Evolutionary relevance facilitates visual information processing.

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Jackson, Russell E; Calvillo, Dusti P

2013-11-03

Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Evolutionary plasticity of habenular asymmetry with a conserved efferent connectivity pattern.

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Aldo Villalón

Full Text Available The vertebrate habenulae (Hb is an evolutionary conserved dorsal diencephalic nuclear complex that relays information from limbic and striatal forebrain regions to the ventral midbrain. One key feature of this bilateral nucleus is the presence of left-right differences in size, cytoarchitecture, connectivity, neurochemistry and/or gene expression. In teleosts, habenular asymmetry has been associated with preferential innervation of left-right habenular efferents into dorso-ventral domains of the midbrain interpeduncular nucleus (IPN. However, the degree of conservation of this trait and its relation to the structural asymmetries of the Hb are currently unknown. To address these questions, we performed the first systematic comparative analysis of structural and connectional asymmetries of the Hb in teleosts. We found striking inter-species variability in the overall shape and cytoarchitecture of the Hb, and in the frequency, strength and to a lesser degree, laterality of habenular volume at the population level. Directional asymmetry of the Hb was either to the left in D. rerio, E. bicolor, O. latipes, P. reticulata, B. splendens, or to the right in F. gardneri females. In contrast, asymmetry was absent in P. scalare and F. gardneri males at the population level, although in these species the Hb displayed volumetric asymmetries at the individual level. Inter-species variability was more pronounced across orders than within a single order, and coexisted with an overall conserved laterotopic representation of left-right habenular efferents into dorso-ventral domains of the IPN. These results suggest that the circuit design involving the Hb of teleosts promotes structural flexibility depending on developmental, cognitive and/or behavioural pressures, without affecting the main midbrain connectivity output, thus unveiling a key conserved role of this connectivity trait in the function of the circuit. We propose that ontogenic plasticity in habenular

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

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Bilsland Elizabeth

2007-08-01

Full Text Available Abstract Background The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. Results We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. Conclusion Evolutionary conservation of uORFs in yeasts can be traced up to 100

An evolutionary model for protein-coding regions with conserved RNA structure

DEFF Research Database (Denmark)

Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

2004-01-01

in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume...... components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

Spatial multiobjective optimization of agricultural conservation practices using a SWAT model and an evolutionary algorithm.

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Rabotyagov, Sergey; Campbell, Todd; Valcu, Adriana; Gassman, Philip; Jha, Manoj; Schilling, Keith; Wolter, Calvin; Kling, Catherine

2012-12-09

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,(5,12,20)) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization. Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods(3,4,9,10,13-15,17-19,22,23,25). In this application, we demonstrate a program which follows Rabotyagov et al.'s approach and integrates a modern and commonly used SWAT water quality model(7) with a

Evolutionary Relevance Facilitates Visual Information Processing

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Russell E. Jackson

2013-07-01

Full Text Available Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

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Scharfe Maren

2010-04-01

Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

Regulation of G-protein coupled receptor traffic by an evolutionary conserved hydrophobic signal.

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Angelotti, Tim; Daunt, David; Shcherbakova, Olga G; Kobilka, Brian; Hurt, Carl M

2010-04-01

Plasma membrane (PM) expression of G-protein coupled receptors (GPCRs) is required for activation by extracellular ligands; however, mechanisms that regulate PM expression of GPCRs are poorly understood. For some GPCRs, such as alpha2c-adrenergic receptors (alpha(2c)-ARs), heterologous expression in non-native cells results in limited PM expression and extensive endoplasmic reticulum (ER) retention. Recently, ER export/retentions signals have been proposed to regulate cellular trafficking of several GPCRs. By utilizing a chimeric alpha(2a)/alpha(2c)-AR strategy, we identified an evolutionary conserved hydrophobic sequence (ALAAALAAAAA) in the extracellular amino terminal region that is responsible in part for alpha(2c)-AR subtype-specific trafficking. To our knowledge, this is the first luminal ER retention signal reported for a GPCR. Removal or disruption of the ER retention signal dramatically increased PM expression and decreased ER retention. Conversely, transplantation of this hydrophobic sequence into alpha(2a)-ARs reduced their PM expression and increased ER retention. This evolutionary conserved hydrophobic trafficking signal within alpha(2c)-ARs serves as a regulator of GPCR trafficking.

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

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

2013-01-01

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

Functional conservation of the Drosophila gooseberry gene and its evolutionary alleles.

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Wei Liu

Full Text Available The Drosophila Pax gene gooseberry (gsb is required for development of the larval cuticle and CNS, survival to adulthood, and male fertility. These functions can be rescued in gsb mutants by two gsb evolutionary alleles, gsb-Prd and gsb-Pax3, which express the Drosophila Paired and mouse Pax3 proteins under the control of gooseberry cis-regulatory region. Therefore, both Paired and Pax3 proteins have conserved all the Gsb functions that are required for survival of embryos to fertile adults, despite the divergent primary sequences in their C-terminal halves. As gsb-Prd and gsb-Pax3 uncover a gsb function involved in male fertility, construction of evolutionary alleles may provide a powerful strategy to dissect hitherto unknown gene functions. Our results provide further evidence for the essential role of cis-regulatory regions in the functional diversification of duplicated genes during evolution.

Integrating Traditional and Evolutionary Knowledge in Biodiversity Conservation: a Population Level Case Study

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Dylan J. Fraser

2006-12-01

Full Text Available Despite their dual importance in the assessment of endangered/threatened species, there have been few attempts to integrate traditional ecological knowledge (TEK and evolutionary biology knowledge (EBK at the population level. We contrasted long-term aboriginal TEK with previously obtained EBK in the context of seasonal migratory habits and population biology of a salmonid fish, brook charr, (Salvelinus fontinalis inhabiting a large, remote postglacial lake. Compilation of TEK spanning four decades involved analytical workshops, semidirective interviews, and collaborative fieldwork with local aboriginal informants and fishing guides. We found that TEK complemented EBK of brook charr by providing concordant and additional information about (1 population viability; (2 breeding areas and migration patterns of divergent populations; and (3 the behavioral ecology of populations within feeding areas; all of which may ultimately affect the maintenance of population diversity. Aboriginal concerns related to human pressures on this species, not revealed by EBK, also help to focus future conservation initiatives for divergent populations and to encourage restoration of traditional fishing practices. However, relative to EBK, the relevance of TEK to salmonid biodiversity conservation was evident mainly at a smaller spatial scale, for example, that of individual rivers occupied by populations or certain lake sectors. Nevertheless, EBK was only collected over a 4-yr period, so TEK provided an essential long-term temporal window to evaluate population differences and persistence. We concluded that, despite different conceptual underpinnings, spatially and temporally varying TEK and EBK both contribute to the knowledge base required to achieve sustainability and effective biodiversity conservation planning for a given species. Such integration may be particularly relevant in many isolated regions, where intraspecific diversity can go unrecognized due to sparse

Evolutionary rescue: linking theory for conservation and medicine.

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Alexander, Helen K; Martin, Guillaume; Martin, Oliver Y; Bonhoeffer, Sebastian

2014-12-01

Evolutionary responses that rescue populations from extinction when drastic environmental changes occur can be friend or foe. The field of conservation biology is concerned with the survival of species in deteriorating global habitats. In medicine, in contrast, infected patients are treated with chemotherapeutic interventions, but drug resistance can compromise eradication of pathogens. These contrasting biological systems and goals have created two quite separate research communities, despite addressing the same central question of whether populations will decline to extinction or be rescued through evolution. We argue that closer integration of the two fields, especially of theoretical understanding, would yield new insights and accelerate progress on these applied problems. Here, we overview and link mathematical modelling approaches in these fields, suggest specific areas with potential for fruitful exchange, and discuss common ideas and issues for empirical testing and prediction.

Phylogenetically-informed priorities for amphibian conservation.

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Isaac, Nick J B; Redding, David W; Meredith, Helen M; Safi, Kamran

2012-01-01

The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

Phylogenetically-informed priorities for amphibian conservation.

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Nick J B Isaac

Full Text Available The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

Evolutionary conservation and changes in insect TRP channels

OpenAIRE

Tominaga Makoto; Kohno Keigo; Sokabe Takaaki; Matsuura Hironori; Kadowaki Tatsuhiko

2009-01-01

Abstract Background TRP (Transient Receptor Potential) channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP c...

Information, conservation and retrieval

Energy Technology Data Exchange (ETDEWEB)

Eng, T [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Norberg, E [National Swedish Archives, Stockholm (Sweden); Torbacke, J [Stockholm Univ. (Sweden). Dept. of History; Jensen, M [Swedish Radiation Protection Inst., Stockholm (Sweden)

1996-12-01

The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: `Active preservation - otherwise no achieves`; `The conservation and dissemination of information - A democratic issue`; and, `Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories`.

Information, conservation and retrieval

International Nuclear Information System (INIS)

Eng, T.; Norberg, E.; Torbacke, J.

1996-12-01

The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: 'Active preservation - otherwise no achieves'; 'The conservation and dissemination of information - A democratic issue'; and, 'Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories'

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

OpenAIRE

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

2013-01-01

Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long-term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and ecological refuges based on our review of the attributes of aquati...

Predicting loss of evolutionary history: Where are we?

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

2017-02-01

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

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...

The importance of immune gene variability (MHC in evolutionary ecology and conservation

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Sommer Simone

2005-10-01

Full Text Available Abstract Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs. However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC. MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I

Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

Science.gov (United States)

Safi, Kamran; Armour-Marshall, Katrina; Baillie, Jonathan E M; Isaac, Nick J B

2013-01-01

Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

Molecular insight into human platelet antigens: structural and evolutionary conservation analyses offer new perspective to immunogenic disorders.

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Landau, Meytal; Rosenberg, Nurit

2011-03-01

Human platelet antigens (HPAs) are polymorphisms in platelet membrane glycoproteins (GPs) that can stimulate production of alloantibodies once exposed to foreign platelets (PLTs) with different HPAs. These antibodies can cause neonatal alloimmune thrombocytopenia, posttransfusion purpura, and PLT transfusion refractoriness. Most HPAs are localized on the main PLT receptors: 1) integrin αIIbβ3, known as the fibrinogen receptor; 2) the GPIb-IX-V complex that functions as the receptor for von Willebrand factor; and 3) integrin α2β1, which functions as the collagen receptor. We analyzed the structural location and the evolutionary conservation of the residues associated with the HPAs to characterize the features that induce immunologic responses but do not cause inherited diseases. We found that all HPAs reside in positions located on the protein surface, apart from the ligand-binding site, and are evolutionary variable. Disease-causing mutations often reside in highly conserved and buried positions. In contrast, the HPAs affect residues on the protein surface that were not conserved throughout evolution; this explains their naive effect on the protein function. Nonetheless, the HPAs involve substitutions of solvent-exposed positions that lead to altered interfaces on the surface of the protein and might present epitopes foreign to the immune system. © 2010 American Association of Blood Banks.

Research on Information Sharing Mechanism of Network Organization Based on Evolutionary Game

Science.gov (United States)

Wang, Lin; Liu, Gaozhi

2018-02-01

This article first elaborates the concept and effect of network organization, and the ability to share information is analyzed, secondly introduces the evolutionary game theory, network organization for information sharing all kinds of limitations, establishes the evolutionary game model, analyzes the dynamic evolution of network organization of information sharing, through reasoning and evolution. The network information sharing by the initial state and two sides of the game payoff matrix of excess profits and information is the information sharing of cost and risk sharing are the influence of network organization node information sharing decision.

Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

Science.gov (United States)

Catania, Francesco; Lynch, Michael

2010-05-04

In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

Directory of Open Access Journals (Sweden)

Kamran Safi

Full Text Available BACKGROUND: Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE. Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. METHODS AND PRINCIPAL FINDINGS: Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. CONCLUSIONS: Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

Evolutionary principles and their practical application

DEFF Research Database (Denmark)

Hendry, A. P.; Kinnison, M. T.; Heino, M.

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...

Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

Directory of Open Access Journals (Sweden)

Lynch Michael

2010-05-01

Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

Aligning science and policy to achieve evolutionarily enlightened conservation.

Science.gov (United States)

Cook, Carly N; Sgrò, Carla M

2017-06-01

There is increasing recognition among conservation scientists that long-term conservation outcomes could be improved through better integration of evolutionary theory into management practices. Despite concerns that the importance of key concepts emerging from evolutionary theory (i.e., evolutionary principles and processes) are not being recognized by managers, there has been little effort to determine the level of integration of evolutionary theory into conservation policy and practice. We assessed conservation policy at 3 scales (international, national, and provincial) on 3 continents to quantify the degree to which key evolutionary concepts, such as genetic diversity and gene flow, are being incorporated into conservation practice. We also evaluated the availability of clear guidance within the applied evolutionary biology literature as to how managers can change their management practices to achieve better conservation outcomes. Despite widespread recognition of the importance of maintaining genetic diversity, conservation policies provide little guidance about how this can be achieved in practice and other relevant evolutionary concepts, such as inbreeding depression, are mentioned rarely. In some cases the poor integration of evolutionary concepts into management reflects a lack of decision-support tools in the literature. Where these tools are available, such as risk-assessment frameworks, they are not being adopted by conservation policy makers, suggesting that the availability of a strong evidence base is not the only barrier to evolutionarily enlightened management. We believe there is a clear need for more engagement by evolutionary biologists with policy makers to develop practical guidelines that will help managers make changes to conservation practice. There is also an urgent need for more research to better understand the barriers to and opportunities for incorporating evolutionary theory into conservation practice. © 2016 Society for Conservation

The use of information theory in evolutionary biology.

Science.gov (United States)

Adami, Christoph

2012-05-01

Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task. © 2012 New York Academy of Sciences.

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.

Evolutionary principles and their practical application.

Science.gov (United States)

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

2011-03-01

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

Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservation.

Science.gov (United States)

Guevara Andino, Juan Ernesto; Pitman, Nigel C A; Ter Steege, Hans; Mogollón, Hugo; Ceron, Carlos; Palacios, Walter; Oleas, Nora; Fine, Paul V A

2017-11-01

Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one-hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.

Patterns of evolutionary conservation of essential genes correlate with their compensability.

Directory of Open Access Journals (Sweden)

Tobias Bergmiller

2012-06-01

Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

Fine-resolution conservation planning with limited climate-change information.

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Shah, Payal; Mallory, Mindy L; Ando, Amy W; Guntenspergen, Glenn R

2017-04-01

Climate-change induced uncertainties in future spatial patterns of conservation-related outcomes make it difficult to implement standard conservation-planning paradigms. A recent study translates Markowitz's risk-diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate-change scenarios for carrying out fine-resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk-return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate-change information and full climate-change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate-change forecasts such that the best possible risk-return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate-change information could be reduced by 17% relative to other iterative approaches. © 2016 Society for Conservation Biology.

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.

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Benjamin R Jack

2016-05-01

Full Text Available Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein-protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes.

Information and knowledge: an evolutionary framework for information science

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Marcia J. Bates

2005-01-01

Full Text Available Background. Many definitions of information, knowledge, and data have been suggested throughout the history of information science. In this article, the objective is to provide definitions that are usable for the physical, biological, and social meanings of the terms, covering the various senses important to our field. Argument. Information 1 is defined as the pattern of organization of matter and energy. Information 2 is defined as some pattern of organization of matter and energy that has been given meaning by a living being. Knowledge is defined as information given meaning and integrated with other contents of understanding. Elaboration. The approach is rooted in an evolutionary framework; that is, modes of information perception, processing, transmission, and storage are seen to have developed as a part of the general evolution of members of the animal kingdom. Brains are expensive for animals to support; consequently, efficient storage, including, particularly, storage at emergent levels-for example, storing the concept of chair, rather than specific memories of all chairs ever seen, is powerful and effective for animals. Conclusion. Thus, rather than being reductionist, the approach taken demonstrates the fundamentally emergent nature of most of what higher animals and human beings, in particular, experience as information.

Identification of an evolutionary conserved SURF-6 domain in a family of nucleolar proteins extending from human to yeast

International Nuclear Information System (INIS)

Polzikov, Mikhail; Zatsepina, Olga; Magoulas, Charalambos

2005-01-01

The mammalian SURF-6 protein is localized in the nucleolus, yet its function remains elusive in the recently characterized nucleolar proteome. We discovered by searching the Protein families database that a unique evolutionary conserved SURF-6 domain is present in the carboxy-terminal of a novel family of eukaryotic proteins extending from human to yeast. By using the enhanced green fluorescent protein as a fusion protein marker in mammalian cells, we show that proteins from distantly related taxonomic groups containing the SURF-6 domain are localized in the nucleolus. Deletion sequence analysis shows that multiple regions of the SURF-6 protein are capable of nucleolar targeting independently of the evolutionary conserved domain. We identified that the Saccharomyces cerevisiae member of the SURF-6 family, named rrp14 or ykl082c, has been categorized in yeast databases to interact with proteins involved in ribosomal biogenesis and cell polarity. These results classify SURF-6 as a new family of nucleolar proteins in the eukaryotic kingdom and point out that SURF-6 has a distinct domain within the known nucleolar proteome that may mediate complex protein-protein interactions for analogous processes between yeast and mammalian cells

Evolutionary conservation of plant gibberellin signalling pathway components

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Reski Ralf

2007-11-01

Full Text Available Abstract Background: Gibberellins (GA are plant hormones that can regulate germination, elongation growth, and sex determination. They ubiquitously occur in seed plants. The discovery of gibberellin receptors, together with advances in understanding the function of key components of GA signalling in Arabidopsis and rice, reveal a fairly short GA signal transduction route. The pathway essentially consists of GID1 gibberellin receptors that interact with F-box proteins, which in turn regulate degradation of downstream DELLA proteins, suppressors of GA-controlled responses. Results: Arabidopsis sequences of the gibberellin signalling compounds were used to screen databases from a variety of plants, including protists, for homologues, providing indications for the degree of conservation of the pathway. The pathway as such appears completely absent in protists, the moss Physcomitrella patens shares only a limited homology with the Arabidopsis proteins, thus lacking essential characteristics of the classical GA signalling pathway, while the lycophyte Selaginella moellendorffii contains a possible ortholog for each component. The occurrence of classical GA responses can as yet not be linked with the presence of homologues of the signalling pathway. Alignments and display in neighbour joining trees of the GA signalling components confirm the close relationship of gymnosperms, monocotyledonous and dicotyledonous plants, as suggested from previous studies. Conclusion: Homologues of the GA-signalling pathway were mainly found in vascular plants. The GA signalling system may have its evolutionary molecular onset in Physcomitrella patens, where GAs at higher concentrations affect gravitropism and elongation growth.

Fine‐resolution conservation planning with limited climate‐change information

Science.gov (United States)

Shah, Payal; Mallory, Mindy L.; Ando , Amy W.; Guntenspergen, Glenn R.

2017-01-01

Climate‐change induced uncertainties in future spatial patterns of conservation‐related outcomes make it difficult to implement standard conservation‐planning paradigms. A recent study translates Markowitz's risk‐diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate‐change scenarios for carrying out fine‐resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk‐return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate‐change information and full climate‐change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate‐change forecasts such that the best possible risk‐return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate‐change information could be reduced by 17% relative to other iterative approaches.

Fixism and conservation science.

Science.gov (United States)

Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

2017-08-01

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

Science.gov (United States)

Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

2012-01-01

Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

Resource Conservation and Recovery Act Information (RCRAInfo)

Data.gov (United States)

U.S. Environmental Protection Agency — The Resource Conservation and Recovery Act Information (RCRAInfo) system contains information reported to the state environmental programs on activities and cleanup...

Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservation

OpenAIRE

Guevara Andino, Juan Ernesto; Pitman, Nigel C. A.; ter Steege, Hans; Mogollón, Hugo; Ceron, Carlos; Palacios, Walter; Oleas, Nora; Fine, Paul V. A.

2017-01-01

Abstract Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one‐hectare plots in terra firme forests of Ecuadorian Amazon. In these plots...

Incorporating evolutionary history into conservation planning in biodiversity hotspots.

Science.gov (United States)

Buerki, Sven; Callmander, Martin W; Bachman, Steven; Moat, Justin; Labat, Jean-Noël; Forest, Félix

2015-02-19

There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

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

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Shirai Leila T

2012-02-01

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

Environmental Performance Information Use by Conservation Agency Staff

Science.gov (United States)

Wardropper, Chloe Bradley

2018-04-01

Performance-based conservation has long been recognized as crucial to improving program effectiveness, particularly when environmental conditions are dynamic. Yet few studies have investigated the use of environmental performance information by staff of conservation organizations. This article identifies attitudinal, policy and organizational factors influencing the use of a type of performance information—water quality information—by Soil and Water Conservation District staff in the Upper Mississippi River Basin region. An online survey ( n = 277) revealed a number of important variables associated with greater information use. Variables included employees' prosocial motivation, or the belief that they helped people and natural resources through their job, the perceived trustworthiness of data, the presence of a U.S. Clean Water Act Total Maximum Daily Load standard designation, and staff discretion to prioritize programs locally. Conservation programs that retain motivated staff and provide them the resources and flexibility to plan and evaluate their work with environmental data may increase conservation effectiveness under changing conditions.

Climate Velocity Can Inform Conservation in a Warming World.

Science.gov (United States)

Brito-Morales, Isaac; García Molinos, Jorge; Schoeman, David S; Burrows, Michael T; Poloczanska, Elvira S; Brown, Christopher J; Ferrier, Simon; Harwood, Tom D; Klein, Carissa J; McDonald-Madden, Eve; Moore, Pippa J; Pandolfi, John M; Watson, James E M; Wenger, Amelia S; Richardson, Anthony J

2018-06-01

Climate change is shifting the ranges of species. Simple predictive metrics of range shifts such as climate velocity, that do not require extensive knowledge or data on individual species, could help to guide conservation. We review research on climate velocity, describing the theory underpinning the concept and its assumptions. We highlight how climate velocity has already been applied in conservation-related research, including climate residence time, climate refugia, endemism, historic and projected range shifts, exposure to climate change, and climate connectivity. Finally, we discuss ways to enhance the use of climate velocity in conservation through tailoring it to be more biologically meaningful, informing design of protected areas, conserving ocean biodiversity in 3D, and informing conservation actions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Conservation Evo-Devo: Preserving Biodiversity by Understanding Its Origins.

Science.gov (United States)

Campbell, Calum S; Adams, Colin E; Bean, Colin W; Parsons, Kevin J

2017-10-01

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

Incorporating phylogenetic information for the definition of floristic districts in hyper-diverse Amazon forests: implications for conservation

NARCIS (Netherlands)

Guevara, J.E.; Pitman, N.C.A.; ter Steege, H.; Mogollón, H.; Ceron, C.; Palacios, W.; Oleas, N.; Fine, P.V.A.

2017-01-01

Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the

Accounting for results: how conservation organizations report performance information.

Science.gov (United States)

Rissman, Adena R; Smail, Robert

2015-04-01

Environmental program performance information is in high demand, but little research suggests why conservation organizations differ in reporting performance information. We compared performance measurement and reporting by four private-land conservation organizations: Partners for Fish and Wildlife in the US Fish and Wildlife Service (national government), Forest Stewardship Council-US (national nonprofit organization), Land and Water Conservation Departments (local government), and land trusts (local nonprofit organization). We asked: (1) How did the pattern of performance reporting relationships vary across organizations? (2) Was political conflict among organizations' principals associated with greater performance information? and (3) Did performance information provide evidence of program effectiveness? Based on our typology of performance information, we found that most organizations reported output measures such as land area or number of contracts, some reported outcome indicators such as adherence to performance standards, but few modeled or measured environmental effects. Local government Land and Water Conservation Departments reported the most types of performance information, while local land trusts reported the fewest. The case studies suggest that governance networks influence the pattern and type of performance reporting, that goal conflict among principles is associated with greater performance information, and that performance information provides unreliable causal evidence of program effectiveness. Challenging simple prescriptions to generate more data as evidence, this analysis suggests (1) complex institutional and political contexts for environmental program performance and (2) the need to supplement performance measures with in-depth evaluations that can provide causal inferences about program effectiveness.

Estimation of body-size traits by photogrammetry in large mammals to inform conservation.

Science.gov (United States)

Berger, Joel

2012-10-01

Photography, including remote imagery and camera traps, has contributed substantially to conservation. However, the potential to use photography to understand demography and inform policy is limited. To have practical value, remote assessments must be reasonably accurate and widely deployable. Prior efforts to develop noninvasive methods of estimating trait size have been motivated by a desire to answer evolutionary questions, measure physiological growth, or, in the case of illegal trade, assess economics of horn sizes; but rarely have such methods been directed at conservation. Here I demonstrate a simple, noninvasive photographic technique and address how knowledge of values of individual-specific metrics bears on conservation policy. I used 10 years of data on juvenile moose (Alces alces) to examine whether body size and probability of survival are positively correlated in cold climates. I investigated whether the presence of mothers improved juvenile survival. The posited latter relation is relevant to policy because harvest of adult females has been permitted in some Canadian and American jurisdictions under the assumption that probability of survival of young is independent of maternal presence. The accuracy of estimates of head sizes made from photographs exceeded 98%. The estimates revealed that overwinter juvenile survival had no relation to the juvenile's estimated mass (p < 0.64) and was more strongly associated with maternal presence (p < 0.02) than winter snow depth (p < 0.18). These findings highlight the effects on survival of a social dynamic (the mother-young association) rather than body size and suggest a change in harvest policy will increase survival. Furthermore, photographic imaging of growth of individual juvenile muskoxen (Ovibos moschatus) over 3 Arctic winters revealed annual variability in size, which supports the idea that noninvasive monitoring may allow one to detect how some environmental conditions ultimately affect body growth. �

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.

Neotropical fish-fruit interactions: eco-evolutionary dynamics and conservation.

Science.gov (United States)

Correa, Sandra Bibiana; Costa-Pereira, Raul; Fleming, Theodore; Goulding, Michael; Anderson, Jill T

2015-11-01

Frugivorous fish play a prominent role in seed dispersal and reproductive dynamics of plant communities in riparian and floodplain habitats of tropical regions worldwide. In Neotropical wetlands, many plant species have fleshy fruits and synchronize their fruiting with the flood season, when fruit-eating fish forage in forest and savannahs for periods of up to 7 months. We conducted a comprehensive analysis to examine the evolutionary origin of fish-fruit interactions, describe fruit traits associated with seed dispersal and seed predation, and assess the influence of fish size on the effectiveness of seed dispersal by fish (ichthyochory). To date, 62 studies have documented 566 species of fruits and seeds from 82 plant families in the diets of 69 Neotropical fish species. Fish interactions with flowering plants are likely to be as old as 70 million years in the Neotropics, pre-dating most modern bird-fruit and mammal-fruit interactions, and contributing to long-distance seed dispersal and possibly the radiation of early angiosperms. Ichthyochory occurs across the angiosperm phylogeny, and is more frequent among advanced eudicots. Numerous fish species are capable of dispersing small seeds, but only a limited number of species can disperse large seeds. The size of dispersed seeds and the probability of seed dispersal both increase with fish size. Large-bodied species are the most effective seed dispersal agents and remain the primary target of fishing activities in the Neotropics. Thus, conservation efforts should focus on these species to ensure continuity of plant recruitment dynamics and maintenance of plant diversity in riparian and floodplain ecosystems. © 2015 Cambridge Philosophical Society.

Insights from life history theory for an explicit treatment of trade-offs in conservation biology.

Science.gov (United States)

Charpentier, Anne

2015-06-01

As economic and social contexts become more embedded within biodiversity conservation, it becomes obvious that resources are a limiting factor in conservation. This recognition is leading conservation scientists and practitioners to increasingly frame conservation decisions as trade-offs between conflicting societal objectives. However, this framing is all too often done in an intuitive way, rather than by addressing trade-offs explicitly. In contrast, the concept of trade-off is a keystone in evolutionary biology, where it has been investigated extensively. I argue that insights from evolutionary theory can provide methodological and theoretical support to evaluating and quantifying trade-offs in biodiversity conservation. I reviewed the diverse ways in which trade-offs have emerged within the context of conservation and how advances from evolutionary theory can help avoid the main pitfalls of an implicit approach. When studying both evolutionary trade-offs (e.g., reproduction vs. survival) and conservation trade-offs (e.g., biodiversity conservation vs. agriculture), it is crucial to correctly identify the limiting resource, hold constant the amount of this resource when comparing different scenarios, and choose appropriate metrics to quantify the extent to which the objectives have been achieved. Insights from studies in evolutionary theory also reveal how an inadequate selection of conservation solutions may result from considering suboptimal rather than optional solutions when examining whether a trade-off exits between 2 objectives. Furthermore, the shape of a trade-off curve (i.e., whether the relationship between 2 objectives follows a concave, convex, or linear form) is known to affect crucially the definition of optimal solutions in evolutionary biology and very likely affects decisions in biodiversity conservation planning too. This interface between evolutionary biology and biodiversity conservation can therefore provide methodological guidance to

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'.

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.

When theory trumps ideology: Lessons from evolutionary psychology.

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Tybur, Joshua M; Navarrete, Carlos David

2015-01-01

Evolutionary psychologists are personally liberal, just as social psychologists are. Yet their research has rarely been perceived as liberally biased--if anything, it has been erroneously perceived as motivated by conservative political agendas. Taking a closer look at evolutionary psychologists might offer the broader social psychology community guidance in neutralizing some of the biases Duarte et al. discuss.

Evolutionary Awareness

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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.

Evolutionary conservation and expression of miR-10a-3p in olive flounder and rock bream.

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Jo, Ara; Im, Jennifer; Lee, Hee-Eun; Jang, Dongmin; Nam, Gyu-Hwi; Mishra, Anshuman; Kim, Woo-Jin; Kim, Won; Cha, Hee-Jae; Kim, Heui-Soo

2017-09-10

MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that mainly bind to the seed sequences located within the 3' untranslated region (3' UTR) of target genes. They perform an important biological function as regulators of gene expression. Different genes can be regulated by the same miRNA, whilst different miRNAs can be regulated by the same genes. Here, the evolutionary conservation and expression pattern of miR-10a-3p in olive flounder and rock bream was examined. Binding sites (AAAUUC) to seed region of the 3' UTR of target genes were highly conserved in various species. The expression pattern of miR-10a-3p was ubiquitous in the examined tissues, whilst its expression level was decreased in gill tissues infected by viral hemorrhagic septicemia virus (VHSV) compared to the normal control. In the case of rock bream, the spleen, kidney, and liver tissues showed dominant expression levels of miR-10a-3p. Only the liver tissues in the rock bream samples infected by the iridovirus indicated a dominant miR-10a-3p expression. The gene ontology (GO) analysis of predicted target genes for miR-10a-3p revealed that multiple genes are related to binding activity, catalytic activity, cell components as well as cellular and metabolic process. Overall the results imply that the miR-10a-3p could be used as a biomarker to detect VHSV infection in olive flounder and iridovirus infection in rock bream. In addition, the data provides fundamental information for further study of the complex interaction between miR-10a-3p and gene expression. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

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Tiancheng Liu

2015-01-01

Full Text Available Evolutionary developmental biology (EVO-DEVO tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA. Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

Domain architecture conservation in orthologs

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2011-01-01

Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

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Gray, Claudia L.; Wearn, Oliver R.; Owen, Nisha R.

2018-01-01

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

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Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

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Maréchal Eric

2005-03-01

Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

DEFF Research Database (Denmark)

Irimia, Manuel; Rukov, Jakob L; Penny, David

2007-01-01

Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern...... in Caenorhabditis nematodes-more than 92% of cassette exons from Caenorhabditis elegans are conserved in Caenorhabditis briggsae and/or Caenorhabditis remanei. High levels of conservation extend to minor-form exons (present in a minority of transcripts) and are particularly pronounced for exons showing complex...... patterns of splicing. The functionality of the vast majority of cassette exons is underscored by various other features. We suggest that differences in conservation between lineages reflect differences in levels of functionality and further suggest that these differences are due to differences in intron...

Expanding the eco-evolutionary context of herbicide resistance research.

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Neve, Paul; Busi, Roberto; Renton, Michael; Vila-Aiub, Martin M

2014-09-01

The potential for human-driven evolution in economically and environmentally important organisms in medicine, agriculture and conservation management is now widely recognised. The evolution of herbicide resistance in weeds is a classic example of rapid adaptation in the face of human-mediated selection. Management strategies that aim to slow or prevent the evolution of herbicide resistance must be informed by an understanding of the ecological and evolutionary factors that drive selection in weed populations. Here, we argue for a greater focus on the ultimate causes of selection for resistance in herbicide resistance studies. The emerging fields of eco-evolutionary dynamics and applied evolutionary biology offer a means to achieve this goal and to consider herbicide resistance in a broader and sometimes novel context. Four relevant research questions are presented, which examine (i) the impact of herbicide dose on selection for resistance, (ii) plant fitness in herbicide resistance studies, (iii) the efficacy of herbicide rotations and mixtures and (iv) the impacts of gene flow on resistance evolution and spread. In all cases, fundamental ecology and evolution have the potential to offer new insights into herbicide resistance evolution and management. © 2014 Society of Chemical Industry.

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...

African wildlife conservation and the evolution of hunting institutions

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't Sas-Rolfes, Michael

2017-11-01

Hunting regulation presents a significant challenge for contemporary global conservation governance. Motivated by various incentives, hunters may act legally or illegally, for or against the interests of conservation. Hunter incentives are shaped by the interactions between unevenly evolving formal and informal institutions, embedded in socio-ecological systems. To work effectively for conservation, regulatory interventions must take these evolving institutional interactions into account. Drawing on analytical tools from evolutionary institutional economics, this article examines the trajectory of African hunting regulation and its consequences. Concepts of institutional dynamics, fit, scale, and interplay are applied to case studies of rhinoceros and lion hunting to highlight issues of significance to conservation outcomes. These include important links between different forms of hunting and dynamic interplay with institutions of trade. The case studies reveal that inappropriate formal regulatory approaches may be undermined by adaptive informal market responses. Poorly regulated hunting may lead to calls for stricter regulations or bans, but such legal restrictions may in turn perversely lead to more intensified and organised illegal hunting activity, further undermining conservation objectives. I conclude by offering insights and recommendations to guide more effective future regulatory interventions and priorities for further research. Specifically, I advocate approaches that move beyond simplistic regulatory interventions toward more complex, but supportive, institutional arrangements that align formal and informal institutions through inclusive stakeholder engagement.

Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation

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Neaves, Linda E.; Frankham, Greta J.; Dennison, Siobhan; FitzGibbon, Sean; Flannagan, Cheyne; Gillett, Amber; Hynes, Emily; Handasyde, Kathrine; Helgen, Kristofer M.; Tsangaras, Kyriakos; Greenwood, Alex D.; Eldridge, Mark D. B.; Johnson, Rebecca N.

2016-01-01

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia’s most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context. PMID:27588685

Phylogeography of the Koala, (Phascolarctos cinereus, and Harmonising Data to Inform Conservation.

Directory of Open Access Journals (Sweden)

Linda E Neaves

Full Text Available The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus, one of Australia's most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA Control Region (CR was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study. The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.

Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation.

Science.gov (United States)

Neaves, Linda E; Frankham, Greta J; Dennison, Siobhan; FitzGibbon, Sean; Flannagan, Cheyne; Gillett, Amber; Hynes, Emily; Handasyde, Kathrine; Helgen, Kristofer M; Tsangaras, Kyriakos; Greenwood, Alex D; Eldridge, Mark D B; Johnson, Rebecca N

2016-01-01

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia's most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.

Are hotspots of evolutionary potential adequately protected in southern California?

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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.

Split diversity in constrained conservation prioritization using integer linear programming.

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Chernomor, Olga; Minh, Bui Quang; Forest, Félix; Klaere, Steffen; Ingram, Travis; Henzinger, Monika; von Haeseler, Arndt

2015-01-01

Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.Depending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator-prey interactions between the species in a community to define viability constraints.Despite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.We exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda.

Multispecies genetic objectives in spatial conservation planning.

Science.gov (United States)

Nielsen, Erica S; Beger, Maria; Henriques, Romina; Selkoe, Kimberly A; von der Heyden, Sophie

2017-08-01

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns. © 2016 Society for Conservation Biology.

Evolutionary conserved neural signature of early life stress affects animal social competence.

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Nyman, Cecilia; Fischer, Stefan; Aubin-Horth, Nadia; Taborsky, Barbara

2018-01-31

In vertebrates, the early social environment can persistently influence behaviour and social competence later in life. However, the molecular mechanisms underlying variation in animal social competence are largely unknown. In rats, high-quality maternal care causes an upregulation of hippocampal glucocorticoid receptors ( gr ) and reduces offspring stress responsiveness. This identifies gr regulation as a candidate mechanism for maintaining variation in animal social competence. We tested this hypothesis in a highly social cichlid fish, Neolamprologus pulcher , reared with or without caring parents. We find that the molecular pathway translating early social experience into later-life alterations of the stress axis is homologous across vertebrates: fish reared with parents expressed the glucocorticoid receptor gr1 more in the telencephalon. Furthermore, expression levels of the transcription factor egr-1 (early growth response 1) were associated with gr1 expression in the telencephalon and hypothalamus. When blocking glucocorticoid receptors (GR) with an antagonist, mifepristone (RU486), parent-reared individuals showed more socially appropriate, submissive behaviour when intruding on a larger conspecific's territory. Remarkably, mifepristone-treated fish were less attacked by territory owners and had a higher likelihood of territory takeover. Our results indicate that early social-environment effects on stress axis programming are mediated by an evolutionary conserved molecular pathway, which is causally involved in environmentally induced variation of animal social competence. © 2018 The Author(s).

Differential Evolutionary Constraints in the Evolution of Chemoreceptors: A Murine and Human Case Study

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Ricardo D’Oliveira Albanus

2014-01-01

Full Text Available Chemoreception is among the most important sensory modalities in animals. Organisms use the ability to perceive chemical compounds in all major ecological activities. Recent studies have allowed the characterization of chemoreceptor gene families. These genes present strikingly high variability in copy numbers and pseudogenization degrees among different species, but the mechanisms underlying their evolution are not fully understood. We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes in Mus musculus, Homo sapiens, and Rattus norvegicus. We have observed significant differences regarding the constraints on the orthologous groups and network topologies of chemoreceptors and signal transduction machinery. Our findings suggest that chemosensory receptor genes are less constrained than their signal transducing machinery, resulting in greater receptor diversity and conservation of information processing pathways. More importantly, we have observed significant differences among the receptors themselves, suggesting that olfactory and bitter taste receptors are more conserved than vomeronasal receptors.

Catchments as conservation units for riverine biodiversity | Wishart ...

African Journals Online (AJOL)

The geological structure and longitudinal nature of river systems provide a possible barrier to the dispersal of lotic organisms. This has the potential to drive evolutionary processes such as genetic differentiation and subsequent allopatric speciation. In the conservation of lotic ecosystems population and evolutionary ...

Exploring the miRNA regulatory network using evolutionary correlations.

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Benedikt Obermayer

2014-10-01

Full Text Available Post-transcriptional regulation by miRNAs is a widespread and highly conserved phenomenon in metazoans, with several hundreds to thousands of conserved binding sites for each miRNA, and up to two thirds of all genes under miRNA regulation. At the same time, the effect of miRNA regulation on mRNA and protein levels is usually quite modest and associated phenotypes are often weak or subtle. This has given rise to the notion that the highly interconnected miRNA regulatory network exerts its function less through any individual link and more via collective effects that lead to a functional interdependence of network links. We present a Bayesian framework to quantify conservation of miRNA target sites using vertebrate whole-genome alignments. The increased statistical power of our phylogenetic model allows detection of evolutionary correlation in the conservation patterns of site pairs. Such correlations could result from collective functions in the regulatory network. For instance, co-conservation of target site pairs supports a selective benefit of combinatorial regulation by multiple miRNAs. We find that some miRNA families are under pronounced co-targeting constraints, indicating a high connectivity in the regulatory network, while others appear to function in a more isolated way. By analyzing coordinated targeting of different curated gene sets, we observe distinct evolutionary signatures for protein complexes and signaling pathways that could reflect differences in control strategies. Our method is easily scalable to analyze upcoming larger data sets, and readily adaptable to detect high-level selective constraints between other genomic loci. We thus provide a proof-of-principle method to understand regulatory networks from an evolutionary perspective.

The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

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Michael K DeSalvo

2014-11-01

Full Text Available AbstractCentral nervous system (CNS function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with FACS and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ABC and SLC transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes.

Science.gov (United States)

DeSalvo, Michael K; Hindle, Samantha J; Rusan, Zeid M; Orng, Souvinh; Eddison, Mark; Halliwill, Kyle; Bainton, Roland J

2014-01-01

Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.

Discovery of Conservation and Diversification of miR171 Genes by Phylogenetic Analysis based on Global Genomes

Directory of Open Access Journals (Sweden)

Xudong Zhu

2015-07-01

Full Text Available The microRNA171 (miR171 family is widely distributed and highly conserved in a range of species and plays critical roles in regulating plant growth and development through repressing expression of ( transcription factors. However, information on the evolutionary conservation and functional diversification of the miRNA171 family members remains scanty. We reconstructed the phylogenetic relationships among miR171 precursor and mature sequences so as to investigate the extent and degree of evolutionary conservation of miR171 in (L. Heynh. (ath, grape ( L. (vvi, poplar ( Torr. & A.Gray ex Hook. (ptc, and rice ( L. (osa. Despite strong conservation of over 80%, some mature miR171 sequences, such as , and and , -, and -, have undergone critical sequence variation, leading to functional diversification, since they target non gene transcript(s. Phylogenetic analyses revealed a combination of old ancestral relationships and recent lineage-specific diversification in the miR171 family within the four model plants. The -regulatory motifs on the upstream promoter sequences of genes were highly divergent and shared some similar elements, indicating their possible contribution to the functional variation observed within the miR171 family. This study will buttress our understanding of the functional differentiation of miRNAs and the relationships of miRNA–target pairs based on the evolutionary history of genes.

Investigating evolutionary conservation of dendritic cell subset identity and functions

Directory of Open Access Journals (Sweden)

Thien-Phong eVu Manh

2015-06-01

Full Text Available Dendritic cells (DC were initially defined as mononuclear phagocytes with a dendritic morphology and an exquisite efficiency for naïve T cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to excel in distinct functions and to develop under the instruction of different transcription factors or cytokines. Very few cell surface molecules are expressed in a specific manner on any immune cell type. Hence, to identify cell types, the sole use of a small number of cell surface markers in classical flow cytometry can be deceiving. Moreover, the markers currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of DC subset identity and in their attribution of specific functions. There is a strong need to identify a rigorous and consensus way to define mononuclear phagocyte subsets, with precise guidelines potentially applicable throughout tissues and species. We will discuss the advantages, drawbacks and complementarities of different methodologies: cell surface phenotyping, ontogeny, functional characterization and molecular profiling. We will advocate that gene expression profiling is a very rigorous, largely unbiased and accessible method to define the identity of mononuclear phagocyte subsets, which strengthens and refines surface phenotyping. It is uniquely powerful to yield new, experimentally testable, hypotheses on the ontogeny or functions of mononuclear phagocyte subsets, their molecular regulation and their evolutionary conservation. We propose defining cell populations based on a combination of cell surface phenotyping, expression analysis of hallmark genes and robust functional assays, in order to reach a consensus and integrate faster the huge but scattered knowledge accumulated by different laboratories on different cell types

How Much Can Evolutionary Psychology Inform the Educational Sciences?

Science.gov (United States)

Halpern, Diane F.

2008-01-01

In response to a stimulating article by David C. Geary on the value of understanding the evolutionary basis of learning as a guide to instruction, I raise several objections. When evolutionary theory is used to explain everything from sex differences in math and reading to why children are bored in school, it loses its explanatory power. There is…

Conservation of transcription factor binding events predicts gene expression across species

Science.gov (United States)

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

Oxfold: Kinetic Folding of RNA using Stochastic Context-Free Grammars and Evolutionary Information

DEFF Research Database (Denmark)

Anderson, James W.J.; Haas, Pierre A.; Mathieson, Leigh-Anne

2013-01-01

Motivation: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods however ignore biophysical factors such as the kinetics of RNA folding; no current...... implementation considers both evolutionary information and folding kinetics, thus losing information which, when considered, might lead to better predictions. Results: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding...

Dynamic conservation of forest genetic resources in 33 European countries

NARCIS (Netherlands)

Lefevre, F.; Koskela, J.; Hubert, J.; Kraigher, H.; Longauer, R.; Olrik, D.C.; Vries, de S.M.G.

2013-01-01

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across

The relationship of protein conservation and sequence length

Directory of Open Access Journals (Sweden)

Panchenko Anna R

2002-11-01

Full Text Available Abstract Background In general, the length of a protein sequence is determined by its function and the wide variance in the lengths of an organism's proteins reflects the diversity of specific functional roles for these proteins. However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints. Results We performed sequence comparisons to distinguish highly conserved and poorly conserved proteins from the bacterium Escherichia coli, the archaeon Archaeoglobus fulgidus, and the eukaryotes Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. For all organisms studied, the conserved and nonconserved proteins have strikingly different length distributions. The conserved proteins are, on average, longer than the poorly conserved ones, and the length distributions for the poorly conserved proteins have a relatively narrow peak, in contrast to the conserved proteins whose lengths spread over a wider range of values. For the two prokaryotes studied, the poorly conserved proteins approximate the minimal length distribution expected for a diverse range of structural folds. Conclusions There is a relationship between protein conservation and sequence length. For all the organisms studied, there seems to be a significant evolutionary trend favoring shorter proteins in the absence of other, more specific functional constraints.

Conservation of transcription factor binding events predicts gene expression across species

OpenAIRE

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to funct...

Preserving the evolutionary potential of floras in biodiversity hotspots.

Science.gov (United States)

Forest, Félix; Grenyer, Richard; Rouget, Mathieu; Davies, T Jonathan; Cowling, Richard M; Faith, Daniel P; Balmford, Andrew; Manning, John C; Procheş, Serban; van der Bank, Michelle; Reeves, Gail; Hedderson, Terry A J; Savolainen, Vincent

2007-02-15

One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

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...

The Modern History of Energy Conservation: An Overview for Information Professionals

OpenAIRE

Wulfinghoff, Donald R.

2000-01-01

The current electricity crisis in California, along with high petroleum and natural gas prices everywhere, reminds us that energy conservation is a key to our survival as a civilization. This critical guide by the author of the Energy Efficiency Manual presents credible information sources on energy conservation.

When Heterotrimeric G Proteins Are Not Activated by G Protein-Coupled Receptors: Structural Insights and Evolutionary Conservation.

Science.gov (United States)

DiGiacomo, Vincent; Marivin, Arthur; Garcia-Marcos, Mikel

2018-01-23

Heterotrimeric G proteins are signal-transducing switches conserved across eukaryotes. In humans, they work as critical mediators of intercellular communication in the context of virtually any physiological process. While G protein regulation by G protein-coupled receptors (GPCRs) is well-established and has received much attention, it has become recently evident that heterotrimeric G proteins can also be activated by cytoplasmic proteins. However, this alternative mechanism of G protein regulation remains far less studied than GPCR-mediated signaling. This Viewpoint focuses on recent advances in the characterization of a group of nonreceptor proteins that contain a sequence dubbed the "Gα-binding and -activating (GBA) motif". So far, four proteins present in mammals [GIV (also known as Girdin), DAPLE, CALNUC, and NUCB2] and one protein in Caenorhabditis elegans (GBAS-1) have been described as possessing a functional GBA motif. The GBA motif confers guanine nucleotide exchange factor activity on Gαi subunits in vitro and activates G protein signaling in cells. The importance of this mechanism of signal transduction is highlighted by the fact that its dysregulation underlies human diseases, such as cancer, which has made the proteins attractive new candidates for therapeutic intervention. Here we discuss recent discoveries on the structural basis of GBA-mediated activation of G proteins and its evolutionary conservation and compare them with the better-studied mechanism mediated by GPCRs.

Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

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Haberer Georg

2009-06-01

Full Text Available Abstract Background The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements. Results In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum. Conclusion Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.

Preservation and conservation of electronic information resources of ...

African Journals Online (AJOL)

The major holdings of the broadcast libraries of the Nigerian Television Authority (NTA) are electronic information resources; therefore, providing safe places for general management of these resources have aroused interest in the industry in Nigeria for sometimes. The need to study the preservation and conservation of ...

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

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

Conservation and retrieval of information

International Nuclear Information System (INIS)

Jensen, M.

1993-01-01

High-level waste from nuclear power generation will remain radioactive for thousands of years even though 99% of the radioactivity will have decayed within the first millennium. For a hypothetical group involved in future actions to retrieve or repair a repository, information about its location, design, and content would be necessary. The need of such groups can be used to design the information that should be kept in a waste archive. Two main strategies exist for long-germ information transfer, one which links information thorough successive transfers of archived material and other forms of knowledge in society, and one - such as marking the site with a monument - relying upon a direct link from the present to the distant future. Digital methods are not recommended for long-term storage, but digital processing may be a valuable tool to structure information summaries, and in the creation of better long-lasting records. Advances in archive management should also be pursued to widen the choice of information carriers of high durability. In the Nordic countries, during the first few thousand years, and perhaps up to the next period of glaciation, monuments at a repository site may be used to warn the public of the presence of dangerous waste. But messages from such markers may pose interpretation problems as we have today for messages left by earlier societies such as rune inscriptions. Since the national borders may change in the time scale relevant for nuclear waste, the creation of an international archive for all radioactive wastes would represent an improvement as regards conservation and retrieval of information. (EG)

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.

Science.gov (United States)

Tang, Haiming; Thomas, Paul D

2016-07-15

PANTHER-PSEP is a new software tool for predicting non-synonymous genetic variants that may play a causal role in human disease. Several previous variant pathogenicity prediction methods have been proposed that quantify evolutionary conservation among homologous proteins from different organisms. PANTHER-PSEP employs a related but distinct metric based on 'evolutionary preservation': homologous proteins are used to reconstruct the likely sequences of ancestral proteins at nodes in a phylogenetic tree, and the history of each amino acid can be traced back in time from its current state to estimate how long that state has been preserved in its ancestors. Here, we describe the PSEP tool, and assess its performance on standard benchmarks for distinguishing disease-associated from neutral variation in humans. On these benchmarks, PSEP outperforms not only previous tools that utilize evolutionary conservation, but also several highly used tools that include multiple other sources of information as well. For predicting pathogenic human variants, the trace back of course starts with a human 'reference' protein sequence, but the PSEP tool can also be applied to predicting deleterious or pathogenic variants in reference proteins from any of the ∼100 other species in the PANTHER database. PANTHER-PSEP is freely available on the web at http://pantherdb.org/tools/csnpScoreForm.jsp Users can also download the command-line based tool at ftp://ftp.pantherdb.org/cSNP_analysis/PSEP/ CONTACT: pdthomas@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An Evolutionary Approach to Adaptive Capacity Assessment: A Case Study of Soufriere, Saint Lucia

Directory of Open Access Journals (Sweden)

James Ryan Hogarth

2016-03-01

Full Text Available This paper assesses the capacity of Soufriere, Saint Lucia to adapt to climate change. A community-based vulnerability assessment was conducted that employed semi-structured interviews with community members. The results were analysed using the Local Adaptive Capacity (LAC framework, which characterises adaptive capacity based on five elements: asset base; institutions and entitlements; knowledge and information; innovation; and flexible forward-looking decision-making and governance. Beyond providing an in-depth analysis of Soufriere’s capacity to adapt to climate change, the paper argues that the elements of the LAC framework largely correspond with an evolutionary perspective on adaptive capacity. However, other evolutionary themes—such as structure, history, path-dependency, scale, agency, conservation of diversity, and the perils of specialisation—should also be taken into account.

Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology.

Science.gov (United States)

Badyaev, Alexander V

2011-07-07

In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.

Identification of extant vertebrate Myxine glutinosa VWF: evolutionary conservation of primary hemostasis.

Science.gov (United States)

Grant, Marianne A; Beeler, David L; Spokes, Katherine C; Chen, Junmei; Dharaneeswaran, Harita; Sciuto, Tracey E; Dvorak, Ann M; Interlandi, Gianluca; Lopez, José A; Aird, William C

2017-12-07

Hemostasis in vertebrates involves both a cellular and a protein component. Previous studies in jawless vertebrates (cyclostomes) suggest that the protein response, which involves thrombin-catalyzed conversion of a soluble plasma protein, fibrinogen, into a polymeric fibrin clot, is conserved in all vertebrates. However, similar data are lacking for the cellular response, which in gnathostomes is regulated by von Willebrand factor (VWF), a glycoprotein that mediates the adhesion of platelets to the subendothelial matrix of injured blood vessels. To gain evolutionary insights into the cellular phase of coagulation, we asked whether a functional vwf gene is present in the Atlantic hagfish, Myxine glutinosa We found a single vwf transcript that encodes a simpler protein compared with higher vertebrates, the most striking difference being the absence of an A3 domain, which otherwise binds collagen under high-flow conditions. Immunohistochemical analyses of hagfish tissues and blood revealed Vwf expression in endothelial cells and thrombocytes. Electron microscopic studies of hagfish tissues demonstrated the presence of Weibel-Palade bodies in the endothelium. Hagfish Vwf formed high-molecular-weight multimers in hagfish plasma and in stably transfected CHO cells. In functional assays, botrocetin promoted VWF-dependent thrombocyte aggregation. A search for vwf sequences in the genome of sea squirts, the closest invertebrate relatives of hagfish, failed to reveal evidence of an intact vwf gene. Together, our findings suggest that VWF evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. © 2017 by The American Society of Hematology.

Evolutionary conserved mechanisms pervade structure and transcriptional modulation of allograft inflammatory factor-1 from sea anemone Anemonia viridis.

Science.gov (United States)

Cuttitta, Angela; Ragusa, Maria Antonietta; Costa, Salvatore; Bennici, Carmelo; Colombo, Paolo; Mazzola, Salvatore; Gianguzza, Fabrizio; Nicosia, Aldo

2017-08-01

Gene family encoding allograft inflammatory factor-1 (AIF-1) is well conserved among organisms; however, there is limited knowledge in lower organisms. In this study, the first AIF-1 homologue from cnidarians was identified and characterised in the sea anemone Anemonia viridis. The full-length cDNA of AvAIF-1 was of 913 bp with a 5' -untranslated region (UTR) of 148 bp, a 3'-UTR of 315 and an open reading frame (ORF) of 450 bp encoding a polypeptide with149 amino acid residues and predicted molecular weight of about 17 kDa. The predicted protein possesses evolutionary conserved EF hand Ca 2+ binding motifs, post-transcriptional modification sites and a 3D structure which can be superimposed with human members of AIF-1 family. The AvAIF-1 transcript was constitutively expressed in all tested tissues of unchallenged sea anemone, suggesting that AvAIF-1 could serve as a general protective factor under normal physiological conditions. Moreover, we profiled the transcriptional activation of AvAIF-1 after challenges with different abiotic/biotic stresses showing induction by warming conditions, heavy metals exposure and immune stimulation. Thus, mechanisms associated to inflammation and immune challenges up-regulated AvAIF-1 mRNA levels. Our results suggest its involvement in the inflammatory processes and immune response of A. viridis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Midwestern US Farmers Perceive Crop Advisers as Conduits of Information on Agricultural Conservation Practices.

Science.gov (United States)

Eanes, Francis R; Singh, Ajay S; Bulla, Brian R; Ranjan, Pranay; Prokopy, Linda S; Fales, Mary; Wickerham, Benjamin; Doran, Patrick J

2017-11-01

Nonpoint source pollution from agricultural land uses continues to pose one of the most significant threats to water quality in the US, with measurable impacts across local, regional, and national scales. The impact and the influence of targeted conservation efforts are directly related to the degree to which farmers are familiar with and trust the entities providing the information and/or outreach. Recent research suggests that farmers consistently rank independent and retail-affiliated crop advisers as among the most trusted and influential sources for agronomic information, but little is understood about whether farmers are willing to receive advice from crop advisers on the use of practices that conserve soil and water, and, if so, whether crop advisers will be perceived as influential. We present survey data from farmers (n = 1461) in Michigan's Saginaw Bay (Lake Huron) watershed to explore these questions. Results suggest that farmers view crop advisers as trustworthy sources of information about conservation, and influential on management practices that have large conservation implications. We discuss these results, along with perceived barriers and opportunities to crop advisers partnering with traditional conservation agencies to enhance the impact of voluntary conservation programs.

Midwestern US Farmers Perceive Crop Advisers as Conduits of Information on Agricultural Conservation Practices

Science.gov (United States)

Eanes, Francis R.; Singh, Ajay S.; Bulla, Brian R.; Ranjan, Pranay; Prokopy, Linda S.; Fales, Mary; Wickerham, Benjamin; Doran, Patrick J.

2017-11-01

Nonpoint source pollution from agricultural land uses continues to pose one of the most significant threats to water quality in the US, with measurable impacts across local, regional, and national scales. The impact and the influence of targeted conservation efforts are directly related to the degree to which farmers are familiar with and trust the entities providing the information and/or outreach. Recent research suggests that farmers consistently rank independent and retail-affiliated crop advisers as among the most trusted and influential sources for agronomic information, but little is understood about whether farmers are willing to receive advice from crop advisers on the use of practices that conserve soil and water, and, if so, whether crop advisers will be perceived as influential. We present survey data from farmers ( n = 1461) in Michigan's Saginaw Bay (Lake Huron) watershed to explore these questions. Results suggest that farmers view crop advisers as trustworthy sources of information about conservation, and influential on management practices that have large conservation implications. We discuss these results, along with perceived barriers and opportunities to crop advisers partnering with traditional conservation agencies to enhance the impact of voluntary conservation programs.

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.

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.

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

Science.gov (United States)

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

2016-01-01

temporary glacial refugia. Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate.

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

Directory of Open Access Journals (Sweden)

Douglas J Shinneman

with discrete temporary glacial refugia. Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design and conservation that promotes haplotype compatibility with projected changes in future climate.

The value and need for long term conservation of information regarding nuclear waste repositories

Energy Technology Data Exchange (ETDEWEB)

Eng, T. [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Jensen, M. [Swedish Radiation Protection Inst., Stockholm (Sweden)

1993-12-31

An important question in safety assessment of all repositories where toxic waste is disposed is how long should information be available to society about the repository and its content? Future societies right to knowledge must be considered and actions must already today be taken to ensure that proper information conservation, transfer and retrieval are provided. Collection of relevant information must be planned for at the research, construction and the operational phase of a repository. One of the main areas for information conservation and transfer is to mitigate future human intrusion. A system for best possible mitigation of human intrusion should with the present knowledge comprise the following parts: (a) development of planning procedures for long-term conservation of gathered information (present and future national and international archives, markers etc.); (b) continuous follow up of the state-of-the-art of information media; (c) preparations for national rules and regulations on nuclear waste information; (d) participation in international cooperation on issues concerning nuclear waste information keeping, transfer and retrieval.

How cultural evolutionary theory can inform social psychology and vice versa.

Science.gov (United States)

Mesoudi, Alex

2009-10-01

Cultural evolutionary theory is an interdisciplinary field in which human culture is viewed as a Darwinian process of variation, competition, and inheritance, and the tools, methods, and theories developed by evolutionary biologists to study genetic evolution are adapted to study cultural change. It is argued here that an integration of the theories and findings of mainstream social psychology and of cultural evolutionary theory can be mutually beneficial. Social psychology provides cultural evolution with a set of empirically verified microevolutionary cultural processes, such as conformity, model-based biases, and content biases, that are responsible for specific patterns of cultural change. Cultural evolutionary theory provides social psychology with ultimate explanations for, and an understanding of the population-level consequences of, many social psychological phenomena, such as social learning, conformity, social comparison, and intergroup processes, as well as linking social psychology with other social science disciplines such as cultural anthropology, archaeology, and sociology.

Inferring repeat-protein energetics from evolutionary information.

Directory of Open Access Journals (Sweden)

Rocío Espada

2017-06-01

Full Text Available Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts.

78 FR 12349 - Proposed Information Collection; Land and Water Conservation Fund State Assistance Program

Science.gov (United States)

2013-02-22

...] Proposed Information Collection; Land and Water Conservation Fund State Assistance Program AGENCY: National.... Abstract The Land and Water Conservation Fund Act of 1965 (LWCF Act) (16 U.S.C. 460l-4 et seq.) was enacted... discussed in detail in the Land and Water Conservation Fund State Assistance Program Federal Financial...

Conserved and variable domains of RNase MRP RNA.

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Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

Science.gov (United States)

Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

2014-01-01

 The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina

Conservation of native Pacific trout diversity in Western North America

Science.gov (United States)

Brooke E. Penaluna; Alicia Abadía-Cardoso; Jason B. Dunham; Francisco J. García-Dé León; Robert E. Gresswell; Arturo Ruiz Luna; Eric B. Taylor; Bradley B. Shepard; Robert Al-Chokhachy; Clint C. Muhlfeld; Kevin R. Bestgen; Kevin Rogers; Marco A. Escalante; Ernest R. Keeley; Gabriel M. Temple; Jack E. Williams; Kathleen R. Matthews; Ron Pierce; Richard L. Mayden; Ryan P. Kovach; John Carlos Garza; Kurt D. Fausch

2016-01-01

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review...

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

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Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they

Evolutionary dynamics of protein domain architecture in plants

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Zhang Xue-Cheng

2012-01-01

Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation

DEFF Research Database (Denmark)

Weinert, Brian T; Wagner, Sebastian A; Horn, Heiko

2011-01-01

Posttranslational modification of proteins by acetylation and phosphorylation regulates most cellular processes in living organisms. Surprisingly, the evolutionary conservation of phosphorylated serine and threonine residues is only marginally higher than that of unmodified serines and threonines....... With high-resolution mass spectrometry, we identified 1981 lysine acetylation sites in the proteome of Drosophila melanogaster. We used data sets of experimentally identified acetylation and phosphorylation sites in Drosophila and humans to analyze the evolutionary conservation of these modification sites...... between flies and humans. Site-level conservation analysis revealed that acetylation sites are highly conserved, significantly more so than phosphorylation sites. Furthermore, comparison of lysine conservation in Drosophila and humans with that in nematodes and zebrafish revealed that acetylated lysines...

78 FR 28619 - Proposed Information Collection; Fish and Wildlife Service Conservation Banking Survey

Science.gov (United States)

2013-05-15

...-FF09E31000] Proposed Information Collection; Fish and Wildlife Service Conservation Banking Survey AGENCY... banking credits. The surveys will benefit the Service by helping to identify constraints in the current... Number: 1018-XXXX. This is a new collection. Title: Fish and Wildlife Service Conservation Banking Survey...

G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

John A Capra

2010-07-01

Full Text Available G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs. Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

In situ conservation and landscape genetics in forest species

Directory of Open Access Journals (Sweden)

Martín L.M.

2012-03-01

Full Text Available Conservation of forest genetic resources is essential for sustaining the environmental and productive values of forests. One of the environmental values is the conservation of the diversity that is assessed through the amount of genetic diversity stored by forests, their structure and dynamics. The current need for forest conservation and management has driven a rapid expansion of landscape genetics discipline that combines tools from molecular genetics, landscape ecology and spatial statistics and is decisive for improving not only ecological knowledge but also for properly managing population genetic resources. The objective of this study is to show the way to establish the safeguard of genetic diversity through this approach using the results obtained in sweet chestnut (Castanea sativa Mill. that has provided a better understanding on the species genetic resources. In this respect, we will show how the information provided by different types of molecular markers (genomic and genic offer more accurate indication on the distribution of the genetic diversity among and within populations assuming different evolutionary drivers.

Bioinformatics education dissemination with an evolutionary problem solving perspective.

Science.gov (United States)

Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

2010-11-01

Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

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.

Information strategies and energy conservation behavior: A meta-analysis of experimental studies from 1975 to 2012

International Nuclear Information System (INIS)

Delmas, Magali A.; Fischlein, Miriam; Asensio, Omar I.

2013-01-01

Strategies that provide information about the environmental impact of activities are increasingly seen as effective to encourage conservation behavior. This article offers the most comprehensive meta-analysis of information based energy conservation experiments conducted to date. Based on evidence from 156 published field trials and 525,479 study subjects from 1975 to 2012, we quantify the energy savings from information based strategies. On average, individuals in the experiments reduced their electricity consumption by 7.4%. Our results also show that strategies providing individualized audits and consulting are comparatively more effective for conservation behavior than strategies that provide historical, peer comparison energy feedback. Interestingly, we find that pecuniary feedback and incentives lead to a relative increase in energy usage rather than induce conservation. We also find that the conservation effect diminishes with the rigor of the study, indicating potential methodological issues in the current literature. - Highlights: • We conduct a meta-analysis of information-based energy conservation experiments. • We analyze 156 published trials and 524,479 study subjects from 1975 to 2012. • On average, individuals in the experiments reduced electricity consumption by 7.4%. • Individualized feedback via audits and consulting results in the largest reductions. Pecuniary feedback and incentives lead to a relative increase in energy usage

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

Reconstruction of caribou evolutionary history in Western North America and its implications for conservation.

Science.gov (United States)

Weckworth, Byron V; Musiani, Marco; McDevitt, Allan D; Hebblewhite, Mark; Mariani, Stefano

2012-07-01

The role of Beringia as a refugium and route for trans-continental exchange of fauna during glacial cycles of the past 2million years are well documented; less apparent is its contribution as a significant reservoir of genetic diversity. Using mitochondrial DNA sequences and 14 microsatellite loci, we investigate the phylogeographic history of caribou (Rangifer tarandus) in western North America. Patterns of genetic diversity reveal two distinct groups of caribou. Caribou classified as a Northern group, of Beringian origin, exhibited greater number and variability in mtDNA haplotypes compared to a Southern group originating from refugia south of glacial ice. Results indicate that subspecies R. t. granti of Alaska and R. t. groenlandicus of northern Canada do not constitute distinguishable units at mtDNA or microsatellites, belying their current status as separate subspecies. Additionally, the Northern Mountain ecotype of woodland caribou (presently R. t. caribou) has closer kinship to caribou classified as granti or groenlandicus. Comparisons of mtDNA and microsatellite data suggest that behavioural and ecological specialization is a more recently derived life history characteristic. Notably, microsatellite differentiation among Southern herds is significantly greater, most likely as a result of human-induced landscape fragmentation and genetic drift due to smaller population sizes. These results not only provide important insight into the evolutionary history of northern species such as caribou, but also are important indicators for managers evaluating conservation measures for this threatened species. © 2012 Blackwell Publishing Ltd.

The single evolutionary origin of chlorinated auxin provides a phylogenetically informative trait in the Fabaceae.

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Lam, Hong Kiat; Ross, John J; McAdam, Erin L; McAdam, Scott A M

2016-07-02

Chlorinated auxin (4-chloroindole-3-acetic acid, 4-Cl-IAA), a highly potent plant hormone, was once thought to be restricted to species of the tribe Fabeae within the Fabaceae, until we recently detected this hormone in the seeds of Medicago, Melilotus and Trifolium species. The absence of 4-Cl-IAA in the seeds of the cultivated species Cicer aeritinum from the Cicerae tribe, immediately basal to the Fabeae and Trifolieae tribes, suggested a single evolutionary origin of 4-Cl-IAA. Here, we provide a more robust phylogenetic placement of the ability to produce chlorinated auxin by screening key species spanning this evolutionary transition. We report no detectable level of 4-Cl-IAA in Cicer echinospermum (a wild relative of C. aeritinum) and 4 species (Galega officinalis, Parochetus communis, Astragalus propinquus and A. sinicus) from tribes or clades more basal or sister to the Cicerae tribe. We did detect 4-Cl-IAA in the dry seeds of 4 species from the genus Ononis that are either basal to the genera Medicago, Melilotus and Trigonella or basal to, but still within, the Fabeae and Trifolieae (ex. Parochetus) clades. We conclude that the single evolutionary origin of this hormone in seeds can be used as a phylogenetically informative trait within the Fabaceae.

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 ...

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Energy Technology Data Exchange (ETDEWEB)

Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

2010-07-01

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

Individual-based modeling of ecological and evolutionary processes

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DeAngelis, Donald L.; Mooij, Wolf M.

2005-01-01

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

Improved quantum-inspired evolutionary algorithm with diversity information applied to economic dispatch problem with prohibited operating zones

International Nuclear Information System (INIS)

Vianna Neto, Julio Xavier; Andrade Bernert, Diego Luis de; Santos Coelho, Leandro dos

2011-01-01

The objective of the economic dispatch problem (EDP) of electric power generation, whose characteristics are complex and highly nonlinear, is to schedule the committed generating unit outputs so as to meet the required load demand at minimum operating cost while satisfying all unit and system equality and inequality constraints. Recently, as an alternative to the conventional mathematical approaches, modern meta-heuristic optimization techniques have been given much attention by many researchers due to their ability to find an almost global optimal solution in EDPs. Research on merging evolutionary computation and quantum computation has been started since late 1990. Inspired on the quantum computation, this paper presented an improved quantum-inspired evolutionary algorithm (IQEA) based on diversity information of population. A classical quantum-inspired evolutionary algorithm (QEA) and the IQEA were implemented and validated for a benchmark of EDP with 15 thermal generators with prohibited operating zones. From the results for the benchmark problem, it is observed that the proposed IQEA approach provides promising results when compared to various methods available in the literature.

Improved quantum-inspired evolutionary algorithm with diversity information applied to economic dispatch problem with prohibited operating zones

Energy Technology Data Exchange (ETDEWEB)

Vianna Neto, Julio Xavier, E-mail: julio.neto@onda.com.b [Pontifical Catholic University of Parana, PUCPR, Undergraduate Program at Mechatronics Engineering, Imaculada Conceicao, 1155, Zip code 80215-901, Curitiba, Parana (Brazil); Andrade Bernert, Diego Luis de, E-mail: dbernert@gmail.co [Pontifical Catholic University of Parana, PUCPR, Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Imaculada Conceicao, 1155, Zip code 80215-901, Curitiba, Parana (Brazil); Santos Coelho, Leandro dos, E-mail: leandro.coelho@pucpr.b [Pontifical Catholic University of Parana, PUCPR, Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Imaculada Conceicao, 1155, Zip code 80215-901, Curitiba, Parana (Brazil)

2011-01-15

The objective of the economic dispatch problem (EDP) of electric power generation, whose characteristics are complex and highly nonlinear, is to schedule the committed generating unit outputs so as to meet the required load demand at minimum operating cost while satisfying all unit and system equality and inequality constraints. Recently, as an alternative to the conventional mathematical approaches, modern meta-heuristic optimization techniques have been given much attention by many researchers due to their ability to find an almost global optimal solution in EDPs. Research on merging evolutionary computation and quantum computation has been started since late 1990. Inspired on the quantum computation, this paper presented an improved quantum-inspired evolutionary algorithm (IQEA) based on diversity information of population. A classical quantum-inspired evolutionary algorithm (QEA) and the IQEA were implemented and validated for a benchmark of EDP with 15 thermal generators with prohibited operating zones. From the results for the benchmark problem, it is observed that the proposed IQEA approach provides promising results when compared to various methods available in the literature.

Improved quantum-inspired evolutionary algorithm with diversity information applied to economic dispatch problem with prohibited operating zones

Energy Technology Data Exchange (ETDEWEB)

Neto, Julio Xavier Vianna [Pontifical Catholic University of Parana, PUCPR, Undergraduate Program at Mechatronics Engineering, Imaculada Conceicao, 1155, Zip code 80215-901, Curitiba, Parana (Brazil); Bernert, Diego Luis de Andrade; Coelho, Leandro dos Santos [Pontifical Catholic University of Parana, PUCPR, Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Imaculada Conceicao, 1155, Zip code 80215-901, Curitiba, Parana (Brazil)

2011-01-15

The objective of the economic dispatch problem (EDP) of electric power generation, whose characteristics are complex and highly nonlinear, is to schedule the committed generating unit outputs so as to meet the required load demand at minimum operating cost while satisfying all unit and system equality and inequality constraints. Recently, as an alternative to the conventional mathematical approaches, modern meta-heuristic optimization techniques have been given much attention by many researchers due to their ability to find an almost global optimal solution in EDPs. Research on merging evolutionary computation and quantum computation has been started since late 1990. Inspired on the quantum computation, this paper presented an improved quantum-inspired evolutionary algorithm (IQEA) based on diversity information of population. A classical quantum-inspired evolutionary algorithm (QEA) and the IQEA were implemented and validated for a benchmark of EDP with 15 thermal generators with prohibited operating zones. From the results for the benchmark problem, it is observed that the proposed IQEA approach provides promising results when compared to various methods available in the literature. (author)

The Automatic Conservative: Ideology-Based Attentional Asymmetries in the Processing of Valenced Information

Science.gov (United States)

Carraro, Luciana; Castelli, Luigi; Macchiella, Claudia

2011-01-01

Research has widely explored the differences between conservatives and liberals, and it has been also recently demonstrated that conservatives display different reactions toward valenced stimuli. However, previous studies have not yet fully illuminated the cognitive underpinnings of these differences. In the current work, we argued that political ideology is related to selective attention processes, so that negative stimuli are more likely to automatically grab the attention of conservatives as compared to liberals. In Experiment 1, we demonstrated that negative (vs. positive) information impaired the performance of conservatives, more than liberals, in an Emotional Stroop Task. This finding was confirmed in Experiment 2 and in Experiment 3 employing a Dot-Probe Task, demonstrating that threatening stimuli were more likely to attract the attention of conservatives. Overall, results support the conclusion that people embracing conservative views of the world display an automatic selective attention for negative stimuli. PMID:22096486

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

NARCIS (Netherlands)

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

2017-01-01

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

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

Science.gov (United States)

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

2016-01-01

discrete temporary glacial refugia. Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate.

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

Science.gov (United States)

Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

2012-01-01

Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

DNA in the conservation and management of African antelope

DEFF Research Database (Denmark)

Lorenzen, Eline

2016-01-01

tool in informed species conservation and sustainable wildlife management. The movement of antelope through translocations, reintroductions, and population augmentations is common practice in wildlife management. DNA-led species identification using genetic barcoding is an effective use of genetic data...... within forensics. DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species....... databases, and represents a valuable reference database of antelope DNA diversity. For the evolution of antelope, sub-Saharan Africa is a region of particular intrigue. The geographic regions of sub-Saharan Africa represent unique evolutionary scenarios. Molecular data have become an increasingly important...

Molecular evolutionary patterns of NAD+/Sirtuin aging signaling pathway across taxa.

Directory of Open Access Journals (Sweden)

Uma Gaur

Full Text Available A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD+/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that MRPS5 and PPARGC1A were under significant constraints because of their functional significance. FOXO3a also displayed strong purifying selection. All three sirtuins, which were SIRT1, SIRT2 and SIRT6, displayed a great degree of conservation between taxa, which is consistent with the previous report. A significant evolutionary constraint is seen on the anti-oxidant gene, SOD3. As expected, TP53 gene was under significant selection pressure in mammals, owing to its major role in tumor progression. Poly-ADP-ribose polymerase (PARP genes displayed the most sites under positive selection. Further 3D structural analysis of PARP1 and PARP2 protein revealed that some of these positively selected sites caused a change in the electrostatic potential of the protein structure, which may allow a change in its interaction with other proteins and molecules ultimately leading to difference in the function. Although the functional significance of the positively selected sites could not be established in the variants databases, yet it will be interesting to see if these sites actually affect the function of PARP1 and PARP2.

Linking diversity and distribution to understand biodiversity gradients and inform conservation assessments

Directory of Open Access Journals (Sweden)

Fabricio Villalobos

2014-03-01

Full Text Available Broad-scale patterns of species richness result from differential coexistence among species in distinct regions of the globe, determined by the species’ ranges and their properties such as size, shape and location. Thus, species richness and ranges are inherently linked. These two biodiversity features also yield primary information for conservation assessments. However, species richness and range size have been usually studied separately and no formal analytical link has been established. In my PhD thesis, I applied and extended a recently developed conceptual and methodological framework to study geographical association among species and similarity among sites. This range–diversity framework, along with stochastic simulation modelling, allowed me to jointly evaluate the relationship between diversity and distribution, to infer potential processes underlying composite patterns of phyllostomid bats, and to use this approach to inform conservation assessments for the Mexican avifauna. I highlight the need to explore composite patterns for understanding biodiversity patterns and show how combining diversity and distributional data can help describe complex biogeographical patterns, providing a transparent and explicit application for initial conservation assessments.

Consequences for diversity when prioritizing animals for conservation with pedigree or genomic information

NARCIS (Netherlands)

Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.

2011-01-01

Up to now, prioritization of animals for conservation has been mainly based on pedigree information; however, genomic information may improve prioritization. In this study, we used two Holstein populations to investigate the consequences for genetic diversity when animals are prioritized with

Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora

Directory of Open Access Journals (Sweden)

Salinas-Saavedra Miguel

2011-12-01

Full Text Available Abstract Background Cytasters (cytoplasmic asters are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes. Presentation of the hypothesis The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria. Testing the hypothesis So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of

Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana.

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Verma, Amit K; Diwan, Danish; Raut, Sandeep; Dobriyal, Neha; Brown, Rebecca E; Gowda, Vinita; Hines, Justin K; Sahi, Chandan

2017-06-07

Heat shock proteins of 70 kDa (Hsp70s) partner with structurally diverse Hsp40s (J proteins), generating distinct chaperone networks in various cellular compartments that perform myriad housekeeping and stress-associated functions in all organisms. Plants, being sessile, need to constantly maintain their cellular proteostasis in response to external environmental cues. In these situations, the Hsp70:J protein machines may play an important role in fine-tuning cellular protein quality control. Although ubiquitous, the functional specificity and complexity of the plant Hsp70:J protein network has not been studied. Here, we analyzed the J protein network in the cytosol of Arabidopsis thaliana and, using yeast genetics, show that the functional specificities of most plant J proteins in fundamental chaperone functions are conserved across long evolutionary timescales. Detailed phylogenetic and functional analysis revealed that increased number, regulatory differences, and neofunctionalization in J proteins together contribute to the emerging functional diversity and complexity in the Hsp70:J protein network in higher plants. Based on the data presented, we propose that higher plants have orchestrated their "chaperome," especially their J protein complement, according to their specialized cellular and physiological stipulations. Copyright © 2017 Verma et al.

Evolutionary conservation and neuronal mechanisms of auditory perceptual restoration.

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Petkov, Christopher I; Sutter, Mitchell L

2011-01-01

Auditory perceptual 'restoration' occurs when the auditory system restores an occluded or masked sound of interest. Behavioral work on auditory restoration in humans began over 50 years ago using it to model a noisy environmental scene with competing sounds. It has become clear that not only humans experience auditory restoration: restoration has been broadly conserved in many species. Behavioral studies in humans and animals provide a necessary foundation to link the insights being obtained from human EEG and fMRI to those from animal neurophysiology. The aggregate of data resulting from multiple approaches across species has begun to clarify the neuronal bases of auditory restoration. Different types of neural responses supporting restoration have been found, supportive of multiple mechanisms working within a species. Yet a general principle has emerged that responses correlated with restoration mimic the response that would have been given to the uninterrupted sound of interest. Using the same technology to study different species will help us to better harness animal models of 'auditory scene analysis' to clarify the conserved neural mechanisms shaping the perceptual organization of sound and to advance strategies to improve hearing in natural environmental settings. © 2010 Elsevier B.V. All rights reserved.

Flotillin-1 is an evolutionary-conserved memory-related protein up-regulated in implicit and explicit learning paradigms.

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Monje, Francisco J; Divisch, Isabella; Demit, Marvie; Lubec, Gert; Pollak, Daniela D

2013-06-01

Studies of synaptic plasticity using the marine mollusk Aplysia californica as model system have been successfully used to identify proteins involved in learning and memory. The importance of molecular elements regulated by the learning- related neurotransmitter serotonin in Aplysia can then be explored in rodent models and finally tested for their relevance for human physiology and pathology. Herein, 2-DE gel-based electrophoresis has been used to investigate protein level changes after treatment with serotonin in Aplysia abdominal ganglia. Twenty-one proteins have been found to be regulated by serotonin, and protein level changes of actin depolymerizing factor (ADF), deleted in azoospermia associated protein (DAZAP-1), and Flotillin-1 have been verified by Western blotting. Flotillin-1, a member of the flotillin/reggie family of scaffolding proteins, has been previously found to be involved in neuritic branching and synapse formation in hippocampal neurons in vitro. However, its importance for hippocampal- dependent learning and memory in the mouse has not been examined. Here, elevated levels of Flotillin-1 in hippocampal tissue of mice trained in the Morris water maze confirmed the relevance of Flotillin-1 for memory-related processes in a mammalian system. Thus, a translational approach-from invertebrates to rodents-led to the identification of Flotillin-1 as evolutionary-conserved memory-related protein.

Archaeogenetics in evolutionary medicine.

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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.

Marine Dispersal Scales Are Congruent over Evolutionary and Ecological Time

KAUST Repository

Pinsky, Malin L.

2016-12-15

The degree to which offspring remain near their parents or disperse widely is critical for understanding population dynamics, evolution, and biogeography, and for designing conservation actions. In the ocean, most estimates suggesting short-distance dispersal are based on direct ecological observations of dispersing individuals, while indirect evolutionary estimates often suggest substantially greater homogeneity among populations. Reconciling these two approaches and their seemingly competing perspectives on dispersal has been a major challenge. Here we show for the first time that evolutionary and ecological measures of larval dispersal can closely agree by using both to estimate the distribution of dispersal distances. In orange clownfish (Amphiprion percula) populations in Kimbe Bay, Papua New Guinea, we found that evolutionary dispersal kernels were 17 km (95% confidence interval: 12–24 km) wide, while an exhaustive set of direct larval dispersal observations suggested kernel widths of 27 km (19–36 km) or 19 km (15–27 km) across two years. The similarity between these two approaches suggests that ecological and evolutionary dispersal kernels can be equivalent, and that the apparent disagreement between direct and indirect measurements can be overcome. Our results suggest that carefully applied evolutionary methods, which are often less expensive, can be broadly relevant for understanding ecological dispersal across the tree of life.

Conservation, biodiversity and infectious disease: scientific evidence and policy implications

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Young, Hillary S.; Wood, Chelsea L.; Kilpatrick, A. Marm; Lafferty, Kevin D.; Nunn, Charles L.; Vincent, Jeffrey R.

2017-01-01

Habitat destruction and infectious disease are dual threats to nature and people. The potential to simultaneously advance conservation and human health has attracted considerable scientific and popular interest; in particular, many authors have justified conservation action by pointing out potential public health benefits . One major focus of this debate—that biodiversity conservation often decreases infectious disease transmission via the dilution effect—remains contentious. Studies that test for a dilution effect often find a negative association between a diversity metric and a disease risk metric, but how such associations should inform conservation policy remains unclear for several reasons. For one, diversity and infection risk have many definitions, making it possible to identify measures that conform to expectations. Furthermore, the premise that habitat destruction consistently reduces biodiversity is in question, and disturbance or conservation can affect disease in many ways other than through biodiversity change. To date, few studies have examined the broader set of mechanisms by which anthropogenic disturbance or conservation might increase or decrease infectious disease risk to human populations. Due to interconnections between biodiversity change, economics and human behaviour, moving from ecological theory to policy action requires understanding how social and economic factors affect conservation.This Theme Issue arose from a meeting aimed at synthesizing current theory and data on ‘biodiversity, conservation and infectious disease’ (4–6 May 2015). Ecologists, evolutionary biologists, economists, epidemiologists, veterinary scientists, public health professionals, and conservation biologists from around the world discussed the latest research on the ecological and socio-economic links between conservation, biodiversity and infectious disease, and the open questions and controversies in these areas. By combining ecological understanding

Evolutionary Algorithms Application Analysis in Biometric Systems

Directory of Open Access Journals (Sweden)

N. Goranin

2010-01-01

Full Text Available Wide usage of biometric information for person identity verification purposes, terrorist acts prevention measures and authenticationprocess simplification in computer systems has raised significant attention to reliability and efficiency of biometricsystems. Modern biometric systems still face many reliability and efficiency related issues such as reference databasesearch speed, errors while recognizing of biometric information or automating biometric feature extraction. Current scientificinvestigations show that application of evolutionary algorithms may significantly improve biometric systems. In thisarticle we provide a comprehensive review of main scientific research done in sphere of evolutionary algorithm applicationfor biometric system parameter improvement.

Design and Implementation of a Research-Informed Water Conservation Education Program

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Thompson, Ruthanne; Coe, Alice; Klaver, Irene; Dickson, Kenneth

2011-01-01

Informed by the results of a baseline research study of regional citizen knowledge and understanding concerning watershed issues, a team of university faculty and classroom teachers designed and implemented a water conservation education program to address lacking areas of watershed knowledge. The authors developed age-appropriate, hands-on…

Proteomics in evolutionary ecology.

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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

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

2008-01-01

Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested...

77 FR 74168 - Information Collection: Youth Conservation Corps Application and Medical History

Science.gov (United States)

2012-12-13

... DEPARTMENT OF AGRICULTURE Forest Service Information Collection: Youth Conservation Corps...-1706), the Forest Service, U.S. Department of Agriculture; the Fish and Wildlife Service, and National... of birth, age, mailing address, telephone numbers, email address, gender, educational background...

USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

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Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

DEFF Research Database (Denmark)

Rukov, Jakob Lewin; Irimia, Manuel; Mørk, Søren

2007-01-01

Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated...... the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae....... Moreover, we find that relative isoform expression levels vary significantly during development for 78% of the AS events and that this quantitative variation is highly conserved between the 2 species. Our results suggest that AS is generally tightly regulated through development and that the regulatory...

Conservation of myeloid surface antigens on primate granulocytes.

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Letvin, N L; Todd, R F; Palley, L S; Schlossman, S F; Griffin, J D

1983-02-01

Monoclonal antibodies reactive with myeloid cell surface antigens were used to study evolutionary changes in granulocyte surface antigens from primate species. Certain of these granulocyte membrane antigens are conserved in phylogenetically distant species, indicating the potential functional importance of these structures. The degree of conservation of these antigens reflects the phylogenetic relationship between primate species. Furthermore, species of the same genus show similar patterns of binding to this panel of anti-human myeloid antibodies. This finding of conserved granulocyte surface antigens suggests that non-human primates may provide a model system for exploring uses of monoclonal antibodies in the treatment of human myeloid disorders.

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-.

Using Home Irrigation Users' Perceptions to Inform Water Conservation Programs

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Warner, Laura A.; Chaudhary, Anil Kumar; Lamm, Alexa J.; Rumble, Joy N.; Momol, Esen

2017-01-01

Targeted agricultural education programs can play a role in solving complex water issues. This article applies importance-performance analysis to examine dimensions of water resources that may inform local water conservation campaigns in the United States. The purpose of this study was to generate a deep understanding of home irrigation users'…

Evolutionary hotspots in the Mojave Desert

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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.

A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

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Maslo, Brooke; Fefferman, Nina H

2015-08-01

Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation. © 2015 Society for Conservation

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

DEFF Research Database (Denmark)

Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel

2015-01-01

Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still...

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information.

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Pai, Priyadarshini P; Dattatreya, Rohit Kadam; Mondal, Sukanta

2017-11-01

Enzyme interactions with ligands are crucial for various biochemical reactions governing life. Over many years attempts to identify these residues for biotechnological manipulations have been made using experimental and computational techniques. The computational approaches have gathered impetus with the accruing availability of sequence and structure information, broadly classified into template-based and de novo methods. One of the predominant de novo methods using sequence information involves application of biological properties for supervised machine learning. Here, we propose a support vector machines-based ensemble for prediction of protein-ligand interacting residues using one of the most important discriminative contributing properties in the interacting residue neighbourhood, i. e., evolutionary information in the form of position-specific- scoring matrix (PSSM). The study has been performed on a non-redundant dataset comprising of 9269 interacting and 91773 non-interacting residues for prediction model generation and further evaluation. Of the various PSSM-based models explored, the proposed method named ROBBY (pRediction Of Biologically relevant small molecule Binding residues on enzYmes) shows an accuracy of 84.0 %, Matthews Correlation Coefficient of 0.343 and F-measure of 39.0 % on 78 test enzymes. Further, scope of adding domain knowledge such as pocket information has also been investigated; results showed significant enhancement in method precision. Findings are hoped to boost the reliability of small-molecule ligand interaction prediction for enzyme applications and drug design. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolutionary Conservation in Genes Underlying Human Psychiatric Disorders

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Lisa Michelle Ogawa

2014-05-01

Full Text Available Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago and thirty one non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant compared to their small-brained sister species. Evidence of differential selection in primates supports the hypothesis that schizophrenia and autism are a cost of higher brain function. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained.

Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.

Directory of Open Access Journals (Sweden)

Martin Poot

2011-05-01

Full Text Available Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.We exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC development.From the 61 syndromes which involve an ACC, 51 human candidate genes have been identified. Through interval mapping, we identified a single significant QTL on mouse chromosome 7 for corpus callosum volume with a QTL peak located between 25.5 and 26.7 Mb. Comparing the genes in this mouse QTL region with those associated with human syndromes (involving ACC and those covered by copy number variations (CNV yielded a single overlap, namely HNRPU in humans and Hnrpul1 in mice. Further analysis of corpus callosum volume in BXD strains revealed that the corpus callosum was significantly larger in BXD mice with a B genotype at the Hnrpul1 locus than in BXD mice with a D genotype at Hnrpul1 (F = 22.48, p<9.87*10(-5.This approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia.

Evolutionary Computing Methods for Spectral Retrieval

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Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

2009-01-01

A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

Reef sharks: recent advances in ecological understanding to inform conservation.

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Osgood, G J; Baum, J K

2015-12-01

Sharks are increasingly being recognized as important members of coral-reef communities, but their overall conservation status remains uncertain. Nine of the 29 reef-shark species are designated as data deficient in the IUCN Red List, and three-fourths of reef sharks had unknown population trends at the time of their assessment. Fortunately, reef-shark research is on the rise. This new body of research demonstrates reef sharks' high site restriction, fidelity and residency on coral reefs, their broad trophic roles connecting reef communities and their high population genetic structure, all information that should be useful for their management and conservation. Importantly, recent studies on the abundance and population trends of the three classic carcharhinid reef sharks (grey reef shark Carcharhinus amblyrhynchos, blacktip reef shark Carcharhinus melanopterus and whitetip reef shark Triaenodon obesus) may contribute to reassessments identifying them as more vulnerable than currently realized. Because over half of the research effort has focused on only these three reef sharks and the nurse shark Ginglymostoma cirratum in only a few locales, there remain large taxonomic and geographic gaps in reef-shark knowledge. As such, a large portion of reef-shark biodiversity remains uncharacterized despite needs for targeted research identified in their red list assessments. A research agenda for the future should integrate abundance, life history, trophic ecology, genetics, habitat use and movement studies, and expand the breadth of such research to understudied species and localities, in order to better understand the conservation requirements of these species and to motivate effective conservation solutions. © 2015 The Fisheries Society of the British Isles.

Conserved sex chromosomes across adaptively radiated Anolis lizards.

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Rovatsos, Michail; Altmanová, Marie; Pokorná, Martina; Kratochvíl, Lukáš

2014-07-01

Vertebrates possess diverse sex-determining systems, which differ in evolutionary stability among particular groups. It has been suggested that poikilotherms possess more frequent turnovers of sex chromosomes than homoiotherms, whose effective thermoregulation can prevent the emergence of the sex reversals induced by environmental temperature. Squamate reptiles used to be regarded as a group with an extensive variability in sex determination; however, we document how the rather old radiation of lizards from the genus Anolis, known for exceptional ecomorphological variability, was connected with stability in sex chromosomes. We found that 18 tested species, representing most of the phylogenetic diversity of the genus, share the gene content of their X chromosomes. Furthermore, we discovered homologous sex chromosomes in species of two genera (Sceloporus and Petrosaurus) from the family Phrynosomatidae, serving here as an outgroup to Anolis. We can conclude that the origin of sex chromosomes within iguanas largely predates the Anolis radiation and that the sex chromosomes of iguanas remained conserved for a significant part of their evolutionary history. Next to therian mammals and birds, Anolis lizards therefore represent another adaptively radiated amniote clade with conserved sex chromosomes. We argue that the evolutionary stability of sex-determining systems may reflect an advanced stage of differentiation of sex chromosomes rather than thermoregulation strategy. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

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.

Evidence Combination From an Evolutionary Game Theory Perspective.

Science.gov (United States)

Deng, Xinyang; Han, Deqiang; Dezert, Jean; Deng, Yong; Shyr, Yu

2016-09-01

Dempster-Shafer evidence theory is a primary methodology for multisource information fusion because it is good at dealing with uncertain information. This theory provides a Dempster's rule of combination to synthesize multiple evidences from various information sources. However, in some cases, counter-intuitive results may be obtained based on that combination rule. Numerous new or improved methods have been proposed to suppress these counter-intuitive results based on perspectives, such as minimizing the information loss or deviation. Inspired by evolutionary game theory, this paper considers a biological and evolutionary perspective to study the combination of evidences. An evolutionary combination rule (ECR) is proposed to help find the most biologically supported proposition in a multievidence system. Within the proposed ECR, we develop a Jaccard matrix game to formalize the interaction between propositions in evidences, and utilize the replicator dynamics to mimick the evolution of propositions. Experimental results show that the proposed ECR can effectively suppress the counter-intuitive behaviors appeared in typical paradoxes of evidence theory, compared with many existing methods. Properties of the ECR, such as solution's stability and convergence, have been mathematically proved as well.

Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

Science.gov (United States)

Richardson, Dale N.; Wiehe, Thomas

Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units

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C. Vásquez-Carrillo; V. Friesen; L. Hall; M.Z. Peery

2013-01-01

Conserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II...

phyloXML: XML for evolutionary biology and comparative genomics.

Science.gov (United States)

Han, Mira V; Zmasek, Christian M

2009-10-27

Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

A study of driver's route choice behavior based on evolutionary game theory.

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Jiang, Xiaowei; Ji, Yanjie; Du, Muqing; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Conservation genetics of otters: Review about the use of non-invasive samples

OpenAIRE

Aristizábal Duque, Sandra L.; Orozco-Jiménez, Luz Y.; Zapata-Escobar, Carolina; Palacio-Baena, Jaime A.

2018-01-01

Abstract: Wild population management programs require determining some fundamental aspects for conservation, including population structure, flow between populations, evolutionary history and kinship, among others. Since sample collection from wild mammals for DNA extraction is a complex task, conservation genetics has developed non-invasive sampling techniques, which allow obtaining DNA without the need to capture individuals. For the genetic characterization of otter populations, stools are...

Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change†

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Xie, Gary; Keyhani, Nemat O.; Bonner; Jensen, Roy A.

2003-01-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

Ancient origin of the tryptophan operon and the dynamics of evolutionary change.

Science.gov (United States)

Xie, Gary; Keyhani, Nemat O; Bonner, Carol A; Jensen, Roy A

2003-09-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

The novel cytochrome c6 of chloroplasts: a case of evolutionary bricolage?

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Howe, Christopher J; Schlarb-Ridley, Beatrix G; Wastl, Juergen; Purton, Saul; Bendall, Derek S

2006-01-01

Cytochrome c6 has long been known as a redox carrier of the thylakoid lumen of cyanobacteria and some eukaryotic algae that can substitute for plastocyanin in electron transfer. Until recently, it was widely accepted that land plants lack a cytochrome c6. However, a homologue of the protein has now been identified in several plant species together with an additional isoform in the green alga Chlamydomonas reinhardtii. This form of the protein, designated cytochrome c6A, differs from the 'conventional' cytochrome c6 in possessing a conserved insertion of 12 amino acids that includes two absolutely conserved cysteine residues. There are conflicting reports of whether cytochrome c6A can substitute for plastocyanin in photosynthetic electron transfer. The evidence for and against this is reviewed and the likely evolutionary history of cytochrome c6A is discussed. It is suggested that it has been converted from a primary role in electron transfer to one in regulation within the chloroplast, and is an example of evolutionary 'bricolage'.

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.

Evolutionary Nephrology

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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.

Conservation of native Pacific trout diversity in western North America

Science.gov (United States)

Penaluna, Brooke E.; Abadía-Cardoso, Alicia; Dunham, Jason B.; García de León, Francisco J; Gresswell, Robert E.; Luna, Arturo Ruiz; Taylor, Eric B.; Shepard, Bradley B.; Al-Chokhachy, Robert K.; Muhlfeld, Clint C.; Bestgen, Kevin R.; Rogers, Kevin H.; Escalante, Marco A; Keeley, Ernest R; Temple, Gabriel; Williams, Jack E.; Matthews, Kathleen; Pierce, Ron; Mayden, Richard L.; Kovach, Ryan; Garza, John Carlos; Fausch, Kurt D.

2016-01-01

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change

OpenAIRE

Schueler, Silvio; Falk, Wolfgang; Koskela, Jarkko; Lefèvre, François; Bozzano, Michele; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C.

2014-01-01

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species p...

Evolutionary algorithms for mobile ad hoc networks

CERN Document Server

Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal

2014-01-01

Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...

Reverse Conservation Analysis Reveals the Specificity Determining Residues of Cytochrome P450 Family 2 (CYP 2

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Tai-Sung Lee

2008-01-01

Full Text Available The concept of conservation of amino acids is widely used to identify important alignment positions of orthologs. The assumption is that important amino acid residues will be conserved in the protein family during the evolutionary process. For paralog alignment, on the other hand, the opposite concept can be used to identify residues that are responsible for specificity. Assuming that the function-specific or ligand-specific residue positions will have higher diversity since they are under evolutionary pressure to fit the target specificity, these function-specific or ligand-specific residues positions will have a lower degree of conservation than other positions in a highly conserved paralog alignment. This study assessed the ability of reverse conservation analysis to identify function-specific and ligand-specific residue positions in closely related paralog. Reverse conservation analysis of paralog alignments successfully identified all six previously reported substrate recognition sites (SRSs in cytochrome P450 family 2 (CYP 2. Further analysis of each subfamily identified the specificity-determining residues (SDRs that have been experimentally found. New potential SDRs were also predicted and await confirmation by further experiments or modeling calculations. This concept may be also applied to identify SDRs in other protein families.

The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

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Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

2018-03-01

Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more

A teleofunctional account of evolutionary mismatch.

Science.gov (United States)

Cofnas, Nathan

When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

Multiobjective Multifactorial Optimization in Evolutionary Multitasking.

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Gupta, Abhishek; Ong, Yew-Soon; Feng, Liang; Tan, Kay Chen

2016-05-03

In recent decades, the field of multiobjective optimization has attracted considerable interest among evolutionary computation researchers. One of the main features that makes evolutionary methods particularly appealing for multiobjective problems is the implicit parallelism offered by a population, which enables simultaneous convergence toward the entire Pareto front. While a plethora of related algorithms have been proposed till date, a common attribute among them is that they focus on efficiently solving only a single optimization problem at a time. Despite the known power of implicit parallelism, seldom has an attempt been made to multitask, i.e., to solve multiple optimization problems simultaneously. It is contended that the notion of evolutionary multitasking leads to the possibility of automated transfer of information across different optimization exercises that may share underlying similarities, thereby facilitating improved convergence characteristics. In particular, the potential for automated transfer is deemed invaluable from the standpoint of engineering design exercises where manual knowledge adaptation and reuse are routine. Accordingly, in this paper, we present a realization of the evolutionary multitasking paradigm within the domain of multiobjective optimization. The efficacy of the associated evolutionary algorithm is demonstrated on some benchmark test functions as well as on a real-world manufacturing process design problem from the composites industry.

An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

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Haddley Kate

2011-05-01

Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

Elemental conservation units: communicating extinction risk without dictating targets for protection.

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Wood, Chris C; Gross, Mart R

2008-02-01

Conservation biologists mostly agree on the need to identify and protect biodiversity below the species level but have not yet resolved the best approach. We addressed 2 issues relevant to this debate. First, we distinguished between the abstract goal of preserving the maximum amount of unique biodiversity and the pragmatic goal of minimizing the loss of ecological goods and services given that further loss of biodiversity seems inevitable. Second, we distinguished between the scientific task of assessing extinction risk and the normative task of choosing targets for protection. We propose that scientific advice on extinction risk be given at the smallest meaningful scale: the elemental conservation unit (ECU). An ECU is a demographically isolated population whose probability of extinction over the time scale of interest (say 100 years) is not substantially affected by natural immigration from other populations. Within this time frame, the loss of an ECU would be irreversible without human intervention. Society's decision to protect an ECU ought to reflect human values that have social, economic, and political dimensions. Scientists can best inform this decision by providing advice about the probability that an ECU will be lost and the ecological and evolutionary consequences of that loss in a form that can be integrated into landscape planning. The ECU approach provides maximum flexibility to decision makers and ensures that the scientific task of assessing extinction risk informs, but remains distinct from, the normative social challenge of setting conservation targets.

Preservation and Conservation of Information Resources in the University of Zambia Library

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Kanyengo, Christine Wamunyima

2009-01-01

Preservation and conservation of library materials is an important aspect of library and information management. Their importance and necessity are more paramount in countries where resources are limited and libraries need to balance them with the needs of an ever increasing number of students hoping to use them. This article reports on the…

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.

Natural history collections as windows on evolutionary processes.

Science.gov (United States)

Holmes, Michael W; Hammond, Talisin T; Wogan, Guinevere O U; Walsh, Rachel E; LaBarbera, Katie; Wommack, Elizabeth A; Martins, Felipe M; Crawford, Jeremy C; Mack, Katya L; Bloch, Luke M; Nachman, Michael W

2016-02-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. © 2016 John Wiley & Sons Ltd.

Conserved family of glycerol kinase loci in Drosophila melanogaster

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Martinez Agosto, Julian A.; McCabe, Edward R.B.

2009-01-01

Glycerol kinase (GK) is an enzyme that catalyzes the formation of glycerol 3-phosphate from ATP and glycerol, the rate-limiting step in glycerol utilization. We analyzed the genome of the model organism Drosophila melanogaster and identified five GK orthologs, including two loci with sequence homology to the mammalian Xp21 GK protein. Using a combination of sequence analysis and evolutionary comparisons of orthologs between species, we characterized functional domains in the protein required for GK activity. Our findings include additional conserved domains that suggest novel nuclear and mitochondrial functions for glycerol kinase in apoptosis and transcriptional regulation. Investigation of GK function in Drosophila will inform us about the role of this enzyme in development and will provide us with a tool to examine genetic modifiers of human metabolic disorders. PMID:16545593

The origin, current diversity and future conservation of the modern lion (Panthera leo)

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Barnett, Ross; Yamaguchi, Nobuyuki; Barnes, Ian; Cooper, Alan

2006-01-01

Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the ‘recent African origin’ model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African–Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration. PMID:16901830

Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

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Saito Shigeru

2010-05-01

Full Text Available Abstract Background Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages. Results In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events. Conclusions Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

On the evolution of misunderstandings about evolutionary psychology.

Science.gov (United States)

Young, J; Persell, R

2000-04-01

Some of the controversy surrounding evolutionary explanations of human behavior may be due to cognitive information-processing patterns that are themselves the result of evolutionary processes. Two such patterns are (1) the tendency to oversimplify information so as to reduce demand on cognitive resources and (2) our strong desire to generate predictability and stability from perceptions of the external world. For example, research on social stereotyping has found that people tend to focus automatically on simplified social-categorical information, to use such information when deciding how to behave, and to rely on such information even in the face of contradictory evidence. Similarly, an undying debate over nature vs. nurture is shaped by various data-reduction strategies that frequently oversimplify, and thus distort, the intent of the supporting arguments. This debate is also often marked by an assumption that either the nature or the nurture domain may be justifiably excluded at an explanatory level because one domain appears to operate in a sufficiently stable and predictable way for a particular argument. As a result, critiques in-veighed against evolutionary explanations of behavior often incorporate simplified--and erroneous--assumptions about either the mechanics of how evolution operates or the inevitable implications of evolution for understanding human behavior. The influences of these tendencies are applied to a discussion of the heritability of behavioral characteristics. It is suggested that the common view that Mendelian genetics can explain the heritability of complex behaviors, with a one-gene-one-trait process, is misguided. Complex behaviors are undoubtedly a product of a more complex interaction between genes and environment, ensuring that both nature and nurture must be accommodated in a yet-to-be-developed post-Mendelian model of genetic influence. As a result, current public perceptions of evolutionary explanations of behavior are

Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.

Science.gov (United States)

Mukherjee, Dola; Mukherjee, Ashutosh; Ghosh, Tapash Chandra

2015-11-10

Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

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Sharmin, Refat; Islam, Abul B M M K

2016-01-01

MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses. We used various in silico tools to predict the conserved antigenic sites. We found that MERS-CoV shared 30 % of its S protein antigenic sites with HKU4 and 70 % with HKU5 bat-CoV. Whereas 100 % of its E, M and N protein's antigenic sites are found to be conserved with those in HKU4 and HKU5. This sharing suggests that in case of pathogenicity MERS-CoV is more closely related to HKU5 bat-CoV than HKU4 bat-CoV. The conserved epitopes indicates their evolutionary relationship and ancestry of pathogenicity.

Evolutionary distance from human homologs reflects allergenicity of animal food proteins.

Science.gov (United States)

Jenkins, John A; Breiteneder, Heimo; Mills, E N Clare

2007-12-01

In silico analysis of allergens can identify putative relationships among protein sequence, structure, and allergenic properties. Such systematic analysis reveals that most plant food allergens belong to a restricted number of protein superfamilies, with pollen allergens behaving similarly. We have investigated the structural relationships of animal food allergens and their evolutionary relatedness to human homologs to define how closely a protein must resemble a human counterpart to lose its allergenic potential. Profile-based sequence homology methods were used to classify animal food allergens into Pfam families, and in silico analyses of their evolutionary and structural relationships were performed. Animal food allergens could be classified into 3 main families--tropomyosins, EF-hand proteins, and caseins--along with 14 minor families each composed of 1 to 3 allergens. The evolutionary relationships of each of these allergen superfamilies showed that in general, proteins with a sequence identity to a human homolog above approximately 62% were rarely allergenic. Single substitutions in otherwise highly conserved regions containing IgE epitopes in EF-hand parvalbumins may modulate allergenicity. These data support the premise that certain protein structures are more allergenic than others. Contrasting with plant food allergens, animal allergens, such as the highly conserved tropomyosins, challenge the capability of the human immune system to discriminate between foreign and self-proteins. Such immune responses run close to becoming autoimmune responses. Exploiting the closeness between animal allergens and their human homologs in the development of recombinant allergens for immunotherapy will need to consider the potential for developing unanticipated autoimmune responses.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

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Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

2013-01-01

WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

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.

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

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Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

2018-04-24

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed

A Study of Driver’s Route Choice Behavior Based on Evolutionary Game Theory

Directory of Open Access Journals (Sweden)

Xiaowei Jiang

2014-01-01

Full Text Available This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers’ route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver’s route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver’s route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

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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.

Beyond the Pleistocene: Using Phylogeny and Constraint to Inform the Evolutionary Psychology of Human Mating

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Eastwick, Paul W.

2009-01-01

Evolutionary psychologists explore the adaptive function of traits and behaviors that characterize modern Homo sapiens. However, evolutionary psychologists have yet to incorporate the phylogenetic relationship between modern Homo sapiens and humans' hominid and pongid relatives (both living and extinct) into their theorizing. By considering the…

Conservation

NARCIS (Netherlands)

Noteboom, H.P.

1985-01-01

The IUCN/WWF Plants Conservation Programme 1984 — 1985. World Wildlife Fund chose plants to be the subject of their fund-raising campaign in the period 1984 — 1985. The objectives were to: 1. Use information techniques to achieve the conservation objectives of the Plants Programme – to save plants;

Conservation endocrinology

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McCormick, Stephen; Romero, L. Michael

2017-01-01

Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species.

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Larkin, Daniel J; Jacobi, Sarah K; Hipp, Andrew L; Kramer, Andrea T

2016-01-01

Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the 'PIECES' index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to

Recording Information on Architectural Heritage Should Meet the Requirements for Conservation Digital Recording Practices at the Summer Palace

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Zhang, L.; Cong, Y.; Wu, C.; Bai, C.; Wu, C.

2017-08-01

The recording of Architectural heritage information is the foundation of research, conservation, management, and the display of architectural heritage. In other words, the recording of architectural heritage information supports heritage research, conservation, management and architectural heritage display. What information do we record and collect and what technology do we use for information recording? How do we determine the level of accuracy required when recording architectural information? What method do we use for information recording? These questions should be addressed in relation to the nature of the particular heritage site and the specific conditions for the conservation work. In recent years, with the rapid development of information acquisition technology such as Close Range Photogrammetry, 3D Laser Scanning as well as high speed and high precision Aerial Photogrammetry, many Chinese universities, research institutes and heritage management bureaux have purchased considerable equipment for information recording. However, the lack of understanding of both the nature of architectural heritage and the purpose for which the information is being collected has led to several problems. For example: some institutions when recording architectural heritage information aim solely at high accuracy. Some consider that advanced measuring methods must automatically replace traditional measuring methods. Information collection becomes the purpose, rather than the means, of architectural heritage conservation. Addressing these issues, this paper briefly reviews the history of architectural heritage information recording at the Summer Palace (Yihe Yuan, first built in 1750), Beijing. Using the recording practices at the Summer Palace during the past ten years as examples, we illustrate our achievements and lessons in recording architectural heritage information with regard to the following aspects: (buildings') ideal status desired, (buildings') current status

International Conference of Intelligence Computation and Evolutionary Computation ICEC 2012

CERN Document Server

Intelligence Computation and Evolutionary Computation

2013-01-01

2012 International Conference of Intelligence Computation and Evolutionary Computation (ICEC 2012) is held on July 7, 2012 in Wuhan, China. This conference is sponsored by Information Technology & Industrial Engineering Research Center.  ICEC 2012 is a forum for presentation of new research results of intelligent computation and evolutionary computation. Cross-fertilization of intelligent computation, evolutionary computation, evolvable hardware and newly emerging technologies is strongly encouraged. The forum aims to bring together researchers, developers, and users from around the world in both industry and academia for sharing state-of-art results, for exploring new areas of research and development, and to discuss emerging issues facing intelligent computation and evolutionary computation.

Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information.

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An, Ji-Yong; Zhang, Lei; Zhou, Yong; Zhao, Yu-Jun; Wang, Da-Fu

2017-08-18

Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Self-interactions detection, one major challenge in the study of prediction SIPs is how to exploit computational approaches for SIPs detection based on evolutionary information contained protein sequence. In the work, we presented a novel computational approach named WELM-LAG, which combined the Weighed-Extreme Learning Machine (WELM) classifier with Local Average Group (LAG) to predict SIPs based on protein sequence. The major improvement of our method lies in presenting an effective feature extraction method used to represent candidate Self-interactions proteins by exploring the evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix (PSSM); and then employing a reliable and robust WELM classifier to carry out classification. In addition, the Principal Component Analysis (PCA) approach is used to reduce the impact of noise. The WELM-LAG method gave very high average accuracies of 92.94 and 96.74% on yeast and human datasets, respectively. Meanwhile, we compared it with the state-of-the-art support vector machine (SVM) classifier and other existing methods on human and yeast datasets, respectively. Comparative results indicated that our approach is very promising and may provide a cost-effective alternative for predicting SIPs. In addition, we developed a freely available web server called WELM-LAG-SIPs to predict SIPs. The web server is available at http://219.219.62.123:8888/WELMLAG/ .

How Should Beta-Diversity Inform Biodiversity Conservation?

Science.gov (United States)

Socolar, Jacob B; Gilroy, James J; Kunin, William E; Edwards, David P

2016-01-01

To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conservation.

Science.gov (United States)

National Audubon Society, New York, NY.

This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

Science.gov (United States)

Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

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 ...

The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.

Science.gov (United States)

Nagy, Vanja; Cole, Tiffany; Van Campenhout, Claude; Khoung, Thang M; Leung, Calvin; Vermeiren, Simon; Novatchkova, Maria; Wenzel, Daniel; Cikes, Domagoj; Polyansky, Anton A; Kozieradzki, Ivona; Meixner, Arabella; Bellefroid, Eric J; Neely, G Gregory; Penninger, Josef M

2015-01-01

PR homology domain-containing member 12 (PRDM12) belongs to a family of conserved transcription factors implicated in cell fate decisions. Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution. Expression of wild-type human PRDM12 in Xenopus induced the expression of sensory neuronal markers, which was reduced using various human PRDM12 mutants. In Drosophila, we identified Hamlet as the functional PRDM12 homolog that controls nociceptive behavior in sensory neurons. Furthermore, expression analysis of human patient fibroblasts with PRDM12 mutations uncovered possible downstream target genes. Knockdown of several of these target genes including thyrotropin-releasing hormone degrading enzyme (TRHDE) in Drosophila sensory neurons resulted in altered cellular morphology and impaired nociception. These data show that PRDM12 and its functional fly homolog Hamlet are evolutionary conserved master regulators of sensory neuronal specification and play a critical role in pain perception. Our data also uncover novel pathways in multiple species that regulate evolutionary conserved nociception.

Evolutionary perspectives on innate immunity from the study of Caenorhabditis elegans.

Science.gov (United States)

Kim, Dennis H; Ausubel, Frederick M

2005-02-01

Genetic and functional genomic approaches have begun to define the molecular determinants of pathogen resistance in Caenorhabditis elegans. Conserved signal transduction components are required for pathogen resistance, including a Toll/IL-1 receptor domain adaptor protein that functions upstream of a conserved p38 MAP kinase pathway. We suggest that this pathway is an ancestral innate immune signaling pathway present in the common ancestor of nematodes, arthropods and vertebrates, which is likely to predate the involvement of canonical Toll signaling pathways in innate immunity. We anticipate that the study of pathogen resistance in C. elegans will continue to provide evolutionary and mechanistic insights into the signal transduction and physiology of innate immunity.

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

Evolutionary ancestry and novel functions of the mammalian glucose transporter (GLUT) family.

Science.gov (United States)

Wilson-O'Brien, Amy L; Patron, Nicola; Rogers, Suzanne

2010-05-21

In general, sugar porters function by proton-coupled symport or facilitative transport modes. Symporters, coupled to electrochemical energy, transport nutrients against a substrate gradient. Facilitative carriers transport sugars along a concentration gradient, thus transport is dependent upon extracellular nutrient levels. Across bacteria, fungi, unicellular non-vertebrates and plants, proton-coupled hexose symport is a crucial process supplying energy under conditions of nutrient flux. In mammals it has been assumed that evolution of whole body regulatory mechanisms would eliminate this need. To determine whether any isoforms bearing this function might be conserved in mammals, we investigated the relationship between the transporters of animals and the proton-coupled hexose symporters found in other species. We took a comparative genomic approach and have performed the first comprehensive and statistically supported phylogenetic analysis of all mammalian glucose transporter (GLUT) isoforms. Our data reveals the mammalian GLUT proteins segregate into five distinct classes. This evolutionary ancestry gives insight to structure, function and transport mechanisms within the groups. Combined with biological assays, we present novel evidence that, in response to changing nutrient availability and environmental pH, proton-coupled, active glucose symport function is maintained in mammalian cells. The analyses show the ancestry, evolutionary conservation and biological importance of the GLUT classes. These findings significantly extend our understanding of the evolution of mammalian glucose transport systems. They also reveal that mammals may have conserved an adaptive response to nutrient demand that would have important physiological implications to cell survival and growth.

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.

Human genomic disease variants: a neutral evolutionary explanation.

Science.gov (United States)

Dudley, Joel T; Kim, Yuseob; Liu, Li; Markov, Glenn J; Gerold, Kristyn; Chen, Rong; Butte, Atul J; Kumar, Sudhir

2012-08-01

Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.

Applying Evolutionary Prototyping In Developing LMIS: A Spatial Web-Based System For Land Management

Science.gov (United States)

Agustiono, W.

2018-01-01

Software development project is a difficult task. Especially for software designed to comply with regulations that are constantly being introduced or changed, it is almost impossible to make just one change during the development process. Even if it is possible, nonetheless, the developers may take bulk of works to fix the design to meet specified needs. This iterative work also means that it takes additional time and potentially leads to failing to meet the original schedule and budget. In such inevitable changes, it is essential for developers to carefully consider and use an appropriate method which will help them carry out software project development. This research aims to examine the implementation of a software development method called evolutionary prototyping for developing software for complying regulation. It investigates the development of Land Management Information System (pseudonym), initiated by the Australian government, for use by farmers to meet regulatory demand requested by Soil and Land Conservation Act. By doing so, it sought to provide understanding the efficacy of evolutionary prototyping in helping developers address frequent changing requirements and iterative works but still within schedule. The findings also offer useful practical insights for other developers who seek to build similar regulatory compliance software.

The evolutionary role of modularity and integration in the hominoid cranium.

Science.gov (United States)

Mitteroecker, Philipp; Bookstein, Fred

2008-04-01

Patterns of morphological integration and modularity among shape features emerge from genetic and developmental factors with varying pleiotropic effects. Factors or processes affecting morphology only locally may respond to selection more easily than common factors that may lead to deleterious side effects and hence are expected to be more conserved. We briefly review evidence for such global factors in primate cranial development as well as for local factors constrained to either the face or the neurocranium. In a sample comprising 157 crania of Homo sapiens, Pan troglodytes, and Gorilla gorilla, we statistically estimated common and local factors of shape variation from Procrustes coordinates of 347 landmarks and semilandmarks. Common factors with pleiotropic effects on both the face and the neurocranium account for a large amount of shape variation, but mainly by extension or truncation of otherwise conserved developmental pathways. Local factors (modular shape characteristics) have more degrees of freedom for evolutionary change than mere ontogenetic scaling. Cranial shape is similarly integrated during development in all three species, but human evolution involves dissociation among several characteristics. The dissociation has probably been achieved by evolutionary alterations and by the novel emergence of local factors affecting characteristics that are controlled at the same time by the common factors.

Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila.

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Caizzi, Ruggiero; Moschetti, Roberta; Piacentini, Lucia; Fanti, Laura; Marsano, Renè Massimiliano; Dimitri, Patrizio

2016-08-01

The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentric heterochromatin, yet little is known about the evolutionary processes through which this has occurred. By combining genome annotation analysis and high-resolution cytology, we have identified and mapped 53 orthologs of D. melanogaster heterochromatic genes in the genomes of two evolutionarily distant species, D. pseudoobscura and D. virilis. Our results show that the orthologs of the D. melanogaster heterochromatic genes are clustered at three main genomic regions in D. virilis and D. pseudoobscura. In D. virilis, the clusters lie in the middle of euchromatin, while those in D. pseudoobscura are located in the proximal portion of the chromosome arms. Some orthologs map to the corresponding Muller C element in D. pseudoobscura and D. virilis, while others localize on the Muller B element, suggesting that chromosomal rearrangements that have been instrumental in the fusion of two separate elements involved the progenitors of genes currently located in D. melanogaster heterochromatin. These results demonstrate an evolutionary repositioning of gene clusters from ancestral locations in euchromatin to the pericentromeric heterochromatin of descendent D. melanogaster chromosomes. Remarkably, in both D. virilis and D. pseudoobscura the gene clusters show a conserved association with the HP1a protein, one of the most highly evolutionarily conserved epigenetic marks. In light of these results, we suggest a new scenario whereby ancestral HP1-like proteins (and possibly other epigenetic marks) may have contributed to the evolutionary repositioning of gene clusters into heterochromatin.

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

OpenAIRE

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 Kom...

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.

Translational environmental biology: cell biology informing conservation.

Science.gov (United States)

Traylor-Knowles, Nikki; Palumbi, Stephen R

2014-05-01

Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Position-specific prediction of methylation sites from sequence conservation based on information theory.

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Shi, Yinan; Guo, Yanzhi; Hu, Yayun; Li, Menglong

2015-07-23

Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

The origins of pedagogy: developmental and evolutionary perspectives.

Science.gov (United States)

Skerry, Amy E; Lambert, Enoch; Powell, Lindsey J; McAuliffe, Katherine

2013-07-18

The question of whether and how information is actively transferred from knowledgeable to ignorant individuals has received much attention in psychology and evolutionary biology. Research in these fields has proceeded largely independently, with studies of nonhuman animals focusing on knowledgeable individuals and whether or not they meet a functional definition of teaching, while studies of children focus on the learner's assumptions and inferences. We argue that a comprehensive theory of teaching will benefit from integrating perspectives and empirical phenomena from evolutionary and developmental disciplines. In this review, we identify cases of seemingly purposeful information transfer (i.e. teaching) in human and nonhuman animals, discuss what is known about the cognitive processes that support teaching in different species, and highlight ways in which each discipline might be informed by extant theories and empirical tools from the other.

Evolutionary Algorithms for Boolean Queries Optimization

Czech Academy of Sciences Publication Activity Database

Húsek, Dušan; Snášel, Václav; Neruda, Roman; Owais, S.S.J.; Krömer, P.

2006-01-01

Roč. 3, č. 1 (2006), s. 15-20 ISSN 1790-0832 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * information retrieval * Boolean query Subject RIV: BA - General Mathematics

Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens.

Science.gov (United States)

Fan, Xiaobo; Supiwong, Weerayuth; Weise, Anja; Mrasek, Kristin; Kosyakova, Nadezda; Tanomtong, Alongkoad; Pinthong, Krit; Trifonov, Vladimir A; Cioffi, Marcelo de Bello; Grothmann, Pierre; Liehr, Thomas; Oliveira, Edivaldo H C de

2015-11-01

Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens

Directory of Open Access Journals (Sweden)

Xiaobo Fan

2015-11-01

Full Text Available Comparative cytogenetic analysis in New World Monkeys (NWMs using human multicolor banding (MCB probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM species, i.e. in Alouatta caraya (ACA, Callithrix jacchus (CJA, Cebus apella (CAP, Saimiri sciureus (SSC, and Chlorocebus aethiops (CAE, respectively. 107 individual evolutionary conserved breakpoints (ECBs among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107 NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99 NWM-ECBs were related with those of Hylobates lar (HLA and 66.3% (71/107 NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS. Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

DNA from the past informs ex situ conservation for the future: an "extinct" species of Galápagos tortoise identified in captivity.

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Michael A Russello

2010-01-01

Full Text Available Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry.We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a "Floreana-like" mitochondrial DNA haplotype.Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C

Amino Acids of Epstein-Barr Virus Nuclear Antigen 3A Essential for Repression of Jκ-Mediated Transcription and Their Evolutionary Conservation

Science.gov (United States)

Dalbiès-Tran, Rozenn; Stigger-Rosser, Evelyn; Dotson, Travis; Sample, Clare E.

2001-01-01

Epstein-Barr virus (EBV) nuclear antigen 3A (EBNA-3A) is essential for virus-mediated immortalization of B lymphocytes in vitro and is believed to regulate transcription of cellular and/or viral genes. One known mechanism of regulation is through its interaction with the cellular transcription factor Jκ. This interaction downregulates transcription mediated by EBNA-2 and Jκ. To identify the amino acids that play a role in this interaction, we have generated mutant EBNA-3A proteins. A mutant EBNA-3A protein in which alanine residues were substituted for amino acids 199, 200, and 202 no longer downregulated transcription. Surprisingly, this mutant protein remained able to coimmunoprecipitate with Jκ. Using a reporter gene assay based on the recruitment of Jκ by various regions spanning EBNA-3A, we have shown that this mutation abolished binding of Jκ to the N-proximal region (amino acids 125 to 222) and that no other region of EBNA-3A alone was sufficient to mediate an association with Jκ. To determine the biological significance of the interaction of EBNA-3A with Jκ, we have studied its conservation in the simian lymphocryptovirus herpesvirus papio (HVP) by cloning HVP-3A, the homolog of EBNA-3A encoded by this virus. This 903-amino-acid protein exhibited 37% identity with its EBV counterpart, mainly within the amino-terminal half. HVP-3A also interacted with Jκ through a region located between amino acids 127 and 223 and also repressed transcription mediated through EBNA-2 and Jκ. The evolutionary conservation of this function, in proteins that have otherwise significantly diverged, argues strongly for an important biological role in virus-mediated immortalization of B lymphocytes. PMID:11119577

Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

Directory of Open Access Journals (Sweden)

Panwar Bharat

2013-02-01

obtained highest MCC of 0.53, 0.48, 0.61, 0.81 for VIRs, VAIRs, VBIRs, PLPIRs respectively, using PSSM-based evolutionary information. All the modules developed in this study have been trained and tested on non-redundant datasets and evaluated using five-fold cross-validation technique. The performances were also evaluated on the balanced and different independent datasets. Conclusions This study demonstrates that it is possible to predict VIRs, VAIRs, VBIRs and PLPIRs from evolutionary information of protein sequence. In order to provide service to the scientific community, we have developed web-server and standalone software VitaPred (http://crdd.osdd.net/raghava/vitapred/.

Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.

Science.gov (United States)

Panwar, Bharat; Gupta, Sudheer; Raghava, Gajendra P S

2013-02-07

.81 for VIRs, VAIRs, VBIRs, PLPIRs respectively, using PSSM-based evolutionary information. All the modules developed in this study have been trained and tested on non-redundant datasets and evaluated using five-fold cross-validation technique. The performances were also evaluated on the balanced and different independent datasets. This study demonstrates that it is possible to predict VIRs, VAIRs, VBIRs and PLPIRs from evolutionary information of protein sequence. In order to provide service to the scientific community, we have developed web-server and standalone software VitaPred (http://crdd.osdd.net/raghava/vitapred/).

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

2016-09-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. © 2016 American Society of Plant Biologists. All rights reserved.

Benefits and limitations of using decision analytic tools to assess uncertainty and prioritize Landscape Conservation Cooperative information needs

Science.gov (United States)

Post van der Burg, Max; Cullinane Thomas, Catherine; Holcombe, Tracy R.; Nelson, Richard D.

2016-01-01

The Landscape Conservation Cooperatives (LCCs) are a network of partnerships throughout North America that are tasked with integrating science and management to support more effective delivery of conservation at a landscape scale. In order to achieve this integration, some LCCs have adopted the approach of providing their partners with better scientific information in an effort to facilitate more effective and coordinated conservation decisions. Taking this approach has led many LCCs to begin funding research to provide the information for improved decision making. To ensure that funding goes to research projects with the highest likelihood of leading to more integrated broad scale conservation, some LCCs have also developed approaches for prioritizing which information needs will be of most benefit to their partnerships. We describe two case studies in which decision analytic tools were used to quantitatively assess the relative importance of information for decisions made by partners in the Plains and Prairie Potholes LCC. The results of the case studies point toward a few valuable lessons in terms of using these tools with LCCs. Decision analytic tools tend to help shift focus away from research oriented discussions and toward discussions about how information is used in making better decisions. However, many technical experts do not have enough knowledge about decision making contexts to fully inform the latter type of discussion. When assessed in the right decision context, however, decision analyses can point out where uncertainties actually affect optimal decisions and where they do not. This helps technical experts understand that not all research is valuable in improving decision making. But perhaps most importantly, our results suggest that decision analytic tools may be more useful for LCCs as way of developing integrated objectives for coordinating partner decisions across the landscape, rather than simply ranking research priorities.

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

Science.gov (United States)

Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

2015-10-01

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further

Conservation Process Model (cpm): a Twofold Scientific Research Scope in the Information Modelling for Cultural Heritage

Science.gov (United States)

Fiorani, D.; Acierno, M.

2017-05-01

The aim of the present research is to develop an instrument able to adequately support the conservation process by means of a twofold approach, based on both BIM environment and ontology formalisation. Although BIM has been successfully experimented within AEC (Architecture Engineering Construction) field, it has showed many drawbacks for architectural heritage. To cope with unicity and more generally complexity of ancient buildings, applications so far developed have shown to poorly adapt BIM to conservation design with unsatisfactory results (Dore, Murphy 2013; Carrara 2014). In order to combine achievements reached within AEC through BIM environment (design control and management) with an appropriate, semantically enriched and flexible The presented model has at its core a knowledge base developed through information ontologies and oriented around the formalization and computability of all the knowledge necessary for the full comprehension of the object of architectural heritage an its conservation. Such a knowledge representation is worked out upon conceptual categories defined above all within architectural criticism and conservation scope. The present paper aims at further extending the scope of conceptual modelling within cultural heritage conservation already formalized by the model. A special focus is directed on decay analysis and surfaces conservation project.

The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate

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Stone Eric A

2011-08-01

Full Text Available Abstract Background Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation. Results Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends. Conclusions We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may

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.

A Neurology of the Conservative-Liberal Dimension of Political Ideology.

Science.gov (United States)

Mendez, Mario F

2017-01-01

Differences in political ideology are a major source of human disagreement and conflict. There is increasing evidence that neurobiological mechanisms mediate individual differences in political ideology through effects on a conservative-liberal axis. This review summarizes personality, evolutionary and genetic, cognitive, neuroimaging, and neurological studies of conservatism-liberalism and discusses how they might affect political ideology. What emerges from this highly variable literature is evidence for a normal right-sided "conservative-complex" involving structures sensitive to negativity bias, threat, disgust, and avoidance. This conservative-complex may be damaged with brain disease, sometimes leading to a pathological "liberal shift" or a reduced tendency to conservatism in political ideology. Although not deterministic, these findings recommend further research on politics and the brain.

Utilizing social media for informal ocean conservation and education: The BioOceanography Project

Science.gov (United States)

Payette, J.

2016-02-01

Science communication through the use of social media is a rapidly evolving and growing pursuit in academic and scientific circles. Online tools and social media are being used in not only scientific communication but also scientific publication, education, and outreach. Standards and usage of social media as well as other online tools for communication, networking, outreach, and publication are always in development. Caution and a conservative attitude towards these novel "Science 2.0" tools is understandable because of their rapidly changing nature and the lack of professional standards for using them. However there are some key benefits and unique ways social media, online systems, and other Open or Open Source technologies, software, and "Science 2.0" tools can be utilized for academic purposes such as education and outreach. Diverse efforts for ocean conservation and education will continue to utilize social media for a variety of purposes. The BioOceanography project is an informal communication, education, outreach, and conservation initiative created for enhancing knowledge related to Oceanography and Marine Science with an unbiased yet conservation-minded approach and in an Open Source format. The BioOceanography project is ongoing and still evolving, but has already contributed to ocean education and conservation communication in key ways through a concerted web presence since 2013, including a curated Twitter account @_Oceanography and BioOceanography blog style website. Social media tools like those used in this project, if used properly can be highly effective and valuable for encouraging students, networking with researchers, and educating the general public in Oceanography.

Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

Energy Technology Data Exchange (ETDEWEB)

Chandonia, John-Marc; Kim, Sung-Hou

2006-03-15

Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

Directory of Open Access Journals (Sweden)

Nolan Priedigkeit

2015-02-01

Full Text Available Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC, is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting "disease map" network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks.

THE THEORY OF THE FIRM AND THE EVOLUTIONARY GAMES

Directory of Open Access Journals (Sweden)

Sirghi Nicoleta

2013-07-01

Full Text Available The neoclassical theory of the firm deals with the pattern of perfect competition, within which the perfect information available to economic agents provides instant allocation of production factors and access to economic goods. The Austrian School (C. Menger, L. von Mises, Hayek, etc. supported the idea of minimal state intervention on the markets, bringing important conceptual developments on the theory of the firm. Hirschleifer (1982 put forward the model of social and institutional functioning, arguing that the game theory is able to predict the outcome of the collective behavior and the human characteristics necessary for building the respective institutions.The evolutionary theory provides the firm and the entrepreneur the recognition of the functions of innovation, of generating and exploiting information and of organizing and coordinating production. The evolutionary perspective of the firm assumes the existence of a body of knowledge that is acquired through and builds up the organizational memory, subsequently found in routines, all choices being made based on these routines (Nelson and Winter, 2002. The evolution of the firm is considered to be similar to natural selection, but unlike the classic market selection, the evolutionists suggest the existence of a plurality of selection media. The present research is structured as follows: a brief introduction into the theories of the firm, the second part of the paper analyzes the theories of the firm from an institutional, neo-institutional and evolutionary perspective. In the third part of the paper the evolutionary games are described and analyzed from the evolutionary perspective of the firm. The last part of the paper represents a study of the “hawk-dove” game dynamic replicator. The final conclusions of the paper show that the evolutionary theory brings valuable contributions to the foundation of explanations regarding economic phenomena, indicating new directions for advanced

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

Science.gov (United States)

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

Tetrahedral gray code for visualization of genome information.

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Natsuhiro Ichinose

Full Text Available We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each [Formula: see text]-mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the [Formula: see text]-mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.

Evolutionary ancestry and novel functions of the mammalian glucose transporter (GLUT family

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Patron Nicola

2010-05-01

Full Text Available Abstract Background In general, sugar porters function by proton-coupled symport or facilitative transport modes. Symporters, coupled to electrochemical energy, transport nutrients against a substrate gradient. Facilitative carriers transport sugars along a concentration gradient, thus transport is dependent upon extracellular nutrient levels. Across bacteria, fungi, unicellular non-vertebrates and plants, proton-coupled hexose symport is a crucial process supplying energy under conditions of nutrient flux. In mammals it has been assumed that evolution of whole body regulatory mechanisms would eliminate this need. To determine whether any isoforms bearing this function might be conserved in mammals, we investigated the relationship between the transporters of animals and the proton-coupled hexose symporters found in other species. Results We took a comparative genomic approach and have performed the first comprehensive and statistically supported phylogenetic analysis of all mammalian glucose transporter (GLUT isoforms. Our data reveals the mammalian GLUT proteins segregate into five distinct classes. This evolutionary ancestry gives insight to structure, function and transport mechanisms within the groups. Combined with biological assays, we present novel evidence that, in response to changing nutrient availability and environmental pH, proton-coupled, active glucose symport function is maintained in mammalian cells. Conclusions The analyses show the ancestry, evolutionary conservation and biological importance of the GLUT classes. These findings significantly extend our understanding of the evolution of mammalian glucose transport systems. They also reveal that mammals may have conserved an adaptive response to nutrient demand that would have important physiological implications to cell survival and growth.

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

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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.

Identifying ambassador species for conservation marketing

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E.A. Macdonald

2017-10-01

Full Text Available Conservation relies heavily on external funding, much of it from a supportive public. Therefore it is important to know which species are most likely to catalyse such funding. Whilst previous work has looked at the physical attributes that contribute to a species' appeal, no previous studies have tried to examine the extent to which a species' sympatriots might contribute to it's potential as flagship for wider conservation. Therefore, here we estimate ‘flexibility’ and ‘appeal’ scores for all terrestrial mammals (n = 4320 and identify which of these might serve as ambassadors (defined as both highly appealing and flexible. Relatively few mammals (between 240 and 331 emerged as ambassadors, with carnivores featuring heavily in this group (representing 5% of terrestrial mammals but 39% of ambassadors. ‘Top ambassadors’ were defined as those with both flexibility and appeal scores greater than 1 standard deviation above the mean. Less than a quarter of the 20 most endangered and evolutionary distinct species in this study were classed as ambassadors, highlighting the need for surrogate species to catalyse conservation effort in areas with such priority species. This is the first global analysis bringing together flexibility and appeal for all terrestrial mammals, and demonstrates an approach for determining how best to market species in order to achieve maximal conservation gain in a world with urgent conservation need but limited resources.

Evolutionary comparison of prenylation pathway in kinetoplastid Leishmania and its sister Leptomonas.

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Chauhan, Indira Singh; Kaur, Jaspreet; Krishna, Shagun; Ghosh, Arpita; Singh, Prashant; Siddiqi, Mohammad Imran; Singh, Neeloo

2015-11-21

Leptomonas is monogenetic kinetoplastid parasite of insects and is primitive in comparison to Leishmania. Comparative studies of these two kinetoplastid may share light on the evolutionary transition to dixenous parasitism in Leishmania. In order to adapt and survive within two hosts, Leishmania species must have acquired virulence factors in addition to mechanisms that mediate susceptibility/resistance to infection in the pathology associated with disease. Rab proteins are key mediators of vesicle transport and contribute greatly to the evolution of complexity of membrane transport system. In this study we used our whole genome sequence data of these two divergent kinetoplastids to analyze the orthologues/paralogues of Rab proteins. During change of lifestyle from monogenetic (Leptomonas) to digenetic (Leishmania), we found that the prenyl machinery remained unchanged. Geranylgeranyl transferase-I (GGTase-I) was absent in both Leishmania and its sister Leptomonas. Farnesyltransferase (FTase) and geranylgeranyl transferase-II (GGTase-II) were identified for protein prenylation. We predict that activity of the missing alpha-subunit (α-subunit) of GGTase-II in Leptomonas was probably contributed by the α-subunit of FTase, while beta-subunit (β-subunit) of GGTase-II was conserved and indicated functional conservation in the evolution of these two kinetoplastids. Therefore the β-subunit emerges as an excellent target for compounds inhibiting parasite activity in clinical cases of co-infections. We also confirmed that during the evolution to digenetic life style in Leishmania, the parasite acquired capabilities to evade drug action and maintain parasite virulence in the host with the incorporation of short-chain dehydrogenase/reductase (SDR/MDR) superfamily in Rab genes. Our study based on whole genome sequences is the first to build comparative evolutionary analysis and identification of prenylation proteins in Leishmania and its sister Leptomonas. The information

Lysosomal enzymes and their receptors in invertebrates: an evolutionary perspective.

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Kumar, Nadimpalli Siva; Bhamidimarri, Poorna M

2015-01-01

Lysosomal biogenesis is an important process in eukaryotic cells to maintain cellular homeostasis. The key components that are involved in the biogenesis such as the lysosomal enzymes, their modifications and the mannose 6-phosphate receptors have been well studied and their evolutionary conservation across mammalian and non-mammalian vertebrates is clearly established. Invertebrate lysosomal biogenesis pathway on the other hand is not well studied. Although, details on mannose 6-phosphate receptors and enzymes involved in lysosomal enzyme modifications were reported earlier, a clear cut pathway has not been established. Recent research on the invertebrate species involving biogenesis of lysosomal enzymes suggests a possible conserved pathway in invertebrates. This review presents certain observations based on these processes that include biochemical, immunological and functional studies. Major conclusions include conservation of MPR-dependent pathway in higher invertebrates and recent evidence suggests that MPR-independent pathway might have been more prominent among lower invertebrates. The possible components of MPR-independent pathway that may play a role in lysosomal enzyme targeting are also discussed here.

An Evolutionary Perspective on Toxic Leadership

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Lucia Ovidia VREJA

2016-12-01

Full Text Available Charles Darwin’s prediction from 1859, that future psychology was going to be built on principles derived from evolutionary theory came at last to be fulfilled. Nowadays, there are at least four disciplines that attempt to explain human behaviours as evolutionary adaptations (or maladaptations to the natural and/or social environment: human sociobiology, human behavioural ecology, evolutionary psychology, memetics and gene–culture coevolution theory (in our view, the most adequate of all. According to gene–culture coevolution theory, articulated language was the singular phenomenon that permitted humans to become a cultural species, and from that moment on culture become itself a selection factor. Culture means transmission of information from one generation to the next and learning from other individuals’ experiences, trough language. So, it is of critical importance to have good criteria for the selection of those individuals from whom we should learn. Yet when humans also choose their leaders from among those role-models, according to the same criteria, this mechanism can become a maladaptation and the result can be toxic leadership.

Information on black-footed ferret biology collected within the framework of ferret conservation

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Biggins, Dean E.

2012-01-01

Once feared to be extinct, black-footed ferrets (Mustela nigripes) were rediscovered near Meeteetse, Wyoming, in 1981, resulting in renewed conservation and research efforts for this highly endangered species. A need for information directly useful to recovery has motivated much monitoring of ferrets since that time, but field activities have enabled collection of data relevant to broader biological themes. This special feature is placed in a context of similar books and proceedings devoted to ferret biology and conservation. Articles include general observations on ferrets, modeling of potential impacts of ferrets on prairie dogs (Cynomys spp.), discussions on relationships of ferrets to prairie dog habitats at several spatial scales (from individual burrows to patches of burrow systems) and a general treatise on the status of black-footed ferret recovery.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

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Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

2016-01-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

Integrating conservation costs into sea level rise adaptive conservation prioritization

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Mingjian Zhu

2015-07-01

Full Text Available Biodiversity conservation requires strategic investment as resources for conservation are often limited. As sea level rises, it is important and necessary to consider both sea level rise and costs in conservation decision making. In this study, we consider costs of conservation in an integrated modeling process that incorporates a geomorphological model (SLAMM, species habitat models, and conservation prioritization (Zonation to identify conservation priorities in the face of landscape dynamics due to sea level rise in the Matanzas River basin of northeast Florida. Compared to conservation priorities that do not consider land costs in the analysis process, conservation priorities that consider costs in the planning process change significantly. The comparison demonstrates that some areas with high conservation values might be identified as lower priorities when integrating economic costs in the planning process and some areas with low conservation values might be identified as high priorities when considering costs in the planning process. This research could help coastal resources managers make informed decisions about where and how to allocate conservation resources more wisely to facilitate biodiversity adaptation to sea level rise.

Do species conservation assessments capture genetic diversity?

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Malin C. Rivers

2014-12-01

Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

CONSERVATION PROCESS MODEL (CPM: A TWOFOLD SCIENTIFIC RESEARCH SCOPE IN THE INFORMATION MODELLING FOR CULTURAL HERITAGE

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D. Fiorani

2017-05-01

Full Text Available The aim of the present research is to develop an instrument able to adequately support the conservation process by means of a twofold approach, based on both BIM environment and ontology formalisation. Although BIM has been successfully experimented within AEC (Architecture Engineering Construction field, it has showed many drawbacks for architectural heritage. To cope with unicity and more generally complexity of ancient buildings, applications so far developed have shown to poorly adapt BIM to conservation design with unsatisfactory results (Dore, Murphy 2013; Carrara 2014. In order to combine achievements reached within AEC through BIM environment (design control and management with an appropriate, semantically enriched and flexible The presented model has at its core a knowledge base developed through information ontologies and oriented around the formalization and computability of all the knowledge necessary for the full comprehension of the object of architectural heritage an its conservation. Such a knowledge representation is worked out upon conceptual categories defined above all within architectural criticism and conservation scope. The present paper aims at further extending the scope of conceptual modelling within cultural heritage conservation already formalized by the model. A special focus is directed on decay analysis and surfaces conservation project.

Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.).

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Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

2015-06-01

The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.

Designing Conservation Corridors in Production Landscapes: Assessment Methods, Implementation Issues, and Lessons Learned

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Amanda T. Lombard

2010-09-01

Full Text Available Designing broad-scale conservation corridors has become increasingly common as a way of conducting an assessment for achieving targets for the representation and persistence of nature. However, since many of these corridors must traverse agricultural and other production landscapes, planning and implementation are not trivial tasks. Most approaches to conservation assessments in the dynamic world of production landscapes are data-intensive and analytically complex. However, in the real world, donor and other external requirements impose time and budget constraints, and dictate strong stakeholder involvement in the entire planning process. In order to accommodate this, assessments must be rapid, cheap, and the approach and products must be comprehensible and acceptable to stakeholders. Here we describe such an assessment aimed at identifying and implementing a network of conservation corridors in the Gouritz Initiative project domain of South Africa's Cape Floristic Region hotspot. We used empirical data and expert knowledge to identify a corridor network hypothesized to sustain key ecological and evolutionary processes. We also consulted experts to provide a spatially explicit assessment of the opportunity costs of conservation associated with agriculture, the predominant land use in the region. We used these products to identify categories of land requiring different actions and instruments to achieve conservation goals, thereby moving from the "where" to the "how" of conservation. This information was then fed into the collaborative strategy development process for the Gouritz Initiative. Our discussion emphasizes the lessons that we learnt from undertaking this assessment, particularly lessons regarding the implementation of the planning products. We conclude that at the outset of any planning project, a consensus on the vision must be achieved, a detailed social assessment of appropriate institutions must be undertaken, and a learning

Evolutionary paths of streptococcal and staphylococcal superantigens

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Okumura Kayo

2012-08-01

Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

Evolutionary conservation of the lipopolysaccharide binding site of β₂-glycoprotein I

NARCIS (Netherlands)

Ağar, Çetin; de Groot, Philip G.; Marquart, J. Arnoud; Meijers, Joost C. M.

2011-01-01

β₂-Glycoprotein I (β₂GPI) is a highly abundant plasma protein and the major antigen for autoantibodies in the antiphospholipid syndrome. Recently, we have described a novel function of β₂GPI as scavenger of lipopolysaccharide (LPS). With this in mind we investigated the conservation of β₂GPI in

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

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Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

2015-01-01

Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

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Kacy L Gordon

2015-05-01

Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

Entropy is conserved in Hawking radiation as tunneling: A revisit of the black hole information loss paradox

International Nuclear Information System (INIS)

Zhang Baocheng; Cai Qingyu; Zhan Mingsheng; You Li

2011-01-01

Research Highlights: → Information is found to be encoded and carried away by Hawking radiations. → Entropy is conserved in Hawking radiation. → We thus conclude no information is lost. → The dynamics of black hole may be unitary. - Abstract: We revisit in detail the paradox of black hole information loss due to Hawking radiation as tunneling. We compute the amount of information encoded in correlations among Hawking radiations for a variety of black holes, including the Schwarzchild black hole, the Reissner-Nordstroem black hole, the Kerr black hole, and the Kerr-Newman black hole. The special case of tunneling through a quantum horizon is also considered. Within a phenomenological treatment based on the accepted emission probability spectrum from a black hole, we find that information is leaked out hidden in the correlations of Hawking radiation. The recovery of this previously unaccounted for information helps to conserve the total entropy of a system composed of a black hole plus its radiations. We thus conclude, irrespective of the microscopic picture for black hole collapsing, the associated radiation process: Hawking radiation as tunneling, is consistent with unitarity as required by quantum mechanics.

Achieving open access to conservation science.

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Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-12-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for

Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories

Energy Technology Data Exchange (ETDEWEB)

Jensen, M [ed.; National Inst. of Radiation Protection, Stockholm (Sweden)

1996-12-01

Two main strategies exist for long-term information transfer, one which links information through successive transfers of archived material and other forms of knowledge in society, and one - such as marking the site with a monument - relying upon a direct link from the present to the distant future. Digital methods are not recommended for long-term storage, but digital processing may be a valuable tool to structure information summaries, and in the creation of better long-lasting records. Advances in archive management should also be pursued to widen the choice of information carriers of high durability. In the Nordic countries, during the first few thousand years, and perhaps up to the next period of glaciation, monuments at a repository site may be used to warn the public of the presence of dangerous waste. But messages from such markers may pose interpretation problems as we have today for messages left by earlier societies such as rune inscriptions. Since the national borders may change in the time scale relevant for nuclear waste, the creation of an international archive for all radioactive wastes would represent an improvement as regards conservation and retrieval of information. (EG).

Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories

International Nuclear Information System (INIS)

Jensen, M.

1996-01-01

Two main strategies exist for long-term information transfer, one which links information through successive transfers of archived material and other forms of knowledge in society, and one - such as marking the site with a monument - relying upon a direct link from the present to the distant future. Digital methods are not recommended for long-term storage, but digital processing may be a valuable tool to structure information summaries, and in the creation of better long-lasting records. Advances in archive management should also be pursued to widen the choice of information carriers of high durability. In the Nordic countries, during the first few thousand years, and perhaps up to the next period of glaciation, monuments at a repository site may be used to warn the public of the presence of dangerous waste. But messages from such markers may pose interpretation problems as we have today for messages left by earlier societies such as rune inscriptions. Since the national borders may change in the time scale relevant for nuclear waste, the creation of an international archive for all radioactive wastes would represent an improvement as regards conservation and retrieval of information. (EG)

Polymorphic Evolutionary Games.

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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.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

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Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-07-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

Incorporating Development Into Evolutionary Psychology

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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.

Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

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Shackelford, Todd K; Liddle, James R

2014-05-01

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

Impacts of Personal Experience: Informing Water Conservation Extension Education

Science.gov (United States)

Huang, Pei-wen; Lamm, Alexa J.

2017-01-01

Extension educators have diligently educated the general public about water conservation. Incorporating audiences' personal experience into educational programming is recommended as an approach to effectively enhance audiences' adoption of water conservation practices. To ensure the impact on the audiences and environment, understanding the…

The ABCs of an evolutionary education science: The academic, behavioral, and cultural implications of an evolutionary approach to education theory and practice

Science.gov (United States)

Kauffman, Rick, Jr.

Calls for improving research-informed policy in education are everywhere. Yet, while there is an increasing trend towards science-based practice, there remains little agreement over which of the sciences to consult and how to organize a collective effort between them. What Education lacks is a general theoretical framework through which policies can be constructed, implemented, and assessed. This dissertation submits that evolutionary theory can provide a suitable framework for coordinating educational policies and practice, and can provide the entire field of education with a clearer sense of how to better manage the learning environment. This dissertation explores two broad paths that outline the conceptual foundations for an Evolutionary Education Science: "Teaching Evolution" and "Using Evolution to Teach." Chapter 1 introduces both of these themes. After describing why evolutionary science is best suited for organizing education research and practice, Chapter 1 proceeds to "teach" an overview of the "evolutionary toolkit"---the mechanisms and principles that underlie the modern evolutionary perspective. The chapter then employs the "toolkit" in examining education from an evolutionary perspective, outlining the evolutionary precepts that can guide theorizing and research in education, describing how educators can "use evolution to teach.". Chapters 2-4 expand on this second theme. Chapters 2 and 3 describe an education program for at-risk 9th and 10th grade students, the Regents Academy, designed entirely with evolutionary principles in mind. The program was rigorously assessed in a randomized control design and has demonstrated success at improving students' academic performance (Chapter 2) and social & behavioral development (Chapter 3). Chapter 4 examines current teaching strategies that underlie effective curriculum-instruction-assessment practices and proposes a framework for organizing successful, evidence-based strategies for neural

Madagascar Conservation & Development

African Journals Online (AJOL)

Madagascar Conservation & Development welcomes the results of original research, field surveys, advances in field and laboratory techniques, book reviews, and informal status reports from research, conservation, development and management programs and in-field projects in Madagascar. In addition, notes on changes ...

Phylogeography and Conservation Genetics of the Ibero-Balearic Three-Spined Stickleback (Gasterosteus aculeatus.

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Marta Vila

Full Text Available Genetic isolation and drift may imperil peripheral populations of wide-ranging species more than central ones. Therefore, information about species genetic variability and population structure is invaluable for conservation managers. The Iberian populations of three-spined stickleback lie at the southwestern periphery of the European distribution of Gasterosteus aculeatus. This teleost is a protected species in Portugal and Spain and local extinctions have been reported in both countries during the last decades. Our objectives were (i to determine whether the Iberian populations of G. aculeatus are unique or composed of any of the major evolutionary lineages previously identified and (ii to assess the evolutionary potential of these peripheral populations. We genotyped 478 individuals from 17 sites at 10 polymorphic microsatellite loci to evaluate the genetic variability and differentiation of the Ibero-Balearic populations. We also sequenced 1,165 bp of the mitochondrial genome in 331 of those individuals in order to complement the estimates of genetic diversity in the Ibero-Balearic region. We predicted the evolutionary potential of the different sites analysed based on the contribution of each of them to total allelic/mitochondrial diversity. An intraspecific phylogeny at European level was reconstructed using our data from the mitochondrial cytochrome b gene (755 bp and published sequences. The so-called Transatlantic, European and Mediterranean mitochondrial lineages were found to be present in the Ibero-Balearic region. Their phylogeography suggests a history of multiple colonisations. The nuclear results show, however, a strong correlation between population structure and drainage system. The following basins should be prioritised by conservation policies in order to preserve those populations with the highest evolutionary potential: the Portuguese Vouga and Tagus as well as the Spanish Majorca and Limia. Maintenance of their connectivity

Phylogeography and Conservation Genetics of the Ibero-Balearic Three-Spined Stickleback (Gasterosteus aculeatus).

Science.gov (United States)

Vila, Marta; Hermida, Miguel; Fernández, Carlos; Perea, Silvia; Doadrio, Ignacio; Amaro, Rafaela; San Miguel, Eduardo

2017-01-01

Genetic isolation and drift may imperil peripheral populations of wide-ranging species more than central ones. Therefore, information about species genetic variability and population structure is invaluable for conservation managers. The Iberian populations of three-spined stickleback lie at the southwestern periphery of the European distribution of Gasterosteus aculeatus. This teleost is a protected species in Portugal and Spain and local extinctions have been reported in both countries during the last decades. Our objectives were (i) to determine whether the Iberian populations of G. aculeatus are unique or composed of any of the major evolutionary lineages previously identified and (ii) to assess the evolutionary potential of these peripheral populations. We genotyped 478 individuals from 17 sites at 10 polymorphic microsatellite loci to evaluate the genetic variability and differentiation of the Ibero-Balearic populations. We also sequenced 1,165 bp of the mitochondrial genome in 331 of those individuals in order to complement the estimates of genetic diversity in the Ibero-Balearic region. We predicted the evolutionary potential of the different sites analysed based on the contribution of each of them to total allelic/mitochondrial diversity. An intraspecific phylogeny at European level was reconstructed using our data from the mitochondrial cytochrome b gene (755 bp) and published sequences. The so-called Transatlantic, European and Mediterranean mitochondrial lineages were found to be present in the Ibero-Balearic region. Their phylogeography suggests a history of multiple colonisations. The nuclear results show, however, a strong correlation between population structure and drainage system. The following basins should be prioritised by conservation policies in order to preserve those populations with the highest evolutionary potential: the Portuguese Vouga and Tagus as well as the Spanish Majorca and Limia. Maintenance of their connectivity, control of

Notes on spectrum and exponential decay in nonautonomous evolutionary equations

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Christian Pötzsche

2016-08-01

Full Text Available We first determine the dichotomy (Sacker-Sell spectrum for certain nonautonomous linear evolutionary equations induced by a class of parabolic PDE systems. Having this information at hand, we underline the applicability of our second result: If the widths of the gaps in the dichotomy spectrum are bounded away from $0$, then one can rule out the existence of super-exponentially decaying (i.e. slow solutions of semi-linear evolutionary equations.

[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.

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

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

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

2013-08-01

Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

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Igor R. Costa

2014-12-01

Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family

OpenAIRE

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...

Using Theory to Inform Water Conservation in Business Communities: Formative Research from a Chamber Initiative

Science.gov (United States)

Sarge, Melanie A.; Daggett, Samantha; VanDyke, Matthew S.

2018-01-01

This study was designed to collect formative information for the development of theoretically driven water conservation communication efforts targeting the business sector of water users. Members from a West Texas Chamber of Commerce were recruited for participation in an online survey. Questionnaire responses were collected from 176 commercial…

The Mangroves of Kenya: general information. Compiled for Netherlands Wetlands Conservation and Training Programme, 1996.

OpenAIRE

Martens, Els

1996-01-01

The report contains general information on mangroves in Kenya with the following main topics: Mangrove ecology, Mangrove distribution, Mangrove vegetation, Mangrove associated flora, Mangrove fauna, Values and utilization, threats. Interactions between mangroves, seagrasses & coral reefs. Main problems related to mangrove management and Conservation. Managing mangroves to insure their survival.

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.

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

Evolutionary and mechanistic drivers of laterality: A review and new synthesis.

Science.gov (United States)

Wiper, Mallory L

2017-11-01

Laterality, best understood as asymmetries of bilateral structures or biases in behaviour, has been demonstrated in species from all major vertebrate classes, and in many invertebrates, showing a large degree of evolutionary conservation across vertebrate groups. Despite the establishment of this phenomenon in so many species, however, the evolutionary and mechanistic study of laterality is uneven with numerous areas in this field requiring greater attention. Here, I present a partial review of how far the study of laterality has come, outlining previous pioneering work, I discuss the hypothesized costs and benefits of a lateralized brain and the suggested path of the evolution of laterality for populations and individuals. I propose an expansion of laterality research into areas that have been touched upon in the past but require stronger evidence from which the field will greatly benefit. Namely, I suggest a continuation of the phylogenetic approach to investigating laterality to better understand its evolutionary path; and a further focus on mechanistic drivers, with special attention to genetic and environmental effects. Putting together the puzzle of laterality using as many pieces as possible will provide a stronger understanding of this field, allowing us to continue to expand the field in novel ways.

Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

Science.gov (United States)

Miklós, István; Zádori, Zoltán

2012-02-01

HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ) and on the carboxy-terminal region of the extracellular domain (CAED) of the human amyloid precursor protein (APP) and a taxonomically well defined group of APP orthologues (APPOs). In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (pHD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1) and Amyloid-like protein 2 (APLP2). Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N) and English (H6R) mutations) in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

Science.gov (United States)

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly.

Directory of Open Access Journals (Sweden)

Tu Anh Nguyen

2018-04-01

Full Text Available Horizontal gene transfer (HGT can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN. Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria. A bacterial OCTIN forms high-order periplasmic oligomers, and inter-molecular disulphide bonds are formed by both fungal and bacterial OCTINs, suggesting that they share elements of a conserved assembly mechanism. However, estimated sedimentation velocities preclude a gravity-sensing function for the bacterial structures. Together, our data suggest that HGT from bacteria into the Mucorales allowed a dramatic increase in assembly scale and emergence of the gravity-sensing function. We conclude that HGT can lead to evolutionary novelties that emerge depending on the physiological and cellular context of protein assembly.

The Neural Systems of Forgiveness: An Evolutionary Psychological Perspective

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Joseph Billingsley

2017-05-01

Full Text Available Evolution-minded researchers posit that the suite of human cognitive adaptations may include forgiveness systems. According to these researchers, forgiveness systems regulate interpersonal motivation toward a transgressor in the wake of harm by weighing multiple factors that influence both the potential gains of future interaction with the transgressor and the likelihood of future harm. Although behavioral research generally supports this evolutionary model of forgiveness, the model’s claims have not been examined with available neuroscience specifically in mind, nor has recent neuroscientific research on forgiveness generally considered the evolutionary literature. The current review aims to help bridge this gap by using evolutionary psychology and cognitive neuroscience to mutually inform and interrogate one another. We briefly summarize the evolutionary research on forgiveness, then review recent neuroscientific findings on forgiveness in light of the evolutionary model. We emphasize neuroscientific research that links desire for vengeance to reward-based areas of the brain, that singles out prefrontal areas likely associated with inhibition of vengeful feelings, and that correlates the activity of a theory-of-mind network with assessments of the intentions and blameworthiness of those who commit harm. In addition, we identify gaps in the existing neuroscientific literature, and propose future research directions that might address them, at least in part.

Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

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Martin H Schaefer

2014-06-01

Full Text Available Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors and the output (transcription factors layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

Dataset on information strategies for energy conservation: A field experiment in India.

Science.gov (United States)

Chen, Victor L; Delmas, Magali A; Locke, Stephen L; Singh, Amarjeet

2018-02-01

The data presented in this article are related to the research article entitled: "Information strategies for energy conservation: a field experiment in India" (Chen et al., 2017) [1]. The availability of high-resolution electricity data offers benefits to both utilities and consumers to understand the dynamics of energy consumption for example, between billing periods or times of peak demand. However, few public datasets with high-temporal resolution have been available to researchers on electricity use, especially at the appliance-level. This article describes data collected in a residential field experiment for 19 apartments at an Indian faculty housing complex during the period from August 1, 2013 to May 12, 2014. The dataset includes detailed information about electricity consumption. It also includes information on apartment characteristics and hourly weather variation to enable further studies of energy performance. These data can be used by researchers as training datasets to evaluate electricity usage consumption.

Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species.

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Rosana Arizmendi-Mejía

Full Text Available The integration of ecological and evolutionary data is highly valuable for conservation planning. However, it has been rarely used in the marine realm, where the adequate design of marine protected areas (MPAs is urgently needed. Here, we examined the interacting processes underlying the patterns of genetic structure and demographic strucuture of a highly vulnerable Mediterranean habitat-forming species (i.e. Paramuricea clavata (Risso, 1826, with particular emphasis on the processes of contemporary dispersal, genetic drift, and colonization of a new population. Isolation by distance and genetic discontinuities were found, and three genetic clusters were detected; each submitted to variations in the relative impact of drift and gene flow. No founder effect was found in the new population. The interplay of ecology and evolution revealed that drift is strongly impacting the smallest, most isolated populations, where partial mortality of individuals was highest. Moreover, the eco-evolutionary analyses entailed important conservation implications for P. clavata. Our study supports the inclusion of habitat-forming organisms in the design of MPAs and highlights the need to account for genetic drift in the development of MPAs. Moreover, it reinforces the importance of integrating genetic and demographic data in marine conservation.

Analysis of Schizosaccharomyces pombe mediator reveals a set of essential subunits conserved between yeast and metazoan cells

DEFF Research Database (Denmark)

Spåhr, H; Samuelsen, C O; Baraznenok, V

2001-01-01

. cerevisiae share an essential protein module, which associates with nonessential speciesspecific subunits. In support of this view, sequence analysis of the conserved yeast Mediator components Med4 and Med8 reveals sequence homology to the metazoan Mediator components Trap36 and Arc32. Therefore, 8 of 10...... essential genes conserved between S. pombe and S. cerevisiae also have a metazoan homolog, indicating that an evolutionary conserved Mediator core is present in all eukaryotic cells. Our data suggest a closer functional relationship between yeast and metazoan Mediator than previously anticipated....

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

Evolutionary modeling-based approach for model errors correction

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S. Q. Wan

2012-08-01

Full Text Available The inverse problem of using the information of historical data to estimate model errors is one of the science frontier research topics. In this study, we investigate such a problem using the classic Lorenz (1963 equation as a prediction model and the Lorenz equation with a periodic evolutionary function as an accurate representation of reality to generate "observational data."

On the basis of the intelligent features of evolutionary modeling (EM, including self-organization, self-adaptive and self-learning, the dynamic information contained in the historical data can be identified and extracted by computer automatically. Thereby, a new approach is proposed to estimate model errors based on EM in the present paper. Numerical tests demonstrate the ability of the new approach to correct model structural errors. In fact, it can actualize the combination of the statistics and dynamics to certain extent.

Synergistic Coherence of Bifurcation Evolutionary Processes of Mergers and Acquisitions of Enterprises

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Ivanchenko Hennadii F.

2016-08-01

Full Text Available The aim of the article is developing information tools for the economic and mathematical modeling of the dynamics of evolutionary processes concerning trophic relationships of populations of enterprises, which allowed to conduct the phase and bifurcation analysis of possible dynamic regimes of the populations’ evolution, determine the mechanisms of influence of the external environment and the internal structure of the system, identify patterns and limits of stability of M&A processes. In the work the main provisions of the evolutionary concept concerning development of the population of enterprises as an economic system are analyzed, the provisions of the evolutionary concept of population systems’ development are considered, the basis of evolutionary modeling methods allowing to analyze the functioning of populations of enterprises in terms of individual strategies of each enterprise’s behavior is studied. The basic principles of synergy of the life cycle evolution for populations of enterprises are determined. An evolutionary approach to the evaluation of a synergistic effect of M & A is proposed. The evolutionary modeling of the scenario for self-organization of populations of dairy industry enterprises through a combination of statistical and expert data is applied. There also created a model of the population of firms reflecting behavioral and resource and technological characteristics of the studied in the work real population of industrial enterprises, which form the input flows of matter, energy and information to the dairy industry, which allows to combine the reflection of main possible options in terms of the external conditions of the population functioning and its internal structure.

Why Do Information Gaps Persist in African Smallholder Agriculture? Perspectives from Farmers Lacking Exposure to Conservation Agriculture

Science.gov (United States)

Brown, Brendan; Llewellyn, Rick; Nuberg, Ian

2018-01-01

Purpose: To explore why substantial agricultural information gaps persist in African smallholder farming communities and how to reduce them. Design/methodology/approach: Using conservation agriculture (CA) as a case study, we deeply explore with 29 smallholder farmers why they are yet to obtain sufficient information to enable practice evaluation.…

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

Evolutionary plasticity of plasma membrane interaction in DREPP family proteins.

Science.gov (United States)

Vosolsobě, Stanislav; Petrášek, Jan; Schwarzerová, Kateřina

2017-05-01

The plant-specific DREPP protein family comprises proteins that were shown to regulate the actin and microtubular cytoskeleton in a calcium-dependent manner. Our phylogenetic analysis showed that DREPPs first appeared in ferns and that DREPPs have a rapid and plastic evolutionary history in plants. Arabidopsis DREPP paralogues called AtMDP25/PCaP1 and AtMAP18/PCaP2 are N-myristoylated, which has been reported as a key factor in plasma membrane localization. Here we show that N-myristoylation is neither conserved nor ancestral for the DREPP family. Instead, by using confocal microscopy and a new method for quantitative evaluation of protein membrane localization, we show that DREPPs rely on two mechanisms ensuring their plasma membrane localization. These include N-myristoylation and electrostatic interaction of a polybasic amino acid cluster. We propose that various plasma membrane association mechanisms resulting from the evolutionary plasticity of DREPPs are important for refining plasma membrane interaction of these signalling proteins under various conditions and in various cells. Copyright © 2017 Elsevier B.V. All rights reserved.

An Angiotensin II type 1 receptor activation switch patch revealed through Evolutionary Trace analysis

DEFF Research Database (Denmark)

Bonde, Marie Mi; Yao, Rong; Ma, Jian-Nong

2010-01-01

to be completely resolved. Evolutionary Trace (ET) analysis is a computational method, which identifies clusters of functionally important residues by integrating information on evolutionary important residue variations with receptor structure. Combined with known mutational data, ET predicted a patch of residues......) displayed phenotypes associated with changed activation state, such as increased agonist affinity or basal activity, promiscuous activation, or constitutive internalization highlighting the importance of testing different signaling pathways. We conclude that this evolutionary important patch mediates...

Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions

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Xiaomei Wu

2017-07-01

Full Text Available As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood. Here, we found that FUN14 domain-containing proteins are present in archaeal, bacterial and eukaryotic genomes, while the family of BNIP3 domain-containing proteins evolved from early animals. We investigated conservation patterns of the critical amino acid residues of the human mitophagy receptors. These residues are involved in receptor regulation, mainly through phosphorylation, and in interaction with LC3 on the phagophore. Whereas FUNDC1 may be able to bind to LC3 under the control of post-translational regulations during the early evolution of vertebrates, BINP3 and NIX had already gained the ability for LC3 binding in early invertebrates. Moreover, FUNDC1 and BNIP3 each lack a layer of phosphorylation regulation in fishes that is conserved in land vertebrates. Molecular evolutionary analysis revealed that BNIP3 and NIX, as the targets of oxygen sensing HIF-1α, showed higher rates of substitution in fishes than in mammals. Conversely, FUNDC1 and its regulator MARCH5 showed higher rates of substitution in mammals. Thus, we postulate that the structural traces of mitophagy receptors in land vertebrates and fishes may reflect the process of vertebrate transition from water onto land, during which the changes in atmospheric oxygen concentrations acted as a selection force in vertebrate evolution. In conclusion, our study, combined with previous experimental results, shows that

In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer

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Poulin, Francis; Nobrega, Marcelo A.; Plajzer-Frick, Ingrid; Holt, Amy; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len

2004-10-01

Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the dachshund gene, which displays a human-Fugu identity of 84 percent over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical between human, mouse, chicken, zebrafish and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424 bp Dc2 conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144 bp 100 percent conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16 bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144 bp 100 percent conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence.

Open Issues in Evolutionary Robotics.

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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.

The concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing.

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Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos

2017-04-01

This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.

The sequence, structure and evolutionary features of HOTAIR in mammals

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2011-01-01

Background An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals

Applying the dark diversity concept to nature conservation

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Lewis, Rob; de Bello, Francesco; A Bennett, Jonathan

2017-01-01

is currently an underappreciated source of information that is valuable for conservation applications ranging from macroscale conservation prioritization to more locally scaled restoration ecology and the management of invasive species. Introduction Conservation biology has strong scientific underpinnings (e...... to improve understanding of how biological diversity is governed and maintained. We illustrate our viewpoint by clarifying how measuring, monitoring, and understanding dark diversity can prove beneficial in the context of 3 facets of conservation biology: biodiversity conservation, habitat restoration......Linking diversity to biological processes is central for developing informed and effective conservation decisions. Unfortunately, observable patterns provide only a proportion of the information necessary for fully understanding the mechanisms and processes acting on a particular population...

The origins and evolutionary history of human non-coding RNA regulatory networks.

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Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

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Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out

Understanding the function of bacterial and eukaryotic thiolases II by integrating evolutionary and functional approaches.

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Fox, Ana Romina; Soto, Gabriela; Mozzicafreddo, Matteo; Garcia, Araceli Nora; Cuccioloni, Massimiliano; Angeletti, Mauro; Salerno, Juan Carlos; Ayub, Nicolás Daniel

2014-01-01

Acetoacetyl-CoA thiolase (EC 2.3.1.9), commonly named thiolase II, condenses two molecules of acetyl-CoA to give acetoacetyl-CoA and CoA. This enzyme acts in anabolic processes as the first step in the biosynthesis of isoprenoids and polyhydroxybutyrate in eukaryotes and bacteria, respectively. We have recently reported the evolutionary and functional equivalence of these enzymes, suggesting that thiolase II could be the rate limiting enzyme in these pathways and presented evidence indicating that this enzyme modulates the availability of reducing equivalents during abiotic stress adaptation in bacteria and plants. However, these results are not sufficient to clarify why thiolase II was evolutionary selected as a critical enzyme in the production of antioxidant compounds. Regarding this intriguing topic, we propose that thiolase II could sense changes in the acetyl-CoA/CoA ratio induced by the inhibition of the tricarboxylic acid cycle under abiotic stress. Thus, the high level of evolutionary and functional constraint of thiolase II may be due to the connection of this enzyme with an ancient and conserved metabolic route. © 2013.

Using insights from animal behaviour and behavioural ecology to inform marine conservation initiatives.

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Brooker, Rohan M; Feeney, William E; White, James R; Manassa, Rachel P; Johansen, Jacob L; Dixson, Danielle L

2016-10-01

The impacts of human activities on the natural world are becoming increasingly apparent, with rapid development and exploitation occurring at the expense of habitat quality and biodiversity. Declines are especially concerning in the oceans, which hold intrinsic value due to their biological uniqueness as well as their substantial sociological and economic importance. Here, we review the literature and investigate whether incorporation of knowledge from the fields of animal behaviour and behavioural ecology may improve the effectiveness of conservation initiatives in marine systems. In particular, we consider (1) how knowledge of larval behaviour and ecology may be used to inform the design of marine protected areas, (2) how protecting species that hold specific ecological niches may be of particular importance for maximizing the preservation of biodiversity, (3) how current harvesting techniques may be inadvertently skewing the behavioural phenotypes of stock populations and whether changes to current practices may lessen this skew and reinforce population persistence, and (4) how understanding the behavioural and physiological responses of species to a changing environment may provide essential insights into areas of particular vulnerability for prioritized conservation attention. The complex nature of conservation programmes inherently results in interdisciplinary responses, and the incorporation of knowledge from the fields of animal behaviour and behavioural ecology may increase our ability to stem the loss of biodiversity in marine environments.

An evolutionary ecology of individual differences

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Dall, Sasha R. X.; Bell, Alison M.; Bolnick, Daniel I.; Ratnieks, Francis L. W.

2014-01-01

Individuals often differ in what they do. This has been recognised since antiquity. Nevertheless, the ecological and evolutionary significance of such variation is attracting widespread interest, which is burgeoning to an extent that is fragmenting the literature. As a first attempt at synthesis, we focus on individual differences in behaviour within populations that exceed the day-to-day variation in individual behaviour (i.e. behavioural specialisation). Indeed, the factors promoting ecologically relevant behavioural specialisation within natural populations are likely to have far-reaching ecological and evolutionary consequences. We discuss such individual differences from three distinct perspectives: individual niche specialisations, the division of labour within insect societies and animal personality variation. In the process, while recognising that each area has its own unique motivations, we identify a number of opportunities for productive ‘crossfertilisation’ among the (largely independent) bodies of work. We conclude that a complete understanding of evolutionarily and ecologically relevant individual differences must specify how ecological interactions impact the basic biological process (e.g. Darwinian selection, development and information processing) that underpin the organismal features determining behavioural specialisations. Moreover, there is likely to be covariation amongst behavioural specialisations. Thus, we sketch the key elements of a general framework for studying the evolutionary ecology of individual differences. PMID:22897772

Evolutionary conservativeness of electric field in the Cu,Zn superoxide dismutase active site. Evidence for co-ordinated mutation of charged amino acid residues.

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Desideri, A; Falconi, M; Polticelli, F; Bolognesi, M; Djinovic, K; Rotilio, G

1992-01-05

Equipotential lines were calculated, using the Poisson-Boltzmann equation, for six Cu,Zn superoxide dismutases with different protein electric charge and various degrees of sequence homology, namely those from ox, pig, sheep, yeast, and the isoenzymes A and B from the amphibian Xenopus laevis. The three-dimensional structures of the porcine and ovine superoxide dismutases were obtained by molecular modelling reconstruction using the structure of the highly homologous bovine enzyme as a template. The three-dimensional structure of the evolutionary distant yeast Cu,Zn superoxide dismutase was recently resolved by us, while computer-modelled structures are available for X. laevis isoenzymes. The six proteins display large differences in the net protein charge and distribution of electrically charged surface residues but the trend of the equipotential lines in the proximity of the active sites was found to be constant in all cases. These results are in line with the very similar catlytic rate constants experimentally measured for the corresponding enzyme activities. This analysis shows that electrostatic guidance for the enzyme-substrate interaction in Cu,Zn superoxide dismutases is related to a spatial distribution of charges, arranged so as to maintain, in the area surrounding the active sites, an identical electrostatic potential distribution, which is conserved in the evolution of this protein family.

Founded: Genetic Reconstruction of Lineage Diversity and Kinship Informs Ex situ Conservation of Cuban Amazon Parrots (Amazona leucocephala).

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Milián-García, Yoamel; Jensen, Evelyn L; Madsen, Jeanette; Álvarez Alonso, Suleiky; Serrano Rodríguez, Aryamne; Espinosa López, Georgina; Russello, Michael A

2015-01-01

Captive breeding is a widespread conservation strategy, yet such programs rarely include empirical genetic data for assessing management assumptions and meeting conservation goals. Cuban Amazon parrots (Amazona leucocephala) are considered vulnerable, and multiple on-island captive populations have been established from wild-caught and confiscated individuals of unknown ancestry. Here, we used mitochondrial haplotypic and nuclear genotypic data at 9 microsatellite loci to quantify the extent and distribution of genetic variation within and among captive populations in Zapata Swamp and Managua, Cuba, and to estimate kinship among breeders (n = 88). Using Bayesian clustering analysis, we detected 2 distinct clusters within the Zapata population, one of which was shared with Managua. Individuals from the cluster unique to Zapata possessed mitochondrial haplotypes with affinities to Cuban subspecies (A. l. leucocephala, A. l. palmarum); the shared cluster was similar, but also included haplotypes closely related to the subspecies restricted to Cayman Brac (A. l. hesterna). Overall mean kinship was low within each captive population (-0.026 to -0.012), with 19 and 11 recommended breeding pairs in Zapata and Managua, respectively, ranked according to mean kinship and informed by molecular sexing. Our results highlight the importance of understanding population history within ex situ management programs, while providing genetic information to directly inform Cuban parrot conservation. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping.

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Yoshinobu Uno

Full Text Available Comparative genome analysis of non-avian reptiles and amphibians provides important clues about the process of genome evolution in tetrapods. However, there is still only limited information available on the genome structures of these organisms. Consequently, the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes in tetrapods remain poorly understood. We constructed chromosome maps of functional genes for the Chinese soft-shelled turtle (Pelodiscus sinensis, the Siamese crocodile (Crocodylus siamensis, and the Western clawed frog (Xenopus tropicalis and compared them with genome and/or chromosome maps of other tetrapod species (salamander, lizard, snake, chicken, and human. This is the first report on the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes inferred from comparative genomic analysis of vertebrates, which cover all major non-avian reptilian taxa (Squamata, Crocodilia, Testudines. The eight largest macrochromosomes of the turtle and chicken were equivalent, and 11 linkage groups had also remained intact in the crocodile. Linkage groups of the chicken macrochromosomes were also highly conserved in X. tropicalis, two squamates, and the salamander, but not in human. Chicken microchromosomal linkages were conserved in the squamates, which have fewer microchromosomes than chicken, and also in Xenopus and the salamander, which both lack microchromosomes; in the latter, the chicken microchromosomal segments have been integrated into macrochromosomes. Our present findings open up the possibility that the ancestral amniotes and tetrapods had at least 10 large genetic linkage groups and many microchromosomes, which corresponded to the chicken macro- and microchromosomes, respectively. The turtle and chicken might retain the microchromosomes of the amniote protokaryotype almost intact. The decrease in number and/or disappearance of microchromosomes by repeated

Integration of 3d Models and Diagnostic Analyses Through a Conservation-Oriented Information System

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Mandelli, A.; Achille, C.; Tommasi, C.; Fassi, F.

2017-08-01

In the recent years, mature technologies for producing high quality virtual 3D replicas of Cultural Heritage (CH) artefacts has grown thanks to the progress of Information Technologies (IT) tools. These methods are an efficient way to present digital models that can be used with several scopes: heritage managing, support to conservation, virtual restoration, reconstruction and colouring, art cataloguing and visual communication. The work presented is an emblematic case of study oriented to the preventive conservation through monitoring activities, using different acquisition methods and instruments. It was developed inside a project founded by Lombardy Region, Italy, called "Smart Culture", which was aimed to realise a platform that gave the users the possibility to easily access to the CH artefacts, using as an example a very famous statue. The final product is a 3D reality-based model that contains a lot of information inside it, and that can be consulted through a common web browser. In the end, it was possible to define the general strategies oriented to the maintenance and the valorisation of CH artefacts, which, in this specific case, must consider the integration of different techniques and competencies, to obtain a complete, accurate and continuative monitoring of the statue.

Evolutionary Trails of Plant Group II Pyridoxal Phosphate-Dependent Decarboxylase Genes.

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Kumar, Rahul

2016-01-01

Type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) enzymes play important metabolic roles during nitrogen metabolism. Recent evolutionary profiling of these genes revealed a sharp expansion of histidine decarboxylase genes in the members of Solanaceae family. In spite of the high sequence homology shared by PLP_deC orthologs, these enzymes display remarkable differences in their substrate specificities. Currently, limited information is available on the gene repertoires and substrate specificities of PLP_deCs which renders their precise annotation challenging and offers technical challenges in the immediate identification and biochemical characterization of their full gene complements in plants. Herein, we explored their evolutionary trails in a comprehensive manner by taking advantage of high-throughput data accessibility and computational approaches. We discussed the premise that has enabled an improved reconstruction of their evolutionary lineage and evaluated the factors offering constraints in their rapid functional characterization, till date. We envisage that the synthesized information herein would act as a catalyst for the rapid exploration of their biochemical specificity and physiological roles in more plant species.

Limitations in global information on species occurrences

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Carsten Meyer

2016-07-01

Full Text Available Detailed information on species distributions is crucial for answering central questions in biogeography, ecology, evolutionary biology and conservation. Millions of species occurrence records have been mobilized via international data-sharing networks, but inherent biases, gaps and uncertainties hamper broader application. In my PhD thesis, I presented the first comprehensive analyses of global patterns and drivers of these limitations across different taxonomic groups and spatial scales. Integrating 300 million occurrence records for terrestrial vertebrates and plants with comprehensive taxonomic databases, expert range maps and regional checklists, I demonstrated extensive taxonomic, geographical and temporal biases, gaps and uncertainties. I identified key socio-economic drivers of data bias across different taxonomic groups and spatial scales. The results of my dissertation provide an empirical baseline for effectively accounting for data limitations in distribution models, as well as for prioritizing and monitoring efforts to collate additional occurrence information.

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

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

2017-01-01

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. PMID:28042784

Recreation economics to inform migratory species conservation: Case study of the northern pintail

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Mattsson, Brady J.; Dubovsky, James A.; Thogmartin, Wayne E.; Bagstad, Kenneth J.; Goldstein, Joshua H.; Loomis, John B.; Diffendorfer, James E.; Semmens, Darius J.; Wiederholt, Ruscena; Lopez-Hoffman, Laura

2018-01-01

Quantification of the economic value provided by migratory species can aid in targeting management efforts and funding to locations yielding the greatest benefits to society and species conservation. Here we illustrate a key step in this process by estimating hunting and birding values of the northern pintail (Anas acuta) within primary breeding and wintering habitats used during the species’ annual migratory cycle in North America. We used published information on user expenditures and net economic values (consumer surplus) for recreational viewing and hunting to determine the economic value of pintail-based recreation in three primary breeding areas and two primary wintering areas. Summed expenditures and consumer surplus for northern pintail viewing were annually valued at $70M, and annual sport hunting totaled $31M (2014 USD). Expenditures for viewing ($42M) were more than twice as high than those for hunting ($18M). Estimates of consumer surplus, defined as the amount consumers are willing to pay above their current expenditures, were $15M greater for viewing ($28M) than for hunting ($13M). We discovered substantial annual consumer surplus ($41M) available for pintail conservation from birders and hunters. We also found spatial differences in economic value among the primary regions used by pintails, with viewing generally valued more in breeding regions than in wintering regions and the reverse being true for hunting. The economic value of pintail-based recreation in the Western wintering region ($26M) exceeded that in any other region by at least a factor of three. Our approach of developing regionally explicit economic values can be extended to other taxonomic groups, and is particularly suitable for migratory game birds because of the availability of large amounts of data. When combined with habitat-linked population models, regionally explicit values could inform development of more effective conservation finance and policy mechanisms to enhance

Recreation economics to inform migratory species conservation: Case study of the northern pintail.

Science.gov (United States)

Mattsson, Brady J; Dubovsky, James A; Thogmartin, Wayne E; Bagstad, Kenneth J; Goldstein, Joshua H; Loomis, John B; Diffendorfer, James E; Semmens, Darius J; Wiederholt, Ruscena; López-Hoffman, Laura

2018-01-15

Quantification of the economic value provided by migratory species can aid in targeting management efforts and funding to locations yielding the greatest benefits to society and species conservation. Here we illustrate a key step in this process by estimating hunting and birding values of the northern pintail (Anas acuta) within primary breeding and wintering habitats used during the species' annual migratory cycle in North America. We used published information on user expenditures and net economic values (consumer surplus) for recreational viewing and hunting to determine the economic value of pintail-based recreation in three primary breeding areas and two primary wintering areas. Summed expenditures and consumer surplus for northern pintail viewing were annually valued at $70M, and annual sport hunting totaled $31M (2014 USD). Expenditures for viewing ($42M) were more than twice as high than those for hunting ($18M). Estimates of consumer surplus, defined as the amount consumers are willing to pay above their current expenditures, were $15M greater for viewing ($28M) than for hunting ($13M). We discovered substantial annual consumer surplus ($41M) available for pintail conservation from birders and hunters. We also found spatial differences in economic value among the primary regions used by pintails, with viewing generally valued more in breeding regions than in wintering regions and the reverse being true for hunting. The economic value of pintail-based recreation in the Western wintering region ($26M) exceeded that in any other region by at least a factor of three. Our approach of developing regionally explicit economic values can be extended to other taxonomic groups, and is particularly suitable for migratory game birds because of the availability of large amounts of data. When combined with habitat-linked population models, regionally explicit values could inform development of more effective conservation finance and policy mechanisms to enhance

Evolutionary Turnover of Kinetochore Proteins: A Ship of Theseus?

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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.

Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

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Toomas Silla

Full Text Available Ultra-conserved genes or elements (UCGs/UCEs in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280 and Italian (n = 501 by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF5% are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

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...

Linkage disequilibrium of evolutionarily conserved regions in the human genome

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Johnson Todd A

2006-12-01

Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

Evolutionary Cell Biology of Proteins from Protists to Humans and Plants.

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Plattner, Helmut

2018-03-01

During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca 2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca 2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca 2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H + -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in

Questioning current practice in brown bear, Ursus arctos, conservation in Europe that undervalues taxonomy

Energy Technology Data Exchange (ETDEWEB)

Gippoliti, S.

2016-07-01

The present paper highlights problems associated with the currently–accepted taxonomy of brown bear, Ursus arctos, and their consequences for conservation at the European level. The enormous morphological variability within Ursus arctos is not acknowledged in current taxonomy and conservation practice. Seven major clades are recognized in Ursus arctos by molecular researchers, and although Western Europe maintains most of the populations belonging to the relict Clade 1 brown bear lineage, no reference to this is made in current conservation policy. Furthermore, the tiny population of Apennine brown bears, characterized by unique skull morphology, is not even recognized as a distinct ESU (evolutionari significant unit) by current European legislation, nor is it included in the IUCN Red List. This may have serious consequences as brown bear conservation in Western Europe has been mainly based on restocking and reintroduction programs. (Author)

The Evolutionary Logic of the Obsessive Trait Complex: Obsessive Compulsive Personality Disorder as a Complementary Behavioral Syndrome

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Steven Charles Hertler

2015-04-01

Full Text Available Freud noted that the obsessive traits of orderliness, parsimony, and obstinacy incontestably belonged together. This observation has been unfailingly justified, but unsatisfactorily explained. Being a highly heritable pattern essentially unaffected by parental influence, it is counterfactual to continue to explain the obsessive trait constellation as a pathological signature of harsh, authoritarian parenting. Alternatively, the present paper, building upon a previously promulgated evolutionary etiological model, describes how obsessive traits work in unison to enable survival within harsh northerly climates. What appears to be a loosely federated inventory of pathology, after the application of evolutionary reasoning, becomes a coherent behavioral package, adaptive suite, or behavioral syndrome. All three of these terms, taken from behavioral biology, suggest that traits strategically covary, such that the adaptive value of each trait is enhanced by the presence of the others. In this vein, the union of anxious tension and conscientiousness drives the obsessive personality to labor incessantly. The fruits of obsessive labor are then conserved through parsimoniousness, hoarding, vigilance, and niggardliness. And so, obsessive personality is a coherent behavioral package in that the drive to work towards the acquisition of necessities is paired with the drive to conserve and defend them.

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

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Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Conservation and co-option in developmental programmes: the importance of homology relationships

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Becker May-Britt

2005-10-01

Full Text Available Abstract One of the surprising insights gained from research in evolutionary developmental biology (evo-devo is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option, and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

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Bruno Pagano

Full Text Available The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

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.

Amphibian molecular ecology and how it has informed conservation.

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McCartney-Melstad, Evan; Shaffer, H Bradley

2015-10-01

Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems. © 2015 John Wiley & Sons Ltd.

Applications of geographic information systems and remote sensing techniques to conservation of amphibians in northwestern Ecuador

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Mariela Palacios González

2015-01-01

Full Text Available The biodiversity of the Andean Chocó in western Ecuador and Colombia is threatened by anthropogenic changes in land cover. The main goal of this study was to contribute to conservation of 12 threatened species of amphibians at a cloud forest site in northwestern Ecuador, by identifying and proposing protection of critical areas. We used Geographic Information Systems (GIS and remote sensing techniques to quantify land cover changes over 35 years and outline important areas for amphibian conservation. We performed a supervised classification of an IKONOS satellite image from 2011 and two aerial photographs from 1977 and 2000. The 2011 IKONOS satellite image classification was used to delineate areas important for conservation of threatened amphibians within a 200 m buffer around rivers and streams. The overall classification accuracy of the three images was ≥80%. Forest cover was reduced by 17% during the last 34 years. However, only 50% of the study area retained the initial (1977 forest cover, as land was cleared for farming and eventually reforested. Finally, using the 2011 IKONOS satellite image, we delineated areas of potential conservation interest that would benefit the long term survival of threatened amphibian species at the Ecuadorian cloud forest site studied.

Evolutionary conservation of dual Sec translocases in the cyanelles of Cyanophora paradoxa

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Löffelhardt Wolfgang

2008-11-01

Full Text Available Abstract Background Cyanelles, the peptidoglycan-armored plastids of glaucocystophytes, occupy a unique bridge position in between free-living cyanobacteria and chloroplasts. In some respects they side with cyanobacteria whereas other features are clearly shared with chloroplasts. The Sec translocase, an example for "conservative sorting" in the course of evolution, is found in the plasma membrane of all prokaryotes, in the thylakoid membrane of chloroplasts and in both these membrane types of cyanobacteria. Results In this paper we present evidence for a dual location of the Sec translocon in the thylakoid as well as inner envelope membranes of the cyanelles from Cyanophora paradoxa, i. e. conservative sorting sensu stricto. The prerequisite was the generation of specific antisera directed against cyanelle SecY that allowed immunodetection of the protein on SDS gels from both membrane types separated by sucrose density gradient floatation centrifugation. Immunoblotting of blue-native gels yielded positive but differential results for both the thylakoid and envelope Sec complexes, respectively. In addition, heterologous antisera directed against components of the Toc/Tic translocons and binding of a labeled precursor protein were used to discriminate between inner and outer envelope membranes. Conclusion The envelope translocase can be envisaged as a prokaryotic feature missing in higher plant chloroplasts but retained in cyanelles, likely for protein transport to the periplasm. Candidate passengers are cytochrome c6 and enzymes of peptidoglycan metabolism. The minimal set of subunits of the Toc/Tic translocase of a primitive plastid is proposed.

A conceptual evolutionary aseismic decision support framework for hospitals

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Hu, Yufeng; Dargush, Gary F.; Shao, Xiaoyun

2012-12-01

In this paper, aconceptual evolutionary framework for aseismic decision support for hospitalsthat attempts to integrate a range of engineering and sociotechnical models is presented. Genetic algorithms are applied to find the optimal decision sets. A case study is completed to demonstrate how the frameworkmay applytoa specific hospital.The simulations show that the proposed evolutionary decision support framework is able to discover robust policy sets in either uncertain or fixed environments. The framework also qualitatively identifies some of the characteristicbehavior of the critical care organization. Thus, by utilizing the proposedframework, the decision makers are able to make more informed decisions, especially toenhance the seismic safety of the hospitals.

Model selection in Bayesian segmentation of multiple DNA alignments.

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Oldmeadow, Christopher; Keith, Jonathan M

2011-03-01

The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model. We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used. Source code and data are available at http://dl.dropbox.com/u/477240/changept.zip.

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

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Grigg, Joseph W; Buckley, Lauren B

2013-04-23

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

Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids

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Alexandra Zinoviev

2012-01-01

Full Text Available Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5 end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3 UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.

Marketing energy conservation options to Northwest manufactured home buyers

Energy Technology Data Exchange (ETDEWEB)

Hendrickson, P.L.; Mohler, B.L.; Taylor, Z.T.; Lee, A.D.; Onisko, S.A.

1985-06-01

This study relies on extensive, existing survey data and new analyses to develop information that would help design a marketing plan to achieve energy conservation in new manufactured homes. Existing surveys present comprehensive information about regional manufactured home occupants and their homes that are relevant to a potential conservation marketing plan. An independent analysis of the cost-effectiveness of various efficiency improvements provides background information for designing a marketing plan. This analysis focuses on the economic impacts of alternative energy conservation options as perceived by the home owner. Identifying impediments to conservation investments is also very important in designing a marketing plan. A recent report suggests that financial constraints and the need for better information and knowledge about conservation pose the major conservation investment barriers. Since loan interest rates for new manufactured homes typically exceed site-built rates by a considerable amount and the buyers tend to have lower incomes, the economics of manufactured home conservation investments are likely to significantly influence their viability. Conservation information and its presentation directly influences the manufactured home buyer's decision. A marketing plan should address these impediments and their implications very clearly. Dealers express a belief that consumer satisfaction is the major advantage to selling energy efficient manufactured homes. This suggests that targeting dealers in a marketing plan and providing them direct information on consumers' indicated attitudes may be important. 74 refs.

Multiscale structure in eco-evolutionary dynamics

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Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

System optimization for HVAC energy management using the robust evolutionary algorithm

International Nuclear Information System (INIS)

Fong, K.F.; Hanby, V.I.; Chow, T.T.

2009-01-01

For an installed centralized heating, ventilating and air conditioning (HVAC) system, appropriate energy management measures would achieve energy conservation targets through the optimal control and operation. The performance optimization of conventional HVAC systems may be handled by operation experience, but it may not cover different optimization scenarios and parameters in response to a variety of load and weather conditions. In this regard, it is common to apply the suitable simulation-optimization technique to model the system then determine the required operation parameters. The particular plant simulation models can be built up by either using the available simulation programs or a system of mathematical expressions. To handle the simulation models, iterations would be involved in the numerical solution methods. Since the gradient information is not easily available due to the complex nature of equations, the traditional gradient-based optimization methods are not applicable for this kind of system models. For the heuristic optimization methods, the continual search is commonly necessary, and the system function call is required for each search. The frequency of simulation function calls would then be a time-determining step, and an efficient optimization method is crucial, in order to find the solution through a number of function calls in a reasonable computational period. In this paper, the robust evolutionary algorithm (REA) is presented to tackle this nature of the HVAC simulation models. REA is based on one of the paradigms of evolutionary algorithm, evolution strategy, which is a stochastic population-based searching technique emphasized on mutation. The REA, which incorporates the Cauchy deterministic mutation, tournament selection and arithmetic recombination, would provide a synergetic effect for optimal search. The REA is effective to cope with the complex simulation models, as well as those represented by explicit mathematical expressions of

The Roles and Evolutionary Patterns of Intronless Genes in Deuterostomes

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Ming Zou

2011-01-01

Full Text Available Genes without introns are a characteristic feature of prokaryotes, but there are still a number of intronless genes in eukaryotes. To study these eukaryotic genes that have prokaryotic architecture could help to understand the evolutionary patterns of related genes and genomes. Our analyses revealed a number of intronless genes that reside in 6 deuterostomes (sea urchin, sea squirt, zebrafish, chicken, platypus, and human. We also determined the conservation for each intronless gene in archaea, bacteria, fungi, plants, metazoans, and other eukaryotes. Proportions of intronless genes that are inherited from the common ancestor of archaea, bacteria, and eukaryotes in these species were consistent with their phylogenetic positions, with more proportions of ancient intronless genes residing in more primitive species. In these species, intronless genes belong to different cellular roles and gene ontology (GO categories, and some of these functions are very basic. Part of intronless genes is derived from other intronless genes or multiexon genes in each species. In conclusion, we showed that a varying number and proportion of intronless genes reside in these 6 deuterostomes, and some of them function importantly. These genes are good candidates for subsequent functional and evolutionary analyses specifically.

Parity-non-conserving nuclear forces

International Nuclear Information System (INIS)

Desplanques, B.

1979-01-01

Theoretical and phenomenological approaches to parity-non-conserving nuclear forces are reviewed. Recent developments in the calculation of weak meson-nucleon coupling constants, whose knowledge is necessary to determine theoretically the parity-non-conserving nucleon-nucleon potential, are described. The consistency of different measurements of parity-non-conserving effects is discussed and the information they provide is compared to theoretical predictions

Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations

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Kumar, Sudhir; Dudley, Joel T.; Filipski, Alan; Liu, Li

2011-01-01

Modern technologies have made the sequencing of personal genomes routine. They have revealed thousands of nonsynonymous (amino-acid altering) single nucleotide variants (nSNVs) of protein coding DNA per genome. What do these variants foretell about an individual’s predisposition to diseases? The experimental technologies required to carry out such evaluations at a genomic scale are not yet available. Fortunately, the process of natural selection has lent us an almost infinite set of tests in nature. During the long-term evolution, new mutations and existing variations have been evaluated for their biological consequences in countless species, and outcomes were readily revealed by multispecies genome comparisons. We review studies that have investigated evolutionary characteristics and in silico functional diagnoses of nSNVs found in thousands of disease-associated genes. We conclude that the patterns of long-term evolutionary conservation and permissible divergence are essential and instructive modalities for functional assessment of human genetic variations. PMID:21764165

Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s.

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Li, Xuyan; Xie, Xin; Li, Ji; Cui, Yuhai; Hou, Yanming; Zhai, Lulu; Wang, Xiao; Fu, Yanli; Liu, Ranran; Bian, Shaomin

2017-02-01

microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or

Soft computing integrating evolutionary, neural, and fuzzy systems

CERN Document Server

Tettamanzi, Andrea

2001-01-01

Soft computing encompasses various computational methodologies, which, unlike conventional algorithms, are tolerant of imprecision, uncertainty, and partial truth. Soft computing technologies offer adaptability as a characteristic feature and thus permit the tracking of a problem through a changing environment. Besides some recent developments in areas like rough sets and probabilistic networks, fuzzy logic, evolutionary algorithms, and artificial neural networks are core ingredients of soft computing, which are all bio-inspired and can easily be combined synergetically. This book presents a well-balanced integration of fuzzy logic, evolutionary computing, and neural information processing. The three constituents are introduced to the reader systematically and brought together in differentiated combinations step by step. The text was developed from courses given by the authors and offers numerous illustrations as

On the evolutionary relationship between chondrocytes and osteoblasts

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Patsy eGomez-Picos

2015-09-01

Full Text Available Vertebrates are the only animals that produce bone, but the molecular genetic basis for this evolutionary novelty remains obscure. Here, we synthesize information from traditional evolutionary and modern molecular genetic studies in order to generate a working hypothesis on the evolution of the gene regulatory network (GRN underlying bone formation. To make this argument, we focus on three skeletal tissues that comprise the majority of the vertebrate skeleton: immature cartilage, mature cartilage, and bone. Immature cartilage is produced during early stages of cartilage differentiation and can persist into adulthood, whereas mature cartilage undergoes additional stages of differentiation, including hypertrophy and mineralization. Functionally, histologically, and embryologically, these three skeletal tissues are very similar, yet unique, suggesting that one might have evolved from another. Traditional studies of the fossil record, comparative anatomy and embryology demonstrate clearly that immature cartilage evolved before mature cartilage or bone. Modern molecular approaches show that the GRNs regulating differentiation of these three skeletal cell fates are similar, yet unique, just like the functional and histological features of the tissues themselves. Intriguingly, the Sox9 GRN driving cartilage formation appears to be dominant to the Runx2 GRN of bone. Emphasizing an embryological and evolutionary transcriptomic view, we hypothesize that the Runx2 GRN underlying bone formation was co-opted from mature cartilage. We discuss how modern molecular genetic experiments, such as comparative transcriptomics, can test this hypothesis directly, meanwhile permitting levels of constraint and adaptation to be evaluated quantitatively. Therefore, comparative transcriptomics may revolutionize understanding of not only the clade-specific evolution of skeletal cells, but also the generation of evolutionary novelties, providing a modern paradigm for the

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.

Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain.

Science.gov (United States)

Ahrens, Collin W; Supple, Megan A; Aitken, Nicola C; Cantrill, David J; Borevitz, Justin O; James, Elizabeth A

2017-06-01

Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation. Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Development of antibiotic regimens using graph based evolutionary algorithms.

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Corns, Steven M; Ashlock, Daniel A; Bryden, Kenneth M

2013-12-01

This paper examines the use of evolutionary algorithms in the development of antibiotic regimens given to production animals. A model is constructed that combines the lifespan of the animal and the bacteria living in the animal's gastro-intestinal tract from the early finishing stage until the animal reaches market weight. This model is used as the fitness evaluation for a set of graph based evolutionary algorithms to assess the impact of diversity control on the evolving antibiotic regimens. The graph based evolutionary algorithms have two objectives: to find an antibiotic treatment regimen that maintains the weight gain and health benefits of antibiotic use and to reduce the risk of spreading antibiotic resistant bacteria. This study examines different regimens of tylosin phosphate use on bacteria populations divided into Gram positive and Gram negative types, with a focus on Campylobacter spp. Treatment regimens were found that provided decreased antibiotic resistance relative to conventional methods while providing nearly the same benefits as conventional antibiotic regimes. By using a graph to control the information flow in the evolutionary algorithm, a variety of solutions along the Pareto front can be found automatically for this and other multi-objective problems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A brief introduction to continuous evolutionary optimization

CERN Document Server

Kramer, Oliver

2014-01-01

Practical optimization problems are often hard to solve, in particular when they are black boxes and no further information about the problem is available except via function evaluations. This work introduces a collection of heuristics and algorithms for black box optimization with evolutionary algorithms in continuous solution spaces. The book gives an introduction to evolution strategies and parameter control. Heuristic extensions are presented that allow optimization in constrained, multimodal, and multi-objective solution spaces. An adaptive penalty function is introduced for constrained optimization. Meta-models reduce the number of fitness and constraint function calls in expensive optimization problems. The hybridization of evolution strategies with local search allows fast optimization in solution spaces with many local optima. A selection operator based on reference lines in objective space is introduced to optimize multiple conflictive objectives. Evolutionary search is employed for learning kernel ...

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

Science.gov (United States)

Awan, Ali R; Manfredo, Amanda; Pleiss, Jeffrey A

2013-07-30

Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in S. pombe reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.

Patterns of intron gain and conservation in eukaryotic genes

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Wolf Yuri I

2007-10-01

Full Text Available Abstract Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions. Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs. Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.

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Subramanian, Sankar; Huynen, Leon; Millar, Craig D; Lambert, David M

2010-12-15

Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

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Huynen Leon

2010-12-01

Full Text Available Abstract Background Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Numerical Simulation of Entropy Growth for a Nonlinear Evolutionary Model of Random Markets

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Mahdi Keshtkar

2016-01-01

Full Text Available In this communication, the generalized continuous economic model for random markets is revisited. In this model for random markets, agents trade by pairs and exchange their money in a random and conservative way. They display the exponential wealth distribution as asymptotic equilibrium, independently of the effectiveness of the transactions and of the limitation of the total wealth. In the current work, entropy of mentioned model is defined and then some theorems on entropy growth of this evolutionary problem are given. Furthermore, the entropy increasing by simulation on some numerical examples is verified.

Evolutionary games on multilayer networks: a colloquium

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Wang, Zhen; Wang, Lin; Szolnoki, Attila; Perc, Matjaž

2015-05-01

Networks form the backbone of many complex systems, ranging from the Internet to human societies. Accordingly, not only is the range of our interactions limited and thus best described and modeled by networks, it is also a fact that the networks that are an integral part of such models are often interdependent or even interconnected. Networks of networks or multilayer networks are therefore a more apt description of social systems. This colloquium is devoted to evolutionary games on multilayer networks, and in particular to the evolution of cooperation as one of the main pillars of modern human societies. We first give an overview of the most significant conceptual differences between single-layer and multilayer networks, and we provide basic definitions and a classification of the most commonly used terms. Subsequently, we review fascinating and counterintuitive evolutionary outcomes that emerge due to different types of interdependencies between otherwise independent populations. The focus is on coupling through the utilities of players, through the flow of information, as well as through the popularity of different strategies on different network layers. The colloquium highlights the importance of pattern formation and collective behavior for the promotion of cooperation under adverse conditions, as well as the synergies between network science and evolutionary game theory.

Exercise, Affect, and Adherence: An Evolutionary Perspective

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Harold Lee

2016-08-01

Full Text Available The low rates of regular exercise and overall physical activity (PA in the general population represent a significant public health challenge. Previous research suggests that, for many people, exercise leads to a negative affective response and, in turn, reduced likelihood of future exercise. The purpose of this paper is to examine this exercise-affect-adherence relationship from an evolutionary perspective. Specifically, we argue that low rates of physical exercise in the general population are a function of the evolved human tendency to avoid unnecessary physical exertion. This innate tendency evolved because it allowed our evolutionary ancestors to conserve energy for physical activities that had immediate adaptive utility such as pursuing prey, escaping predators, and engaging in social and reproductive behaviors. The commonly observed negative affective response to exercise is an evolved proximate psychological mechanism through which humans avoid unnecessary energy expenditure. The fact that the human tendencies toward negative affective response to and avoidance of unnecessary physical activities are innate does not mean that they are unchangeable. Indeed, it is only because of human-engineered changes in our environmental conditions (i.e., it is no longer necessary for us to work for our food that our predisposition to avoid unnecessary physical exertion has become a liability. Thus, it is well within our capabilities to reengineer our environments to once again make PA necessary or, at least, to serve an immediate functional purpose. We propose a two-pronged approach to PA promotion based on this evolutionary functional perspective: First, to promote exercise and other physical activities that are perceived to have an immediate purpose, and second, to instill greater perceived purpose for a wider range of physical activities. We posit that these strategies are more likely to result in more positive (or at least less negative affective

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.

Consciousness, crosstalk, and the mereological fallacy: An evolutionary perspective

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Wallace, Rodrick

2012-12-01

The cross-sectional decontextualization afflicting contemporary neuroscience - attributing to ‘the brain’ what is the province of the whole organism - is mirrored by an evolutionary decontextualization exceptionalizing consciousness. The living state is characterized by cognitive processes at all scales and levels of organization. Many can be associated with dual information sources that ‘speak’ a ‘language’ of behavior-in-context. Shifting global broadcasts analogous to consciousness, albeit far slower - wound healing, tumor control, immune function, gene expression, etc. - have emerged through repeated evolutionary exaptation of the crosstalk and noise inherent to all information transmission. These recruit ‘unconscious’ cognitive modules into tunable arrays as needed to meet threats and opportunities across multiple frames of reference. The development is straightforward, based on the powerful necessary conditions imposed by the asymptotic limit theorems of communication theory, in the same sense that the Central Limit Theorem constrains sums of stochastic variates. Recognition of information as a form of free energy instantiated by physical processes that consume free energy permits analogs to phase transition and nonequilibrium thermodynamic arguments, leading to ‘dynamic regression models’ useful for data analysis.

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

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Lespinet Olivier

2007-11-01

Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

Algorithmic Mechanism Design of Evolutionary Computation.

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Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach.

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Shaar-Moshe, Lidor; Hübner, Sariel; Peleg, Zvi

2015-05-03

Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism. Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved

The value of information in conservation planning: Selecting retention trees for lichen conservation

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Karin Perhans; Robert G. Haight; Lena Gustafsson

2014-01-01

Conservation planning studies at small scales such as forest stands and below are uncommon. However, for retention forestry, developed during the last two decades and with current wide and increasing application in boreal and temperate regions, the need for cost-effective selection of individual trees is evident. In retention forestry certain trees are left at final...

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

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Raherison, Elie S M; Giguère, Isabelle; Caron, Sébastien; Lamara, Mebarek; MacKay, John J

2015-07-01

Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Tapir health and conservation medicine.

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Mangini, Paulo Rogerio; Medici, Emilia Patrícia; Fernandes-Santos, Renata Carolina

2012-12-01

Tapirs have unique nutritional needs, as well as anatomical, physiological, behavioral and ecological adaptations that must be considered when managing their health, both in the wild and in captivity. Information about how tapirs live in their natural habitats can provide crucial knowledge to prevent many of the health problems found in captivity such as infectious and parasitic diseases, reproductive issues and nutritional and behavioral disorders. Likewise, proper management in captivity can significantly contribute to in situ conservation programs. Conservation medicine is a science created to address the global health crisis that jeopardizes biodiversity causing imbalances among ecosystem, human, animal and vegetal health. In this context, common threats to tapir health and conservation, such as isolated and small populations surrounded by human activity, chemical pollution, domestic animals and their pathogenic agents, need to be better understood. This manuscript provides information about the health of tapirs both in captivity and in the wild and aims to encourage tapir conservationists worldwide to gather information about pathogen and disease dynamics and manifestation, as well as implications for tapir conservation. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Evolutionary Explanations of Eating Disorders

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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.

A new conservation strategy for China-A model starting with primates.

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Pan, Ruliang; Oxnard, Charles; Grueter, Cyril C; Li, Baoguo; Qi, Xiaoguang; He, Gang; Guo, Songtao; Garber, Paul A

2016-11-01

Although the evolutionary history of primates in China dates to the Eocene, and includes major radiations of lorisids, hominoids, cercopithecines, and colobines during the Miocene, Pliocene, and Pleistocene, extensive human-induced habitat change and deforestation over the past few centuries has resulted in 22 of 25 extant species listed as threatened or endangered, and two species of gibbons extirpated in the last few years. This commentary briefly reviews factors that have contributed to the decline of primates in China over the past 400 years, and in particular how major social events and economic development in modern China have resulted in unsustainable environmental change. In response, we describe our efforts to develop a strategic scientific, educational and conservation partnership in China, focusing on primates, in which GIS technology will be used to integrate geographical profiles, climatic information, and changes in land use patterns and human and nonhuman primate distributions to highlight issues of immediate concern and to develop priority-based conservation solutions. Our goal is to evaluate how human-induced environmental change has impacted primates over time and to predict the likelihood of primate population extinctions in the near future. This model represents an early warning system that will be widely available to the Chinese government, public, educational institutions, researchers, and NGOs through social media and educational videos in order to arouse public awareness and promote wildlife conservation. We encourage colleagues across a broad range of academic disciplines, political ideologies, and the public to help move this strategy into reality, the sooner the better. Am. J. Primatol. 78:1137-1148, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Evolutionary Science as a Method to Facilitate Higher Level Thinking and Reasoning in Medical Training.

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Graves, Joseph L; Reiber, Chris; Thanukos, Anna; Hurtado, Magdalena; Wolpaw, Terry

2016-10-15

Evolutionary science is indispensable for understanding biological processes. Effective medical treatment must be anchored in sound biology. However, currently the insights available from evolutionary science are not adequately incorporated in either pre-medical or medical school curricula. To illuminate how evolution may be helpful in these areas, examples in which the insights of evolutionary science are already improving medical treatment and ways in which evolutionary reasoning can be practiced in the context of medicine are provided. In order to facilitate the learning of evolutionary principles, concepts derived from evolutionary science that medical students and professionals should understand are outlined. These concepts are designed to be authoritative and at the same time easily accessible for anyone with the general biological knowledge of a first-year medical student. Thus we conclude that medical practice informed by evolutionary principles will be more effective and lead to better patient outcomes.Furthermore, it is argued that evolutionary medicine complements general medical training because it provides an additional means by which medical students can practice the critical thinking skills that will be important in their future practice. We argue that core concepts from evolutionary science have the potential to improve critical thinking and facilitate more effective learning in medical training. © The Author(s) 2016. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.

The citation field of evolutionary economics

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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

Subjective risk assessment for planning conservation projects

International Nuclear Information System (INIS)

Game, Edward T; Fitzsimons, James A; Lipsett-Moore, Geoff; McDonald-Madden, Eve

2013-01-01

Conservation projects occur under many types of uncertainty. Where this uncertainty can affect achievement of a project’s objectives, there is risk. Understanding risks to project success should influence a range of strategic and tactical decisions in conservation, and yet, formal risk assessment rarely features in the guidance or practice of conservation planning. We describe how subjective risk analysis tools can be framed to facilitate the rapid identification and assessment of risks to conservation projects, and how this information should influence conservation planning. Our approach is illustrated with an assessment of risks to conservation success as part of a conservation plan for the work of The Nature Conservancy in northern Australia. Risks can be both internal and external to a project, and occur across environmental, social, economic and political systems. Based on the relative importance of a risk and the level of certainty in its assessment we propose a series of appropriate, project level responses including research, monitoring, and active amelioration. Explicit identification, prioritization, and where possible, management of risks are important elements of using conservation resources in an informed and accountable manner. (letter)

Information requirements of young women with breast cancer treated with mastectomy or breast conserving surgery: A systematic review.

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Recio-Saucedo, Alejandra; Gerty, Sue; Foster, Claire; Eccles, Diana; Cutress, Ramsey I

2016-02-01

Young women with breast cancer have poorer prognosis, greater lifetime risk of local recurrence, contralateral recurrence, and distant disease, regardless of surgery received. Here we systematically review published evidence relating to the information requirements and preferences of young women diagnosed with early-stage breast cancer offered a choice between mastectomy and Breast Conservation Surgery (BCS). Findings will inform the development of a surgical decision aid for young women. Eight databases were searched to identify research examining information requirements of young women facing breast oncological surgery treatment decisions (MESH headings). Twelve studies met the inclusion criteria. Data were extracted and summarised in a narrative synthesis. Findings indicate that young women prefer greater and more detailed information regarding treatment side effects, sexuality, and body image. Younger age of diagnosis leads to an increased risk perception of developing a second breast cancer. Young women's choices are influenced by factors associated with family and career. Information is required in a continuum throughout the treatment experience and not only at diagnosis when treatment decisions are made. Young women show differing levels of participation preferences. Young women find decision-making challenging when the characteristics of diagnosis provide a surgical choice between mastectomy and breast conservation surgery. Efforts should be made to provide information regarding sexuality, body image, reconstruction, fertility and likelihood of familial predisposition. Further research is needed to identify the specific level and information requirements of this young-onset group. The low number of studies indicate a need to design studies targeting specifically this age group of breast cancer patients. Copyright © 2015 Elsevier Ltd. All rights reserved.

A genetic linkage map of sole (Solea solea: a tool for evolutionary and comparative analyses of exploited (flatfishes.

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Eveline Diopere

Full Text Available Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L. is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes, Nile tilapia (Oreochromis niloticus, three-spined stickleback (Gasterosteus aculeatus and green spotted pufferfish (Tetraodon nigroviridis. This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus, another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

Towards a mechanistic foundation of evolutionary theory.

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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.

A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.

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Sagar Darvekar

Full Text Available Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or "reader" modules. The nuclear proteins SPBP and RAI1 are composed of several putative "reader" modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif. Interactions studies in vitro and in yeast cells suggested that despite the extraordinary long loop region in their ePHD/ADD-like chromatin binding domains, the C-terminal region of both proteins seem to adopt a cross-braced topology of zinc finger interactions similar to other structurally determined ePHD/ADD structures. Both their ePHD/ADD-like domain and their novel nucleosome binding domain are highly conserved in vertebrate evolution, and construction of a phylogenetic tree displayed two well supported clusters representing SPBP and RAI1, respectively. Their genome and domain organisation suggest that SPBP and RAI1 have occurred from a gene duplication event. The phylogenetic tree suggests that this duplication has happened early in vertebrate evolution, since only one gene was identified in insects and lancelet. Finally, experimental data confirm that the conserved novel nucleosome binding region of RAI1 has the ability to bind the nucleosome core and histones. However, an adjacent conserved AT-hook motif as identified in SPBP is not present in RAI1, and deletion of the novel nucleosome binding region of RAI1 did not significantly affect its nuclear localisation.

Nonprice incentives and energy conservation.

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Asensio, Omar I; Delmas, Magali A

2015-02-10

In the electricity sector, energy conservation through technological and behavioral change is estimated to have a savings potential of 123 million metric tons of carbon per year, which represents 20% of US household direct emissions in the United States. In this article, we investigate the effectiveness of nonprice information strategies to motivate conservation behavior. We introduce environment and health-based messaging as a behavioral strategy to reduce energy use in the home and promote energy conservation. In a randomized controlled trial with real-time appliance-level energy metering, we find that environment and health-based information strategies, which communicate the environmental and public health externalities of electricity production, such as pounds of pollutants, childhood asthma, and cancer, outperform monetary savings information to drive behavioral change in the home. Environment and health-based information treatments motivated 8% energy savings versus control and were particularly effective on families with children, who achieved up to 19% energy savings. Our results are based on a panel of 3.4 million hourly appliance-level kilowatt-hour observations for 118 residences over 8 mo. We discuss the relative impacts of both cost-savings information and environmental health messaging strategies with residential consumers.

Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792 in a Fragmented Landscape: Implications for Conservation Management.

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Péter Takács

Full Text Available The European mudminnow (Umbra krameri is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.

Conserving what, where and how? Cost-efficient measures to conserve biodiversity in Denmark

DEFF Research Database (Denmark)

Petersen, Anders Højgård; Strange, Niels; Anthon, Signe

2016-01-01

Biodiversity conservation efforts in Europe have traditionally focused on farmland and open nature areas such as grasslands, heathlands and meadows, while little attention has been devoted to conservation actions in forest. Using detailed information on the geographical distribution of about 900...... terrestrial species in Denmark we apply systematic conservation planning techniques to identify how to protect biodiversity at the lowest cost to society. The results suggest that conservation actions in forest should be given a higher priority. Thus, three to four times the number of forest species...... are protected per million € compared with species living in open land natural areas. Furthermore, a gap analysis finds the current designation of Natura 2000 and other protected areas is skewed toward open land natural areas, and insufficient to meet the conservation targets on forest species....

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

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Achal Rastogi

2015-07-01

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

Conserved domains and SINE diversity during animal evolution.

Science.gov (United States)

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Overview topic paper on mass media energy conservation communications

Energy Technology Data Exchange (ETDEWEB)

Vertinsky, P; Vertinsky, I

1979-02-01

The utilization of information diffusion strategies to increase energy conservation knowledge and practices among the general population in Canada is discussed in terms of 5 media functions: information dissemination, remedial behavior modification, lifestyle decisions, initiating conservation action, and crisis management. Each of these functions is critically addressed in terms of media mix, message content and form, timing and intensity, exposure, and specific target populations. The diffusion strategies are then organized into a matrix of policy options to enable the appropriate one to be selected. Four major categories of energy conservation information considered are the nature of the energy problem, methods of conservation, results of conservation, and the individual consumer decision-making process. Heavy television exposure suggests this medium has enormous potential for informing Canadians on conservation issues. Print seems to be the main source of detailed, specialized, and sophisticated kinds of information. However, despite wide media availability, large numbers of the population consistently escape contact with widely reported information. Behavioral modification to change undesirable energy habits is examined from the perspectives of initial change and cultural/social change required to sustain new lifestyles. The use of mass media during crisis situations may be of essential importance for implementation of future energy policies. Information dissemination and responses to the mass media do not appear to have the same patterns during crisis and non-crisis situations. 279 refs.

Energy conservation in industry

International Nuclear Information System (INIS)

Pembleton, P.

1992-01-01

Energy Conservation in Industry is the first number in the Energy and Environmental Series of the Industrial and Technological Information Bank (INTIB). The Series supersedes the INECA Journal and reflects the broader information programme undertaken by INTIB. The present number of the Series contains contributions from three major international databases and five topic-specific sources, including three United Nations Organizations. The present publication consists of a recent technical report on a current topic: reducing energy loss in four industrial sectors and improving energy conservation through waste-heat recovery, followed by two sections containing abstracts of technical materials

Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

Science.gov (United States)

Hunt, Tam

2014-12-01

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

Where Evolutionary Psychology Meets Cognitive Neuroscience: A Précis to Evolutionary Cognitive Neuroscience1

Directory of Open Access Journals (Sweden)

Austen L. Krill

2007-01-01

Full Text Available Cognitive neuroscience, the study of brain-behavior relationships, has long attempted to map the brain. The discipline is flourishing, with an increasing number of functional neuroimaging studies appearing in the scientific literature daily. Unlike biology and even psychology, the cognitive neurosciences have only recently begun to apply evolutionary meta-theory and methodological guidance. Approaching cognitive neuroscience from an evolutionary perspective allows scientists to apply biologically based theoretical guidance to their investigations and can be conducted in both humans and nonhuman animals. In fact, several investigations of this sort are underway in laboratories around the world. This paper and two new volumes (Platek, Keenan, and Shackelford [Eds.], 2007; Platek and Shackelford [Eds.], under contract represent the first formal attempts to document the burgeoning field of evolutionary cognitive neuroscience. Here, we briefly review the current state of the science of evolutionary cognitive neuroscience, the methods available to the evolutionary cognitive neuroscientist, and what we foresee as the future directions of the discipline.

communities` attitudes towards conservation in gashakagumti

African Journals Online (AJOL)

Tersor

JOURNAL OF RESEARCH IN FORESTRY, WILDLIFE AND ENVIRONMENT VOLUME 7, No.2 SEPTEMBER, 2015. ... and the impact of conservation interventions, as well as to inform the ... The conservation attitudes of local people residing ...

Evolutionary conservatism and convergence both lead to striking similarity in ecology, morphology and performance across continents in frogs.

Science.gov (United States)

Moen, Daniel S; Irschick, Duncan J; Wiens, John J

2013-12-22

Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and South America), assessing the importance of dispersal and convergent evolution in explaining similarity across regions. We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems.

Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses.

Science.gov (United States)

Durrant, Matthew; Boyer, Justin; Zhou, Wenwu; Baldwin, Ian T; Xu, Shuqing

2017-08-01

Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes. Highly conserved and evolutionarily ancient genes of primary metabolism were activated at intermediate time points (2-6 h) after elicitation, while less constrained and young genes associated with defense signaling and biosynthesis of specialized metabolites were activated at early (before 2 h) and late (after 6 h) stages of the induced response, respectively - a pattern resembling the evolutionary hourglass pattern observed during embryogenesis in animals and the developmental process in plants and fungi. The hourglass patterns found in herbivory-induced defense responses and developmental process are both likely to be a result of signaling modularization and differential evolutionary constraints on the modules involved in the signaling cascade. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

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

Lamarck and the adaptive conservation of life

Directory of Open Access Journals (Sweden)

Galera, Andrés

2009-12-01

Full Text Available This paper studies Lamarck’s evolutionary thought through four analytic elements. Firstly, Lamarckian construction of a founding evolutionary archetype. Secondly, the interpretation of nature as a material system where the organic change represents a continuous process aimed at the adaptative conservation of life. Thirdly, the definition of a genealogical process on the origin of species which identifies the natural method. Fourthly, the redefinition of the concept of species applying the arguments of temporary relativity and individual instability.

En este artículo se estudia el ideario evolucionista lamarckiano desarrollando cuatro elementos analíticos. Primero, la elaboración de un arquetipo evolutivo fundacional. Segundo, la interpretación de la naturaleza como un sistema material donde el cambio orgánico da sentido a un proceso continuo dirigido a la conservación de la vida. Tercero, la definición de un principio genealógico sobre el origen de las especies que identifica el método natural. Cuarto, la reformulación del concepto de especie utilizando los argumentos de relatividad temporal e inestabilidad individual.

Optimal conservation of migratory species.

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Tara G Martin

Full Text Available BACKGROUND: Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea-regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity bringing into question the utility and efficiency of current conservation efforts. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. CONCLUSIONS/SIGNIFICANCE: We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of

Resembling a viper: implications of mimicry for conservation of the endangered smooth snake.

Science.gov (United States)

Valkonen, Janne K; Mappes, Johanna

2014-12-01

The phenomenon of Batesian mimicry, where a palatable animal gains protection against predation by resembling an unpalatable model, has been a core interest of evolutionary biologists for 150 years. An extensive range of studies has focused on revealing mechanistic aspects of mimicry (shared education and generalization of predators) and the evolutionary dynamics of mimicry systems (co-operation vs. conflict) and revealed that protective mimicry is widespread and is important for individual fitness. However, according to our knowledge, there are no case studies where mimicry theories have been applied to conservation of mimetic species. Theoretically, mimicry affects, for example, frequency dependency of predator avoidance learning and human induced mortality. We examined the case of the protected, endangered, nonvenomous smooth snake (Coronella austriaca) that mimics the nonprotected venomous adder (Vipera berus), both of which occur in the Åland archipelago, Finland. To quantify the added predation risk on smooth snakes caused by the rarity of vipers, we calculated risk estimates from experimental data. Resemblance of vipers enhances survival of smooth snakes against bird predation because many predators avoid touching venomous vipers. Mimetic resemblance is however disadvantageous against human predators, who kill venomous vipers and accidentally kill endangered, protected smooth snakes. We found that the effective population size of the adders in Åland is very low relative to its smooth snake mimic (28.93 and 41.35, respectively).Because Batesian mimicry is advantageous for the mimic only if model species exist in sufficiently high numbers, it is likely that the conservation program for smooth snakes will fail if adders continue to be destroyed. Understanding the population consequences of mimetic species may be crucial to the success of endangered species conservation. We suggest that when a Batesian mimic requires protection, conservation planners should

Adapting the bioblitz to meet conservation needs.

Science.gov (United States)

Parker, Sophie S; Pauly, Gregory B; Moore, James; Fraga, Naomi S; Knapp, John J; Principe, Zachary; Brown, Brian V; Randall, John M; Cohen, Brian S; Wake, Thomas A

2018-03-01

When conservation strategies require new, field-based information, practitioners must find the best ways to rapidly deliver high-quality survey data. To address this challenge, several rapid-assessment approaches have been developed since the early 1990s. These typically involve large areas, take many months to complete, and are not appropriate when conservation-relevant survey data are urgently needed for a specific locale. In contrast, bioblitzes are designed for quick collection of site-specific survey data. Although bioblitzes are commonly used to achieve educational or public-engagement goals, conservation practitioners are increasingly using a modified bioblitz approach to generate conservation-relevant data while simultaneously enhancing research capacity and building working partnerships focused on conservation concerns. We term these modified events expert bioblitzes. Several expert bioblitzes have taken place on lands of conservation concern in Southern California and have involved collaborative efforts of government agencies, nonprofit organizations, botanic gardens, museums, and universities. The results of expert bioblitzes directly informed on-the-ground conservation and decision-making; increased capacity for rapid deployment of expert bioblitzes in the future; and fostered collaboration and communication among taxonomically and institutionally diverse experts. As research and conservation funding becomes increasingly scarce, expert bioblitzes can play an increasingly important role in biodiversity conservation. © 2018 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Conservation genetics of the genus Martes: Assessing within-species movements, units to conserve, and connectivity across ecological and evolutionary time [Chapter 17

Science.gov (United States)

Michael K. Schwartz; Aritz Ruiz-Gonzalez; Ryuchi Masuda; Cino Pertoldi

2012-01-01

Understanding the physical and temporal factors that structure Martes populations is essential to the conservation and management of the 8 recognized Martes species. Recently, advances in 3 distinct subdisciplines in molecular ecology have provided insights into historical and contemporary environmental factors that have created population substructure and influenced...

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.

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.

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.

Clonality and evolutionary history of rhabdomyosarcoma.

Directory of Open Access Journals (Sweden)

Li Chen

2015-03-01

Full Text Available To infer the subclonality of rhabdomyosarcoma (RMS and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS.

Lattice-work corridors for climate change: a conceptual framework for biodiversity conservation and social-ecological resilience in a tropical elevational gradient

Directory of Open Access Journals (Sweden)

Patricia A. Townsend

2015-06-01

Full Text Available Rapid climate change poses complex challenges for conservation, especially in tropical developing countries where biodiversity is high while financial and technical resources are limited. The complexity is heightened by uncertainty in predicted effects, both for ecological systems and human communities that depend heavily on natural resource extraction and use. Effective conservation plans and measures must be inexpensive, fast-acting, and able to increase the resilience of both the ecosystem and the social-ecological system. We present conservation practitioners with a framework that strategically integrates climate change planning into connectivity measures for tropical mountain ecosystems in Costa Rica. We propose a strategy for doubling the amount of habitat currently protected in riparian corridors using measures that are relatively low cost and fast-acting, and will employ and expand human capital. We argue that habitat connectivity must be enhanced along latitudinal gradients, but also within the same elevational bands, via a lattice-work corridor system. This is needed to facilitate range shifts for mobile species and evolutionary adaptation for less mobile species. We think that conservation measures within the elevational bands must include conservation-friendly land uses that improve current and future human livelihoods under dynamic conditions. Key components include community involvement, habitat priority-setting, forest landscape restoration, and environmental services payments. Our approach is fundamentally adaptive in that the conservation measures employed are informed by on-the-ground successes and failures and modified accordingly, but are relatively low risk and fast-acting. Our proposal, if implemented, would satisfy tenets of climate-smart conservation, improve the resilience of human and ecological communities, and be a model for other locations facing similar challenges.

Comparative Advantages of Spin-off Firms: An Evolutionary Perspective

Directory of Open Access Journals (Sweden)

Bilgehan Uzunca

2011-11-01

Full Text Available As predicted by evolutionary economics, historical antecedents matter when it comes to the relationship between survival of entrants and organizational capabilities. Spinoff firms provide an exemplary case of such relationship where the founders’ pre-entry capabilities that are inherited from the parent firm increases their survival chances. Looking closer and deeper to the evolutionary spinoff success mechanisms, I examine three specific genetic features which make spinoff firms more advantageous compared to other entrants; namely 1 Genotype: Transfer of blueprint, 2 Phenotype: Organizational learning, and 3 Memes: Informal relations and social capital. A detailed theoretical analysis of each mechanism prevails how they function and provide sustainable competitive advantage to spinoff firms. Testable hypotheses are provided about each mechanism.

Predicting Greater Prairie-Chicken Lek Site Suitability to Inform Conservation Actions.

Directory of Open Access Journals (Sweden)

Torre J Hovick

Full Text Available The demands of a growing human population dictates that expansion of energy infrastructure, roads, and other development frequently takes place in native rangelands. Particularly, transmission lines and roads commonly divide rural landscapes and increase fragmentation. This has direct and indirect consequences on native wildlife that can be mitigated through thoughtful planning and proactive approaches to identifying areas of high conservation priority. We used nine years (2003-2011 of Greater Prairie-Chicken (Tympanuchus cupido lek locations totaling 870 unique leks sites in Kansas and seven geographic information system (GIS layers describing land cover, topography, and anthropogenic structures to model habitat suitability across the state. The models obtained had low omission rates (0.81, indicating high model performance and reliability of predicted habitat suitability for Greater Prairie-Chickens. We found that elevation was the most influential in predicting lek locations, contributing three times more predictive power than any other variable. However, models were improved by the addition of land cover and anthropogenic features (transmission lines, roads, and oil and gas structures. Overall, our analysis provides a hierarchal understanding of Greater Prairie-Chicken habitat suitability that is broadly based on geomorphological features followed by land cover suitability. We found that when land features and vegetation cover are suitable for Greater Prairie-Chickens, fragmentation by anthropogenic sources such as roadways and transmission lines are a concern. Therefore, it is our recommendation that future human development in Kansas avoid areas that our models identified as highly suitable for Greater Prairie-Chickens and focus development on land cover types that are of lower conservation concern.

Case study of building of conservation coalitions to conserve ecological interactions.

Science.gov (United States)

Chen, Gao; Luo, Shihong; Mei, Nianshu; Shen, Dingfang; Sun, Weibang

2015-12-01

We engaged experts in various fields of study (pollination ecology, chemical ecology, and ethnobotany), invited community participation, and provided environmental education in an effort to conserve an endangered birthwort (Aristolochia delavayi) and a vulnerable pipevine swallowtail (Byasa daemonius). Scientists studied the uptake and sequestration of the secondary metabolites aristolochic acids from A. delavayi leaves by different stages of pipevine swallowtail as a defense mechanism; low fruit set of the myophilous A. delavayi due to pollinator limitation; and the emission of chemical signals that attract parasitic wasps by the prepupae of B. daemonius. The results of these studies were part of an education program delivered by personnel of non-governmental organizations. The program was devised to deliver information to the public about the health risks of consuming A. delavayi individuals (aristolochic-acid-associated cancers) and to establish a bridge between the public and scientific research. Following delivery of the program, the behavior of residents changed considerably. Community residents were involved in management activities, including participation in a program to promote understanding of ecological interactions between A. delavayi and B. daemonius; designing an in situ conservation site; monitoring A. delavayi and B. daemonius individuals; and promoting the natural fruit set of A. delavayi by scattering animal excrement to attract fly pollinators. The integration of scientific information and community participation appears to have resulted in an increase in abundance of threatened A. delavayi and B. daemonius populations. We believe the involvement of local people in conservation is necessary for successful species conservation. © 2015 Society for Conservation Biology.

Determination of non-market values to inform conservation strategies for the threatened Alistana-Sanabresa cattle breed.

Science.gov (United States)

Martin-Collado, D; Diaz, C; Drucker, A G; Carabaño, M J; Zander, K K

2014-08-01

Livestock breed-related public good functions are often used to justify support for endangered breed conservation despite the fact that little is known about such non-market values. We show how stated preference techniques can be used to assess the non-market values that people place on livestock breeds. Through the application of a case study choice experiment survey in Zamora province, Spain, the total economic value (TEV) of the threatened Alistana-Sanabresa (AS) cattle breed was investigated. An analysis of the relative importance of the non-market components of its TEV and an assessment of the socio-economic variables that influence people's valuation of such components is used to inform conservation strategy design. Overall, the findings reveal that the AS breed had significant non-market values associated with it and that the value that respondents placed on each specific public good function also varied significantly. Functions related with indirect use cultural and existence values were much more highly valued than landscape maintenance values. These high cultural and existence values (totalling over 80% of TEV) suggest that an AS in situ conservation strategy will be required to secure such values. As part of such a strategy, incentive mechanisms will be needed to permit farmers to capture some of these public good values and thus be able to afford to maintain breed population numbers at socially desirable levels. One such mechanism could be related to the development of breed-related agritourism initiatives, with a view to enhancing private good values and providing an important addition to continued direct support. Where linked with cultural dimensions, niche product market development, including through improving AS breed-related product quality and brand recognition may also have a role to play as part of such an overall conservation and use strategy. We conclude that livestock breed conservation strategies with the highest potential to maximise

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

(ICTs) And Environmental Conservation

African Journals Online (AJOL)

ICTs have a potential for improving the accessibility of environmental information, and if appropriately applied, they can empower local people to make informed decisions regarding environmental issues, thus enhancing environmental conservation. However, the challenge is on how to define particular roles that ...

Evidence of at least two evolutionary lineages in Melipona subnitida (Apidae, Meliponini) suggested by mtDNA variability and geometric morphometrics of forewings

Science.gov (United States)

Bonatti, Vanessa; Simões, Zilá Luz Paulino; Franco, Fernando Faria; Francoy, Tiago Mauricio

2014-01-01

Melipona subnitida, a tropical stingless bee, is an endemic species of the Brazilian northeast and exhibits great potential for honey and pollen production in addition to its role as one of the main pollinators of the Caatinga biome. To understand the genetic structure and better assist in the conservation of this species, we characterized the population variability of M. subnitida using geometric morphometrics of the forewing and cytochrome c oxidase I gene fragment sequencing. We collected workers from six localities in the northernmost distribution. Both methodologies indicated that the variability among the sampled populations is related both to the environment in which samples were collected and the geographical distance between the sampling sites, indicating that differentiation among the populations is due to the existence of at least evolutionary lineages. Molecular clock data suggest that this differentiation may have begun in the middle Pleistocene, approximately 396 kya. The conservation of all evolutionary lineages is important since they can present differential resistance to environmental changes, as resistance to drought and diseases.

The neuro-immunological interface in an evolutionary perspective: the dynamic relationship between effector and recognition systems.

Science.gov (United States)

Ottaviani, E; Valensin, S; Franceschi, C

1998-04-16

The evolutionary perspective indicates that an immune-neuroendocrine effector system integrating innate immunity, stress and inflammation is present in invertebrates. This defense network, centered on the macrophage and exerting primitive and highly promiscuous recognition units, is very effective, ancestral and appears to have been conserved throughout evolution from invertebrates to higher vertebrates. It would seem that there was a "big bang" in the recognition system of lower vertebrates, and T and B cell repertoires, MHC and antibodies suddenly appeared. We argue that this phenomenon is the counterpart of the increasing complexity of the internal circuitry and recognition units in the effector system. The immediate consequences were a progressive enlargement of the pathogen repertoire and new problems regarding self/not-self discrimination. Probably not by chance, a new organ appeared, capable of purging cells able of excessive self recognition. This organ, the thymus, appears to be the result of a well known evolutionary strategy of re-using pre-existing material (neuroendocrine cells and mediators constituting the thymic microenvironment). This bricolage at an organ level is similar to the effect we have already described at the level of molecules and functions of the defense network, and has a general counterpart at genetic level. Thus, in vertebrates, the conserved immune-neuroendocrine effector system remains of fundamental importance in defense against pathogens, while its efficiency has increased through synergy with the new, clonotipical recognition repertoire.

Calculating evolutionary dynamics in structured populations.

Directory of Open Access Journals (Sweden)

Charles G Nathanson

2009-12-01

Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

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...

CDMetaPOP: An individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

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Landguth, Erin L; Bearlin, Andrew; Day, Casey; Dunham, Jason B.

2016-01-01

1. Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco-evolutionary applications.2. Using two illustrative examples, we present Cost–Distance Meta-POPulation, a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers.3. Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

Beyond biology: toward a more public ecology for conservation

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David P. Robertson; R. Bruce Hull

2001-01-01

The ultimate purpose of conservation science is to inform and affect conservation policy. Therefore, conservation biologists and all the people who produce, review, and apply conservation research should evaluate the success of their knowledge according to its ability to influence conservation decisions. In addition to possessing conventional "scientific"...

Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

Directory of Open Access Journals (Sweden)

Jeffrey K Noel

2016-01-01

Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

Use of sibling relationship reconstruction to complement traditional monitoring in fisheries management and conservation of brown trout.

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Ozerov, Mikhail; Jürgenstein, Tauno; Aykanat, Tutku; Vasemägi, Anti

2015-08-01

Declining trends in the abundance of many fish urgently call for more efficient and informative monitoring methods that would provide necessary demographic data for the evaluation of existing conservation, restoration, and management actions. We investigated how genetic sibship reconstruction from young-of-the-year brown trout (Salmo trutta L.) juveniles provides valuable, complementary demographic information that allowed us to disentangle the effects of habitat quality and number of breeders on juvenile density. We studied restored (n = 15) and control (n = 15) spawning and nursery habitats in 16 brown trout rivers and streams over 2 consecutive years to evaluate the effectiveness of habitat restoration activities. Similar juvenile densities both in restored and control spawning and nursery grounds were observed. Similarly, no differences in the effective number of breeders, Nb(SA) , were detected between habitats, indicating that brown trout readily used recently restored spawning grounds. Only a weak relationship between the Nb(SA) and juvenile density was observed, suggesting that multiple factors affect juvenile abundance. In some areas, very low estimates of Nb(SA) were found at sites with high juvenile density, indicating that a small number of breeders can produce a high number of progeny in favorable conditions. In other sites, high Nb(SA) estimates were associated with low juvenile density, suggesting low habitat quality or lack of suitable spawning substrate in relation to available breeders. Based on these results, we recommend the incorporation of genetic sibship reconstruction to ongoing and future fish evaluation and monitoring programs to gain novel insights into local demographic and evolutionary processes relevant for fisheries management, habitat restoration, and conservation. © 2015 Society for Conservation Biology.

Phylogenetic distribution and evolutionary dynamics of the sex determination genes doublesex and transformer in insects.

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Geuverink, E; Beukeboom, L W

2014-01-01

Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects. © 2013 S. Karger AG, Basel.

Assessing ecological correlates of marine bird declines to inform marine conservation

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Vilchis, L Ignacio; Johnson, Christine K; Evenson, Joseph R; Pearson, Scott F; Barry, Karen L; Davidson, Peter; Raphael, Martin G; Gaydos, Joseph K

2015-01-01

Identifying drivers of ecosystem change in large marine ecosystems is central for their effective management and conservation. This is a sizable challenge, particularly in ecosystems transcending international borders, where monitoring and conservation of long-range migratory species and their habitats are logistically and financially problematic. Here, using tools borrowed from epidemiology, we elucidated common drivers underlying species declines within a marine ecosystem, much in the way epidemiological analyses evaluate risk factors for negative health outcomes to better inform decisions. Thus, we identified ecological traits and dietary specializations associated with species declines in a community of marine predators that could be reflective of ecosystem change. To do so, we integrated count data from winter surveys collected in long-term marine bird monitoring programs conducted throughout the Salish Sea—a transboundary large marine ecosystem in North America's Pacific Northwest. We found that decadal declines in winter counts were most prevalent among pursuit divers such as alcids (Alcidae) and grebes (Podicipedidae) that have specialized diets based on forage fish, and that wide-ranging species without local breeding colonies were more prone to these declines. Although a combination of factors is most likely driving declines of diving forage fish specialists, we propose that changes in the availability of low-trophic prey may be forcing wintering range shifts of diving birds in the Salish Sea. Such a synthesis of long-term trends in a marine predator community not only provides unique insights into the types of species that are at risk of extirpation and why, but may also inform proactive conservation measures to counteract threats—information that is paramount for species-specific and ecosystem-wide conservation. Evaluación de las Correlaciones Ecológicas de las Declinaciones de Aves Marinas para Informar a la Conservación Marina Resumen La

The evolutionary portrait of metazoan NAD salvage.

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Carneiro, João; Duarte-Pereira, Sara; Azevedo, Luísa; Castro, L Filipe C; Aguiar, Paulo; Moreira, Irina S; Amorim, António; Silva, Raquel M

2013-01-01

Nicotinamide Adenine Dinucleotide (NAD) levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs) and Nicotinamidases (PNCs) have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.

Asymmetric Evolutionary Games

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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

Genome-wide identification of nuclear receptor (NR) genes and the evolutionary significance of the NR1O subfamily in the monogonont rotifer Brachionus spp.

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Kim, Duck-Hyun; Kim, Hui-Su; Hwang, Dae-Sik; Kim, Hee-Jin; Hagiwara, Atsushi; Lee, Jae-Seong; Jeong, Chang-Bum

2017-10-01

Nuclear receptors (NRs) are a large family of transcription factors that are involved in many fundamental biological processes. NRs are considered to have originated from a common ancestor, and are highly conserved throughout the whole animal taxa. Therefore, the genome-wide identification of NR genes in an animal taxon can provide insight into the evolutionary tendencies of NRs. Here, we identified all the NR genes in the monogonont rotifer Brachionus spp., which are considered an ecologically key species due to their abundance and world-wide distribution. The NR family was composed of 40, 32, 29, and 32 genes in the genomes of the rotifers B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, respectively, which were classified into seven distinct subfamilies. The composition of each subfamily was highly conserved between species, except for NR1O genes, suggesting that they have undergone sporadic evolutionary processes for adaptation to their different environmental pressures. In addition, despite the dynamics of NR evolution, the significance of the conserved endocrine system, particularly for estrogen receptor (ER)-signaling, in rotifers was discussed on the basis of phylogenetic analyses. The results of this study may help provide a better understanding the evolution of NRs, and expand our knowledge of rotifer endocrine systems. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

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Zarrineh, Peyman; Sánchez-Rodríguez, Aminael; Hosseinkhan, Nazanin; Narimani, Zahra; Marchal, Kathleen; Masoudi-Nejad, Ali

2014-01-01

Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica. PMID:25101984

Network evolution: rewiring and signatures of conservation in signaling.

Directory of Open Access Journals (Sweden)

Mark G F Sun

Full Text Available The analysis of network evolution has been hampered by limited availability of protein interaction data for different organisms. In this study, we investigate evolutionary mechanisms in Src Homology 3 (SH3 domain and kinase interaction networks using high-resolution specificity profiles. We constructed and examined networks for 23 fungal species ranging from Saccharomyces cerevisiae to Schizosaccharomyces pombe. We quantify rates of different rewiring mechanisms and show that interaction change through binding site evolution is faster than through gene gain or loss. We found that SH3 interactions evolve swiftly, at rates similar to those found in phosphoregulation evolution. Importantly, we show that interaction changes are sufficiently rapid to exhibit saturation phenomena at the observed timescales. Finally, focusing on the SH3 interaction network, we observe extensive clustering of binding sites on target proteins by SH3 domains and a strong correlation between the number of domains that bind a target protein (target in-degree and interaction conservation. The relationship between in-degree and interaction conservation is driven by two different effects, namely the number of clusters that correspond to interaction interfaces and the number of domains that bind to each cluster leads to sequence specific conservation, which in turn results in interaction conservation. In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules.

Biophysics of protein evolution and evolutionary protein biophysics

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Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots.

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de Bruyn, Mark; Rüber, Lukas; Nylinder, Stephan; Stelbrink, Björn; Lovejoy, Nathan R; Lavoué, Sébastien; Tan, Heok Hui; Nugroho, Estu; Wowor, Daisy; Ng, Peter K L; Siti Azizah, M N; Von Rintelen, Thomas; Hall, Robert; Carvalho, Gary R

2013-05-01

Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region's dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts.

Core principles of evolutionary medicine: A Delphi study.

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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.

Conceptual Barriers to Progress Within Evolutionary Biology.

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Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

2009-08-01

In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

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

Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

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Silla, Toomas; Kepp, Katrin; Tai, E Shyong; Goh, Liang; Davila, Sonia; Catela Ivkovic, Tina; Calin, George A; Voorhoeve, P Mathijs

2014-01-01

Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAFpower for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

Information Management Systems for Cultural Heritage and Conservation of World Heritage Sites. The Silk Roads Case Study

Directory of Open Access Journals (Sweden)

Ona Vileikis

2011-12-01

Full Text Available This paper discusses the application of Information Management Systems (IMS in cultural heritage. IMS offer a set of tools for understanding, inventorying and documenting national, regional and World Heritage properties.  Information Management Systems can assist State Parties, stakeholders and heritage site managers involved in cultural heritage management and conservation by easily mining, sharing and exchanging information from multiple sources based on international standards. Moreover, they aim to record, manage, visualize, analyze and disseminate heritage information. In close collaboration with five Central Asian countries, namely, Turkmenistan, Kazakhstan, Kyrgyzstan, Uzbekistan and Tajikistan; a Belgian consortium headed by the Raymond Lemaire International Centre for Conservation (RLICC, K.U.Leuven is developing the Silk Roads Cultural Heritage Resource Information System (CHRIS. This Web-based Information Management System supports the preparation of the Central Asia Silk Roads serial and transnational nominations on the UNESCO World Heritage list. The project has been set up thanks to the financial support of the Belgian Federal Science Policy Office (BELSPO and in collaboration with UNESCO World Heritage Centre in conjunction with the People’s Republic of China and the Japanese Funds-in-Trust UNESCO project. It provides a holistic approach for the recording, documenta tion, protection and monitoring tasks as part of the management of these potential World Heritage Properties. The Silk Roads CHRIS is easily accessible to the general user, presented in a bilingual English and Russian frame and interoperable, i.e. open for other applications to connect to. In this way, all information for the nomination dossiers is easily verified regarding consistency and quality and ready for managing, periodic reporting and monitoring processes in the respect to the property listed. Fina lly, this study provides a general framework to establish

Evolutionary origins of hepatitis A virus in small mammals.

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Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

2015-12-08

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

Estimating the ratios of the stationary distribution values for Markov chains modeling evolutionary algorithms.

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Mitavskiy, Boris; Cannings, Chris