From a thrust standpoint, a nozzle designed to give uniform parallel flow at the exit had no advantage over the simple geometric design with conical convergent and divergent sections. The rapid-divergent nozzles might be competitive with the more gradual-divergent nozzles since the relatively short length of these nozzles would be advantageous from a weight standpoint and might result in smaller thrust losses due to friction. The thrusts, with friction losses neglected, were predicted satisfactorily by one-dimensional theory for the nozzles with relatively gradual divergence. The thrusts of the rapid-divergent designs were several percentages below the theoretical values at the design pressure ratio or above, while at low pressure ratios there was a considerable effect of free-stream Mach number, with thrusts considerably above theoretical values at subsonic speeds and somewhat above theoretical values at supersonic speeds. This Mach numb effect appeared to be related to the variation of the model base pressure with free-stream Mach number.

  20. Towards a mechanistic foundation of evolutionary theory.

    Science.gov (United States)

    Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

    2017-02-15

    Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

  1. Applied evolutionary economics and economic geography

    NARCIS (Netherlands)

    Frenken, K.

    2007-01-01

    Applied Evolutionary Economics and Economic Geography" aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and

  2. Evolutionary biology of bacterial and fungal pathogens

    National Research Council Canada - National Science Library

    Baquero, F

    2008-01-01

    ... and Evolutionary Dynamics of Pathogens * 21 Keith A. Crandall and Marcos Pérez-Losada II. Evolutionary Genetics of Microbial Pathogens 4. Environmental and Social Influences on Infectious Disea...

  3. Cancellation of soft and collinear divergences in noncommutative QED

    International Nuclear Information System (INIS)

    Mirza, B.; Zarei, M.

    2006-01-01

    In this paper, we investigate the behavior of noncommutative IR divergences and will also discuss their cancellation in the physical cross sections. The commutative IR (soft) divergences existing in the nonplanar diagrams will be examined in order to prove an all-order cancellation of these divergences using the Weinberg's method. In noncommutative QED, collinear divergences due to triple photon splitting vertex, were encountered, which are shown to be canceled out by the noncommutative version of KLN theorem. This guarantees that there is no mixing between the Collinear, soft divergences and noncommutative IR divergences

  4. Evolutionary relationships and functional diversity of plant sulfate transporters.

    Science.gov (United States)

    Takahashi, Hideki; Buchner, Peter; Yoshimoto, Naoko; Hawkesford, Malcolm J; Shiu, Shin-Han

    2011-01-01

    Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR, and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal SUL and animal anion exchangers (SLC26). The lineage of plant SULTR family is expanded into four subfamilies (SULTR1-SULTR4) in land plant species. By contrast, the putative SULTR homologs from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4), and the other diverged before the appearance of lineages for SUL, SULTR, and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13) and plant tonoplast-localized dicarboxylate transporters (TDT). The putative sulfur-sensing protein (SAC1) and SAC1-like transporters (SLT) of Chlorophyte green algae, bryophyte, and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  5. Evolutionary relationships and functional diversity of plant sulfate transporters

    Directory of Open Access Journals (Sweden)

    Hideki eTakahashi

    2012-01-01

    Full Text Available Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal sulfate transporters (SUL and animal anion exchangers (SLC26. The lineage of plant SULTR family is expanded into four subfamilies (SULTR1 to SULTR4 in land plant species. By contrast, the putative SULTR homologues from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4, and the other diverged before the appearance of lineages for SUL, SULTR and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13 and plant tonoplast-localized dicarboxylate transporters (TDT. The putative sulfur-sensing protein (SAC1 and SAC1-like transporters (SLT of Chlorophyte green algae, bryophyte and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is completely absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.

  6. The citation field of evolutionary economics

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal

  7. Essays on nonlinear evolutionary game dynamics

    NARCIS (Netherlands)

    Ochea, M.I.

    2010-01-01

    Evolutionary game theory has been viewed as an evolutionary repair of rational actor game theory in the hope that a population of boundedly rational players may attain convergence to classic rational solutions, such as the Nash Equilibrium, via some learning or evolutionary process. In this thesis

  8. Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus.

    Directory of Open Access Journals (Sweden)

    Anssi Karvonen

    Full Text Available Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

  9. Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Karvonen, Anssi; Lucek, Kay; Marques, David A; Seehausen, Ole

    2015-01-01

    Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

  10. Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra).

    Science.gov (United States)

    Moritz, Craig C; Pratt, Renae C; Bank, Sarah; Bourke, Gayleen; Bragg, Jason G; Doughty, Paul; Keogh, J Scott; Laver, Rebecca J; Potter, Sally; Teasdale, Luisa C; Tedeschi, Leonardo G; Oliver, Paul M

    2018-01-01

    Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  11. Morphological divergence of breeders and helpers in wild Damaraland mole-rat societies.

    Science.gov (United States)

    Young, Andrew J; Bennett, Nigel C

    2010-11-01

    The specialization of body shape to an individual's role within society represents a pinnacle of social evolution. Although commonplace among social insects, divergence in the body shapes of breeders and helpers has to date been documented in just one social vertebrate, the naked mole-rat, Heterocephalus glaber; an extraordinary species in which large colony size and frequent inbreeding may have favored the evolution of such specialization. Here, we present new evidence of morphological divergence between breeders and helpers in the Damaraland mole-rat, Fukomys damarensis; a much less socially extreme species that reflects an independent evolutionary origin of sociality. Using longitudinal data from wild populations, we show that dominant female Damaraland mole-rats, like many social insect queens, have a significantly more elongate body shape than subordinates. This difference arises not from a pre-existing difference in the body shapes of subordinates that do, and those that do not, become dominant, but from a modification to the growth trajectory of subordinates on dominance acquisition. Our findings reveal a wider role for morphological divergence within vertebrate societies and, as Damaraland mole-rats neither live in unusually large groups nor inbreed, suggest that circumstances favoring the evolution of such specializations may be more widespread among vertebrates than previously supposed. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  12. Niche divergence builds the case for ecological speciation in skinks of the Plestiodon skiltonianus species complex

    Science.gov (United States)

    Wogan, Guinevere O.U.; Richmond, Jonathan Q.

    2015-01-01

    Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate-based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by-product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size-divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.

  13. Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Sinha Amit

    2012-06-01

    Full Text Available Abstract Background An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans. Results We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance. Conclusion Our data set provides a catalog for future functional investigations and indicates novel insight

  14. Schroedinger operators and evolutionary strategies

    International Nuclear Information System (INIS)

    Asselmeyer, T.

    1997-01-01

    First we introduce a simple model for the description of evolutionary algorithms, which is based on 2nd order partial differential equations for the distribution function of the individuals. Then we turn to the properties of Boltzmann's and Darwin's strategy. the next chapter is dedicated to the mathematical properties of Schroedinger operators. Both statements on the spectral density and their reproducibility during the simulation are summarized. The remaining of this chapter are dedicated to the analysis of the kernel as well as the dependence of the Schroedinger operator on the potential. As conclusion from the results of this chapter we obtain the classification of the strategies in dependence of the fitness. We obtain the classification of the evolutionary strategies, which are described by a 2nd order partial differential equation, in relation to their solution behaviour. Thereafter we are employed with the variation of the mutation distribution

  15. Exponential Expansion in Evolutionary Economics

    DEFF Research Database (Denmark)

    Frederiksen, Peter; Jagtfelt, Tue

    2013-01-01

    This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...

  16. Preventive evolutionary medicine of cancers.

    Science.gov (United States)

    Hochberg, Michael E; Thomas, Frédéric; Assenat, Eric; Hibner, Urszula

    2013-01-01

    Evolutionary theory predicts that once an individual reaches an age of sufficiently low Darwinian fitness, (s)he will have reduced chances of keeping cancerous lesions in check. While we clearly need to better understand the emergence of precursor states and early malignancies as well as their mitigation by the microenvironment and tissue architecture, we argue that lifestyle changes and preventive therapies based in an evolutionary framework, applied to identified high-risk populations before incipient neoplasms become clinically detectable and chemoresistant lineages emerge, are currently the most reliable way to control or eliminate early tumours. Specifically, the relatively low levels of (epi)genetic heterogeneity characteristic of many if not most incipient lesions will mean a relatively limited set of possible adaptive traits and associated costs compared to more advanced cancers, and thus a more complete and predictable understanding of treatment options and outcomes. We propose a conceptual model for preventive treatments and discuss the many associated challenges.

  17. Phenotypic Divergence in the Reproductive Traits of Marbled ...

    African Journals Online (AJOL)

    Overall, the results indicated some level of phenotypic divergence of the fish ... divergence cannot be partitioned between fishing mortality, genetic .... female fish was estimated from the egg counts ..... that greatly improved the quality of the.

  18. Endemic infrared divergences in QED3 at finite temperature

    International Nuclear Information System (INIS)

    Lo, Pok Man; Swanson, Eric S.

    2011-01-01

    We demonstrate that massless QED in three dimensions contains endemic infrared divergences. It is argued that these divergences do not affect observables; furthermore, it is possible to choose a gauge that renders the theory finite.

  19. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu; Shamma, Jeff S.; Martins, Nuno C.

    2018-01-01

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  20. Passivity and Evolutionary Game Dynamics

    KAUST Repository

    Park, Shinkyu

    2018-03-21

    This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.

  1. PUBLIC INTEGRITY AND THE DIVERGENCE FROM IT

    Directory of Open Access Journals (Sweden)

    Simona‐Roxana ULMAN

    2013-12-01

    Full Text Available Public Integrity is one of the public sector’s essential objectives to attain. In contradiction, as a divergence from it, corruption is one of the persistent problems of the societies over years and it affects the credibility of public institutions and its ambassadors in front of the citizens and of the other related countries. All nations complain of corruption and, as it is observed in the Corruption Perception Index 2012, no country has a maximum score which shows that a country is totally clean. In this context, the study of the most important elements of the public integrity concept, the identification of what causes the divergence from it and the solutions detection become a relevant option for economic literature. In this context, the main objective of this paper is to emphasize the public integrity concept and its main aspects and to make a comparison between countries to achieve a large perspective of the world’s public integrity juncture.

  2. Flow over convergent and divergent wall riblets

    Energy Technology Data Exchange (ETDEWEB)

    Koeltzsch, K.; Dinkelacker, A.; Grundmann, R. [Institut fuer Luft- und Raumfahrttechnik, Technische Universitaet Dresden, 36460 Merkers (Germany)

    2002-08-01

    Fast swimming sharks have small riblets on their skin, which are assumed to improve the swimming performance of the fish. Fluid dynamic experiments in water as well as in air confirm this assumption. With riblet surfaces as compared to smooth surfaces, drag reductions up to about 10% were measured. The overall riblet pattern on sharks shows parallel riblets directed from head to tail, but besides this overall pattern fast swimming sharks have also small areas with converging riblets and others with diverging riblets. In the present study the velocity field over convergent and divergent riblet patterns is investigated by hot-wire measurements in turbulent pipe flow. Significant changes in the near wall velocity field were found. (orig.)

  3. Gluon mass generation without seagull divergences

    International Nuclear Information System (INIS)

    Aguilar, Arlene C.; Papavassiliou, Joannis

    2010-01-01

    Dynamical gluon mass generation has been traditionally plagued with seagull divergences, and all regularization procedures proposed over the years yield finite but scheme-dependent gluon masses. In this work we show how such divergences can be eliminated completely by virtue of a characteristic identity, valid in dimensional regularization. The ability to trigger the aforementioned identity hinges crucially on the particular Ansatz employed for the three-gluon vertex entering into the Schwinger-Dyson equation governing the gluon propagator. The use of the appropriate three-gluon vertex brings about an additional advantage: one obtains two separate (but coupled) integral equations, one for the effective charge and one for the gluon mass. This system of integral equations has a unique solution, which unambiguously determines these two quantities. Most notably, the effective charge freezes in the infrared, and the gluon mass displays power-law running in the ultraviolet, in agreement with earlier considerations.

  4. Increasing interpersonal trust through divergent thinking

    Directory of Open Access Journals (Sweden)

    Roberta eSellaro

    2014-06-01

    Full Text Available Interpersonal trust is an essential ingredient of many social relationships but how stable is it actually, and how is it controlled? There is evidence that the degree of trust into others might be rather volatile and can be affected by manipulations like drawing attention to personal interdependence or independence. Here we investigated whether the degree of interpersonal trust can be biased by inducing either a more integrative or a more cognitive-control mode by means of a creativity task requiring divergent or convergent thinking, respectively. Participants then performed the Trust Game, which provides an index of interpersonal trust by assessing the money units one participant (the trustor transfers to another participant (the trustee. As expected, participants transferred significantly more money to the trustee after engaging in divergent thinking as compared to convergent thinking. This observation provides support for the idea that interpersonal trust is controlled by domain-general (i.e., not socially dedicated cognitive states.

  5. High temperature phase transitions without infrared divergences

    International Nuclear Information System (INIS)

    Tetradis, N.; Wetterich, C.

    1993-09-01

    The most commonly used method for the study of high temperature phase transitions is based on the perturbative evaluation of the temperature dependent effective potential. This method becomes unreliable in the case of a second order or weakly first order phase transition, due to the appearance of infrared divergences. These divergences can be controlled through the method of the effective average action which employs renormalization group ideas. We report on the study of the high temperature phase transition for the N-component φ 4 theory. A detailed quantitative picture of the second order phase transition is presented, including the critical exponents for the behaviour in the vicinity of the critical temperature. An independent check of the results is obtained in the large N limit, and contact with the perturbative approach is established through the study of the Schwinger-Dyson equations. (orig.)

  6. [Evolutionary perspective in precocious puberty].

    Science.gov (United States)

    Hochberg, Ze'ev

    2014-10-01

    Pubertal development is subject to substantial heritability, but much variation remains to be explained, including fast changes over the last 150 years, that cannot be explained by changes of gene frequency in the population. This article discusses the influence of environmental factors to adjust maturational tempo in the service of fitness goals. Utilizing evolutionary development thinking (evo-devo), the author examines adolescence as an evolutionary life-history stage in its developmental context. The transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, social needs of adolescence and maturation toward youth and adulthood. Using Belsky's evolutionary theory of socialization, I show that familial psychosocial environment during the infancy-childhood and childhood-juvenility transitions foster a fast life-history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. The implications of the evo-devo framework for theory building, illuminates new directions in the understanding of precocious puberty other than a diagnosis of a disease.

  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. Testing evolutionary convergence on Europa

    Energy Technology Data Exchange (ETDEWEB)

    Chela-Flores, Julian [Instituto de Estudios Avanzados, Caracas (Venezuela); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)

    2002-11-01

    A major objective in solar system exploration is the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. Based on numerous examples, we argue in favour of the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe. We have suggested how to obtain preliminary insights into the question of the distribution of life in the universe. Universal evolution of intelligent behaviour is at the end of an evolutionary pathway, in which evolution of ion channels in the membrane of microorganisms occurs in its early stages. Further, we have argued that a preliminary test of this conjecture is feasible with experiments on the Europan surface or ocean, involving evolutionary biosignatures (ion channels). This aspect of the exploration for life in the solar system should be viewed as a complement to the astronomical approach for the search of evidence of the later stages of the evolutionary pathways towards intelligent behaviour. (author)

  9. Evolutionary ecology of virus emergence.

    Science.gov (United States)

    Dennehy, John J

    2017-02-01

    The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

  10. Evolutionary Roots and Diversification of the Genus Aeromonas.

    Science.gov (United States)

    Sanglas, Ariadna; Albarral, Vicenta; Farfán, Maribel; Lorén, J G; Fusté, M C

    2017-01-01

    Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available. More recently, several methods based on molecular sequence data have been developed to estimate speciation and extinction rates from phylogenies reconstructed from contemporary taxa. In this work, we determined the divergence time and temporal diversification of the genus Aeromonas by applying these methods widely used with eukaryotic taxa. Our analysis involved 150 Aeromonas strains using the concatenated sequences of two housekeeping genes (approximately 2,000 bp). Dating and diversification model analyses were performed using two different approaches: obtaining the consensus sequence from the concatenated sequences corresponding to all the strains belonging to the same species, or generating the species tree from multiple alignments of each gene. We used BEAST to perform a Bayesian analysis to estimate both the phylogeny and the divergence times. A global molecular clock cannot be assumed for any gene. From the chronograms obtained, we carried out a diversification analysis using several approaches. The results suggest that the genus Aeromonas began to diverge approximately 250 millions of years (Ma) ago. All methods used to determine Aeromonas diversification gave similar results, suggesting that the speciation process in this bacterial genus followed a rate-constant (Yule) diversification model, although there is a small probability that a slight

  11. COMPARATIVE FINANCIAL STATEMENTS. CONVERGENCE VERSUS DIVERGENCE

    Directory of Open Access Journals (Sweden)

    Nicolae ECOBICI

    2010-09-01

    Full Text Available In this paper I compared the Romanian financial statements with the US GAAP financial statements in terms of two criteria: first the reference period and secondly the shape, structure and content of financial statements. Nowadays the two accounting systems, the French and Anglo-Saxon, tend to harmonize. I will present the convergences and the divergences between the financial statements of Romania, subject to OMFP 3055/2009, in parallel with the Anglo-Saxon accounting system.

  12. Divergent Effects of Dendritic Cells on Pancreatitis

    Science.gov (United States)

    2015-09-01

    role of dendritic cells in pancreatitis. Dendritic cells are professional antigen presenting cells which initiate innate and adaptive immune... Lymphoid -tissue-specific homing of bone- marrow-derived dendritic cells . Blood. 113:6638–6647. http://dx.doi .org/10.1182/blood-2009-02-204321 Dapito...Award Number: W81XWH-12-1-0313 TITLE: Divergent Effects of Dendritic Cells on Pancreatitis PRINCIPAL INVESTIGATOR: Dr. George Miller

  13. Initial States: IR and Collinear Divergences

    International Nuclear Information System (INIS)

    Lavelle, Martin; McMullan, David

    2007-01-01

    The standard approach to the infra-red problem is to use the Bloch-Nordsieck trick to handle soft divergences and the Lee-Nauenberg (LN) theorem for collinear singularities. We show that this is inconsistent in the presence of massless initial particles. Furthermore, we show that using the LN theorem with such initial states introduces a non-convergent infinite series of diagrams at any fixed order in perturbation theory

  14. Carnot efficiency at divergent power output

    Science.gov (United States)

    Polettini, Matteo; Esposito, Massimiliano

    2017-05-01

    The widely debated feasibility of thermodynamic machines achieving Carnot efficiency at finite power has been convincingly dismissed. Yet, the common wisdom that efficiency can only be optimal in the limit of infinitely slow processes overlooks the dual scenario of infinitely fast processes. We corroborate that efficient engines at divergent power output are not theoretically impossible, framing our claims within the theory of Stochastic Thermodynamics. We inspect the case of an electronic quantum dot coupled to three particle reservoirs to illustrate the physical rationale.

  15. Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

    Science.gov (United States)

    McNamara, K B; Simmons, L W

    2017-09-01

    Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  16. Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus

    Science.gov (United States)

    Fan, Wentao; Sun, Zhaoyu; Shen, Tongtong; Xu, Danning; Huang, Kehe; Zhou, Jiyong; Song, Suquan; Yan, Liping

    2017-01-01

    Waterfowl parvoviruses are classified into goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) according to their antigenic features and host preferences. A novel duck parvovirus (NDPV), identified as a new variant of GPV, is currently infecting ducks, thus causing considerable economic loss. This study analyzed the molecular evolution and population dynamics of the emerging parvovirus capsid gene to investigate the evolutionary processes concerning the host shift of NDPV. Two important amino acids changes (Asn-489 and Asn-650) were identified in NDPV, which may be responsible for host shift of NDPV. Phylogenetic analysis indicated that the currently circulating NDPV originated from the GPV lineage. The Bayesian Markov chain Monte Carlo tree indicated that the NDPV diverged from GPV approximately 20 years ago. Evolutionary rate analyses demonstrated that GPV evolved with 7.674 × 10-4 substitutions/site/year, and the data for MDPV was 5.237 × 10-4 substitutions/site/year, whereas the substitution rate in NDPV branch was 2.25 × 10-3 substitutions/site/year. Meanwhile, viral population dynamics analysis revealed that the GPV major clade, including NDPV, grew exponentially at a rate of 1.717 year-1. Selection pressure analysis showed that most sites are subject to strong purifying selection and no positively selected sites were found in NDPV. The unique immune-epitopes in waterfowl parvovirus were also estimated, which may be helpful for the prediction of antibody binding sites against NDPV in ducks. PMID:28352261

  17. 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.

  18. 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.

  19. Evolutionary analysis of FAM83H in vertebrates.

    Directory of Open Access Journals (Sweden)

    Wushuang Huang

    Full Text Available Amelogenesis imperfecta is a group of disorders causing abnormalities in enamel formation in various phenotypes. Many mutations in the FAM83H gene have been identified to result in autosomal dominant hypocalcified amelogenesis imperfecta in different populations. However, the structure and function of FAM83H and its pathological mechanism have yet to be further explored. Evolutionary analysis is an alternative for revealing residues or motifs that are important for protein function. In the present study, we chose 50 vertebrate species in public databases representative of approximately 230 million years of evolution, including 1 amphibian, 2 fishes, 7 sauropsidas and 40 mammals, and we performed evolutionary analysis on the FAM83H protein. By sequence alignment, conserved residues and motifs were indicated, and the loss of important residues and motifs of five special species (Malayan pangolin, platypus, minke whale, nine-banded armadillo and aardvark was discovered. A phylogenetic time tree showed the FAM83H divergent process. Positive selection sites in the C-terminus suggested that the C-terminus of FAM83H played certain adaptive roles during evolution. The results confirmed some important motifs reported in previous findings and identified some new highly conserved residues and motifs that need further investigation. The results suggest that the C-terminus of FAM83H contain key conserved regions critical to enamel formation and calcification.

  20. Fast algorithms for computing phylogenetic divergence time.

    Science.gov (United States)

    Crosby, Ralph W; Williams, Tiffani L

    2017-12-06

    The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.

  1. Two families of astrophysical diverging lens models

    Science.gov (United States)

    Er, Xinzhong; Rogers, Adam

    2018-03-01

    In the standard gravitational lensing scenario, rays from a background source are bent in the direction of a foreground lensing mass distribution. Diverging lens behaviour produces deflections in the opposite sense to gravitational lensing, and is also of astrophysical interest. In fact, diverging lensing due to compact distributions of plasma has been proposed as an explanation for the extreme scattering events that produce frequency-dependent dimming of extragalactic radio sources, and may also be related to the refractive radio wave phenomena observed to affect the flux density of pulsars. In this work we study the behaviour of two families of astrophysical diverging lenses in the geometric optics limit, the power law, and the exponential plasma lenses. Generally, the members of these model families show distinct behaviour in terms of image formation and magnification, however the inclusion of a finite core for certain power-law lenses can produce a caustic and critical curve morphology that is similar to the well-studied Gaussian plasma lens. Both model families can produce dual radial critical curves, a novel distinction from the tangential distortion usually produced by gravitational (converging) lenses. The deflection angle and magnification of a plasma lens vary with the observational frequency, producing wavelength-dependent magnifications that alter the amplitudes and the shape of the light curves. Thus, multiwavelength observations can be used to physically constrain the distribution of the electron density in such lenses.

  2. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

    Science.gov (United States)

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

    2015-10-13

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

  3. The direct Flow parametric Proof of Gauss' Divergence Theorem revisited

    DEFF Research Database (Denmark)

    Markvorsen, Steen

    The standard proof of the divergence theorem in undergraduate calculus courses covers the theorem for static domains between two graph surfaces. We show that within first year undergraduate curriculum, the flow proof of the dynamic version of the divergence theorem - which is usually considered...... we apply the key instrumental concepts and verify the various steps towards this alternative proof of the divergence theorem....

  4. Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

    Science.gov (United States)

    Preston, Jill C.; Kellogg, Elizabeth A.

    2006-01-01

    Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

  5. Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.

    Directory of Open Access Journals (Sweden)

    Guillaume Chevereau

    Full Text Available The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the "morbidostat", a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations-an almost paradoxical behavior since this drug causes DNA damage and increases the mutation

  6. Characteristics, causes and evolutionary consequences of male-biased mutation.

    Science.gov (United States)

    Ellegren, Hans

    2007-01-07

    Mutation has traditionally been considered a random process, but this paradigm is challenged by recent evidence of divergence rate heterogeneity in different genomic regions. One facet of mutation rate variation is the propensity for genetic change to correlate with the number of germ cell divisions, reflecting the replication-dependent origin of many mutations. Haldane was the first to connect this association of replication and mutation to the difference in the number of cell divisions in oogenesis (low) and spermatogenesis (usually high), and the resulting sex difference in the rate of mutation. The concept of male-biased mutation has been thoroughly analysed in recent years using an evolutionary approach, in which sequence divergence of autosomes and/or sex chromosomes are compared to allow inference about the relative contribution of mothers and fathers in the accumulation of mutations. For instance, assuming that a neutral sequence is analysed, that rate heterogeneity owing to other factors is cancelled out by the investigation of many loci and that the effect of ancestral polymorphism is properly taken into account, the male-to-female mutation rate ratio, alpham, can be solved from the observed difference in rate of X and Y chromosome divergence. The male mutation bias is positively correlated with the relative excess of cell divisions in the male compared to the female germ line, as evidenced by a generation time effect: in mammals, alpham is estimated at approximately 4-6 in primates, approximately 3 in carnivores and approximately 2 in small rodents. Another life-history correlate is sexual selection: when there is intense sperm competition among males, increased sperm production will be associated with a larger number of mitotic cell divisions in spermatogenesis and hence an increase in alpham. Male-biased mutation has implications for important aspects of evolutionary biology such as mate choice in relation to mutation load, sexual selection and the

  7. Dinosaurs reveal the geographical signature of an evolutionary radiation.

    Science.gov (United States)

    O'Donovan, Ciara; Meade, Andrew; Venditti, Chris

    2018-03-01

    Dinosaurs dominated terrestrial ecosystems across the globe for over 100 million years and provide a classic example of an evolutionary radiation. However, little is known about how these animals radiated geographically to become globally distributed. Here, we use a biogeographical model to reconstruct the dinosaurs' ancestral locations, revealing the spatial mechanisms that underpinned this 170-million-year-long radiation. We find that dinosaurs spread rapidly initially, followed by a significant continuous and gradual reduction in their speed of movement towards the Cretaceous/Tertiary boundary (66 million years ago). This suggests that the predominant mode of dinosaur speciation changed through time with speciation originally largely driven by geographical isolation-when dinosaurs speciated more, they moved further. This was gradually replaced by increasing levels of sympatric speciation (species taking advantage of ecological opportunities within their existing environment) as terrestrial space became a limiting factor. Our results uncover the geographical signature of an evolutionary radiation.

  8. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  9. Hybrid fitness, adaptation and evolutionary diversification: lessons learned from Louisiana Irises.

    Science.gov (United States)

    Arnold, M L; Ballerini, E S; Brothers, A N

    2012-03-01

    Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a 'model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes.

  10. Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.

    Science.gov (United States)

    Medina-Carmona, Encarnación; Fuchs, Julian E; Gavira, Jose A; Mesa-Torres, Noel; Neira, Jose L; Salido, Eduardo; Palomino-Morales, Rogelio; Burgos, Miguel; Timson, David J; Pey, Angel L

    2017-09-15

    Human proteins are vulnerable towards disease-associated single amino acid replacements affecting protein stability and function. Interestingly, a few studies have shown that consensus amino acids from mammals or vertebrates can enhance protein stability when incorporated into human proteins. Here, we investigate yet unexplored relationships between the high vulnerability of human proteins towards disease-associated inactivation and recent evolutionary site-specific divergence of stabilizing amino acids. Using phylogenetic, structural and experimental analyses, we show that divergence from the consensus amino acids at several sites during mammalian evolution has caused local protein destabilization in two human proteins linked to disease: cancer-associated NQO1 and alanine:glyoxylate aminotransferase, mutated in primary hyperoxaluria type I. We demonstrate that a single consensus mutation (H80R) acts as a disease suppressor on the most common cancer-associated polymorphism in NQO1 (P187S). The H80R mutation reactivates P187S by enhancing FAD binding affinity through local and dynamic stabilization of its binding site. Furthermore, we show how a second suppressor mutation (E247Q) cooperates with H80R in protecting the P187S polymorphism towards inactivation through long-range allosteric communication within the structural ensemble of the protein. Our results support that recent divergence of consensus amino acids may have occurred with neutral effects on many functional and regulatory traits of wild-type human proteins. However, divergence at certain sites may have increased the propensity of some human proteins towards inactivation due to disease-associated mutations and polymorphisms. Consensus mutations also emerge as a potential strategy to identify structural hot-spots in proteins as targets for pharmacological rescue in loss-of-function genetic diseases. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please

  11. Intraspecific ecological niche divergence and reproductive shifts foster cytotype displacement and provide ecological opportunity to polyploids.

    Science.gov (United States)

    Karunarathne, Piyal; Schedler, Mara; Martínez, Eric J; Honfi, Ana I; Novichkova, Anastasiia; Hojsgaard, Diego

    2018-05-11

    Niche divergence between polyploids and their lower ploidy progenitors is one of the primary mechanisms fostering polyploid establishment and adaptive divergence. However, within-species chromosomal and reproductive variability have usually been neglected in community ecology and biodiversity analyses even though they have been recognized to play a role in the adaptive diversification of lineages. We used Paspalum intermedium, a grass species with diverging genetic systems (diploidy vs. autopolyploidy, allogamy vs. autogamy and sexuality vs. apomixis), to recognize the causality of biogeographic patterns, adaptation and ecological flexibility of cytotypes. Chromosome counts and flow cytometry were used to characterize within-species genetic systems diversity. Environmental niche modelling was used to evaluate intraspecific ecological attributes associated with environmental and climatic factors and to assess correlations among ploidy, reproductive modes and ecological conditions ruling species' population dynamics, range expansion, adaptation and evolutionary history. Two dominant cytotypes non-randomly distributed along local and regional geographical scales displayed niche differentiation, a directional shift in niche optima and signs of disruptive selection on ploidy-related ecological aptitudes for the exploitation of environmental resources. Ecologically specialized allogamous sexual diploids were found in northern areas associated with higher temperature, humidity and productivity, while generalist autogamous apomictic tetraploids occurred in southern areas, occupying colder and less productive environments. Four localities with a documented shift in ploidy and four mixed populations in a zone of ecological transition revealed an uneven replacement between cytotypes. Polyploidy and contrasting reproductive traits between cytotypes have promoted shifts in niche optima, and increased ecological tolerance and niche divergence. Ecologically specialized diploids

  12. Variational divergence in wave scattering theory with Kirchhoffean trial functions

    Science.gov (United States)

    Bird, J. F.

    1986-01-01

    In a recent study of variational improvement of the Kirchhoff approximation for electromagnetic scattering by rough surfaces, a key ingredient in the variational principle was found to diverge for important configurations (e.g., backscatter) if the polarization had any vertical component. The cause and a cure of this divergence are discussed here. The divergence is demonstrated to occur for arbitrary perfectly conducting scatterers and its universal characterstics are determined, by means of a general divergence criterion that is derived. A variational cure for the divergence is prescribed, and it is tested successfully on a standard scattering model.

  13. Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes.

    Science.gov (United States)

    Torres-Dowdall, Julián; Pierotti, Michele E R; Härer, Andreas; Karagic, Nidal; Woltering, Joost M; Henning, Frederico; Elmer, Kathryn R; Meyer, Axel

    2017-10-01

    Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only a few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted toward shorter wavelengths compared with the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution. © 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.

  14. Unexpected Functional Divergence of Bat Influenza Virus NS1 Proteins.

    Science.gov (United States)

    Turkington, Hannah L; Juozapaitis, Mindaugas; Tsolakos, Nikos; Corrales-Aguilar, Eugenia; Schwemmle, Martin; Hale, Benjamin G

    2018-03-01

    recent discovery of influenza A-like viruses in bats has raised questions over whether these entities could be a threat to humans. Understanding unique properties of the newly described bat influenza A-like viruses, such as their mechanisms to infect cells or how they manipulate host functions, is critical to assess their likelihood of causing disease. Here, we characterized the bat influenza A-like virus NS1 protein, a key virulence factor, and found unexpected functional divergence of this protein from counterparts in other influenza A viruses. Our study dissects the molecular changes required by bat influenza A-like virus NS1 to adopt classical influenza A virus properties and suggests consequences of bat influenza A-like virus infection, potential future evolutionary trajectories, and intriguing virus-host biology in bat species. Copyright © 2018 Turkington et al.

  15. Molecular evolution of the Bovini tribe (Bovidae, Bovinae: Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

    Directory of Open Access Journals (Sweden)

    McCulloch Alan

    2009-04-01

    Full Text Available Abstract Background If mutation within the coding region of the genome is largely not adaptive, the ratio of nonsynonymous (dN to synonymous substitutions (dS per site (dN/dS should be approximately equal among closely related species. Furthermore, dN/dS in divergence between species should be equivalent to dN/dS in polymorphisms. This hypothesis is of particular interest in closely related members of the Bovini tribe, because domestication has promoted rapid phenotypic divergence through strong artificial selection of some species while others remain undomesticated. We examined a number of genes that may be involved in milk production in Domestic cattle and a number of their wild relatives for evidence that domestication had affected molecular evolution. Elevated rates of dN/dS were further queried to determine if they were the result of positive selection, low effective population size (Ne or reduced selective constraint. Results We have found that the domestication process has contributed to higher dN/dS ratios in cattle, especially in the lineages leading to the Domestic cow (Bos taurus and Mithan (Bos frontalis and within some breeds of Domestic cow. However, the high rates of dN/dS polymorphism within B. taurus when compared to species divergence suggest that positive selection has not elevated evolutionary rates in these genes. Likewise, the low rate of dN/dS in Bison, which has undergone a recent population bottleneck, indicates a reduction in population size alone is not responsible for these observations. Conclusion The effect of selection depends on effective population size and the selection coefficient (Nes. Typically under domestication both selection pressure for traits important in fitness in the wild and Ne are reduced. Therefore, reduced selective constraint could be responsible for the observed elevated evolutionary ratios in domesticated species, especially in B. taurus and B. frontalis, which have the highest dN/dS in the

  16. Introduced species as evolutionary traps

    Science.gov (United States)

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  17. Multidimensional extended spatial evolutionary games.

    Science.gov (United States)

    Krześlak, Michał; Świerniak, Andrzej

    2016-02-01

    The goal of this paper is to study the classical hawk-dove model using mixed spatial evolutionary games (MSEG). In these games, played on a lattice, an additional spatial layer is introduced for dependence on more complex parameters and simulation of changes in the environment. Furthermore, diverse polymorphic equilibrium points dependent on cell reproduction, model parameters, and their simulation are discussed. Our analysis demonstrates the sensitivity properties of MSEGs and possibilities for further development. We discuss applications of MSEGs, particularly algorithms for modelling cell interactions during the development of tumours. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Feminist Encounters with Evolutionary Psychology

    OpenAIRE

    O'Neill, Rachel

    2016-01-01

    This Section of Australian Feminist Studies is the product of an event that took place at King’s College London in January 2015, hosted as part of the UK-based ‘Critical Sexology’ seminar series. Participants at this event – feminist scholars working across the fields of lin- guistics, cultural studies, sociology, and psychology – were invited to reflect on their encounters with evolutionary psychology (EP). As the event organiser, I was interested to prompt a discussion about how EP shapes t...

  19. Improving processes through evolutionary optimization.

    Science.gov (United States)

    Clancy, Thomas R

    2011-09-01

    As systems evolve over time, their natural tendency is to become increasingly more complex. Studies on complex systems have generated new perspectives on management in social organizations such as hospitals. Much of this research appears as a natural extension of the cross-disciplinary field of systems theory. This is the 18th in a series of articles applying complex systems science to the traditional management concepts of planning, organizing, directing, coordinating, and controlling. In this article, I discuss methods to optimize complex healthcare processes through learning, adaptation, and evolutionary planning.

  20. Historical change and evolutionary theory.

    Science.gov (United States)

    Masters, Roger D

    2007-09-01

    Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological