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Sample records for facilitate adaptive evolution

  1. Developmental evolution facilitates rapid adaptation.

    Science.gov (United States)

    Lin, Hui; Kazlauskas, Romas J; Travisano, Michael

    2017-11-21

    Developmental evolution has frequently been identified as a mode for rapid adaptation, but direct observations of the selective benefits and associated mechanisms of developmental evolution are necessarily challenging to obtain. Here we show rapid evolution of greatly increased rates of dispersal by developmental changes when populations experience stringent selection. Replicate populations of the filamentous fungus Trichoderma citrinoviride underwent 85 serial transfers, under conditions initially favoring growth but not dispersal. T. citrinoviride populations shifted away from multicellular growth toward increased dispersal by producing one thousand times more single-celled asexual conidial spores, three times sooner than the ancestral genotype. Conidia of selected lines also germinated fifty percent faster. Gene expression changed substantially between the ancestral and selected fungi, especially for spore production and growth, demonstrating rapid evolution of tight regulatory control for down-regulation of growth and up-regulation of conidia production between 18 and 24 hours of growth. These changes involved both developmentally fixed and plastic changes in gene expression, showing that complex developmental changes can serve as a mechanism for rapid adaptation.

  2. Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts.

    Science.gov (United States)

    Siepielski, Adam M; Beaulieu, Jeremy M

    2017-04-01

    Most species have evolved adaptations to reduce the chances of predation. In many cases, adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis that adaptive evolution to live with a novel predator facilitates range size shifts. Our results suggest that the evolution of Enallagma shifting from living in ancestral lakes with fish as top predators, to living in lakes with dragonflies as predators, may have facilitated an increase in their range sizes. This increased range size likely arose because lakes with dragonflies were widespread, but unavailable as a habitat throughout much of the evolutionary history of Enallagma because they were historically maladapted to coexist with dragonfly predators. Additionally, the traits that have evolved as defenses against dragonflies also likely enhanced damselfly dispersal abilities. While many factors underlie the evolutionary history of species ranges, these results suggest a role for the evolution of predator-prey interactions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  3. The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation.

    Science.gov (United States)

    Finn, Roderick Nigel; Chauvigné, François; Hlidberg, Jón Baldur; Cutler, Christopher P; Cerdà, Joan

    2014-01-01

    A major physiological barrier for aquatic organisms adapting to terrestrial life is dessication in the aerial environment. This barrier was nevertheless overcome by the Devonian ancestors of extant Tetrapoda, but the origin of specific molecular mechanisms that solved this water problem remains largely unknown. Here we show that an ancient aquaporin gene cluster evolved specifically in the sarcopterygian lineage, and subsequently diverged into paralogous forms of AQP2, -5, or -6 to mediate water conservation in extant Tetrapoda. To determine the origin of these apomorphic genomic traits, we combined aquaporin sequencing from jawless and jawed vertebrates with broad taxon assembly of >2,000 transcripts amongst 131 deuterostome genomes and developed a model based upon Bayesian inference that traces their convergent roots to stem subfamilies in basal Metazoa and Prokaryota. This approach uncovered an unexpected diversity of aquaporins in every lineage investigated, and revealed that the vertebrate superfamily consists of 17 classes of aquaporins (Aqp0 - Aqp16). The oldest orthologs associated with water conservation in modern Tetrapoda are traced to a cluster of three aqp2-like genes in Actinistia that likely arose >500 Ma through duplication of an aqp0-like gene present in a jawless ancestor. In sea lamprey, we show that aqp0 first arose in a protocluster comprised of a novel aqp14 paralog and a fused aqp01 gene. To corroborate these findings, we conducted phylogenetic analyses of five syntenic nuclear receptor subfamilies, which, together with observations of extensive genome rearrangements, support the coincident loss of ancestral aqp2-like orthologs in Actinopterygii. We thus conclude that the divergence of sarcopterygian-specific aquaporin gene clusters was permissive for the evolution of water conservation mechanisms that facilitated tetrapod terrestrial adaptation.

  4. The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation.

    Directory of Open Access Journals (Sweden)

    Roderick Nigel Finn

    Full Text Available A major physiological barrier for aquatic organisms adapting to terrestrial life is dessication in the aerial environment. This barrier was nevertheless overcome by the Devonian ancestors of extant Tetrapoda, but the origin of specific molecular mechanisms that solved this water problem remains largely unknown. Here we show that an ancient aquaporin gene cluster evolved specifically in the sarcopterygian lineage, and subsequently diverged into paralogous forms of AQP2, -5, or -6 to mediate water conservation in extant Tetrapoda. To determine the origin of these apomorphic genomic traits, we combined aquaporin sequencing from jawless and jawed vertebrates with broad taxon assembly of >2,000 transcripts amongst 131 deuterostome genomes and developed a model based upon Bayesian inference that traces their convergent roots to stem subfamilies in basal Metazoa and Prokaryota. This approach uncovered an unexpected diversity of aquaporins in every lineage investigated, and revealed that the vertebrate superfamily consists of 17 classes of aquaporins (Aqp0 - Aqp16. The oldest orthologs associated with water conservation in modern Tetrapoda are traced to a cluster of three aqp2-like genes in Actinistia that likely arose >500 Ma through duplication of an aqp0-like gene present in a jawless ancestor. In sea lamprey, we show that aqp0 first arose in a protocluster comprised of a novel aqp14 paralog and a fused aqp01 gene. To corroborate these findings, we conducted phylogenetic analyses of five syntenic nuclear receptor subfamilies, which, together with observations of extensive genome rearrangements, support the coincident loss of ancestral aqp2-like orthologs in Actinopterygii. We thus conclude that the divergence of sarcopterygian-specific aquaporin gene clusters was permissive for the evolution of water conservation mechanisms that facilitated tetrapod terrestrial adaptation.

  5. The Lineage-Specific Evolution of Aquaporin Gene Clusters Facilitated Tetrapod Terrestrial Adaptation

    OpenAIRE

    Finn, Roderick Nigel; Chauvigné, François; Hlidberg, Jón Baldur; Cutler, Christopher P.; Cerdà, Joan

    2014-01-01

    A major physiological barrier for aquatic organisms adapting to terrestrial life is dessication in the aerial environment. This barrier was nevertheless overcome by the Devonian ancestors of extant Tetrapoda, but the origin of specific molecular mechanisms that solved this water problem remains largely unknown. Here we show that an ancient aquaporin gene cluster evolved specifically in the sarcopterygian lineage, and subsequently diverged into paralogous forms of AQP2, -5, or -6 to mediate wa...

  6. Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments.

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    David A Marques

    2017-04-01

    Full Text Available Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

  7. Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments.

    Science.gov (United States)

    Marques, David A; Taylor, John S; Jones, Felicity C; Di Palma, Federica; Kingsley, David M; Reimchen, Thomas E

    2017-04-01

    Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

  8. Adaptability and evolution.

    Science.gov (United States)

    Bateson, Patrick

    2017-10-06

    The capacity of organisms to respond in their own lifetimes to new challenges in their environments probably appeared early in biological evolution. At present few studies have shown how such adaptability could influence the inherited characteristics of an organism's descendants. In part, this has been because organisms have been treated as passive in evolution. Nevertheless, their effects on biological evolution are likely to have been important and, when they occurred, accelerated the pace of evolution. Ways in which this might have happened have been suggested many times since the 1870s. I review these proposals and discuss their relevance to modern thought.

  9. Sleep facilitates long-term face adaptation.

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    Ditye, Thomas; Javadi, Amir Homayoun; Carbon, Claus-Christian; Walsh, Vincent

    2013-10-22

    Adaptation is an automatic neural mechanism supporting the optimization of visual processing on the basis of previous experiences. While the short-term effects of adaptation on behaviour and physiology have been studied extensively, perceptual long-term changes associated with adaptation are still poorly understood. Here, we show that the integration of adaptation-dependent long-term shifts in neural function is facilitated by sleep. Perceptual shifts induced by adaptation to a distorted image of a famous person were larger in a group of participants who had slept (experiment 1) or merely napped for 90 min (experiment 2) during the interval between adaptation and test compared with controls who stayed awake. Participants' individual rapid eye movement sleep duration predicted the size of post-sleep behavioural adaptation effects. Our data suggest that sleep prevented decay of adaptation in a way that is qualitatively different from the effects of reduced visual interference known as 'storage'. In the light of the well-established link between sleep and memory consolidation, our findings link the perceptual mechanisms of sensory adaptation--which are usually not considered to play a relevant role in mnemonic processes--with learning and memory, and at the same time reveal a new function of sleep in cognition.

  10. Adaptive evolution in ecological communities.

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    Martin M Turcotte

    Full Text Available Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

  11. Adaptive evolution in ecological communities.

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    Turcotte, Martin M; Corrin, Michael S C; Johnson, Marc T J

    2012-01-01

    Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.

  12. Adaptive evolution of Mediterranean pines.

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    Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

    2013-09-01

    Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Adaptation and evolution of drug-resistant Mycobacterium tuberculosis

    NARCIS (Netherlands)

    Bergval, I.L.

    2013-01-01

    Many studies have been conducted on drug resistance and the evolution of Mycobacterium tuberculosis. Notwithstanding, many molecular mechanisms facilitating the emergence, adaptation and spread of drug-resistant tuberculosis have yet to be discovered. This thesis reports studies of the adaptive

  14. Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

    Science.gov (United States)

    Christie, Joshua R; Beekman, Madeleine

    2017-03-01

    Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Adapting perspectives to facilitate knowledge assimilation

    Energy Technology Data Exchange (ETDEWEB)

    Kelsey, R.L.; Webster, R.B.

    1998-12-31

    The notion of perspective when supported in knowledge representation can allow the representation of multiple and varying points of view, some of which may even be inconsistent with one another. In an object-based knowledge representation methodology created and used by the authors, a perspective is defined by consolidating a number of objects and a number of those objects` associated attributes and methods into a view. This view can help partition a knowledge domain into separate portions. A separate portion represents an individual`s view of the knowledge domain. Representation of multiple and varying perspectives may add to the existing knowledge as well as reveal paths to additional knowledge. A simple example is presented where perspectives are used to represent game playing strategies and levels of expertise in those strategies. Players` perspectives are adapted and changed to provide additional knowledge and insight into further game playing strategies. Results show improvement in the playing of the games. Additionally, a more complex problem for applying these techniques is introduced.

  16. Adaptive Evolution of Gene Expression in Drosophila

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    Armita Nourmohammad

    2017-08-01

    Full Text Available Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.

  17. Directed evolution of adaptive traits

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    As a species, switchgrass is adapted to an amazingly broad range of environments, spanning hardiness zones ranging from HZ3 to HZ9 (Canada to Mexico), from the mid-grass prairie to the Atlantic Seaboard, from sandy soils to heavy clay soils, from acid to alkaline soils, and from wetland to dryland h...

  18. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    OpenAIRE

    Dixon, JL; Stringer, LC; Challinor, AJ

    2014-01-01

    Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1) similar trends in farming system evolution have had diff...

  19. Adaptive genic evolution in the Drosophila genomes

    DEFF Research Database (Denmark)

    Shapiro, Joshua A; Huang, Wei; Zhang, Chenhui

    2007-01-01

    . melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss......Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large...... sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species...

  20. Facilitated variation: how evolution learns from past environments to generalize to new environments.

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    Merav Parter

    2008-11-01

    Full Text Available One of the striking features of evolution is the appearance of novel structures in organisms. Recently, Kirschner and Gerhart have integrated discoveries in evolution, genetics, and developmental biology to form a theory of facilitated variation (FV. The key observation is that organisms are designed such that random genetic changes are channeled in phenotypic directions that are potentially useful. An open question is how FV spontaneously emerges during evolution. Here, we address this by means of computer simulations of two well-studied model systems, logic circuits and RNA secondary structure. We find that evolution of FV is enhanced in environments that change from time to time in a systematic way: the varying environments are made of the same set of subgoals but in different combinations. We find that organisms that evolve under such varying goals not only remember their history but also generalize to future environments, exhibiting high adaptability to novel goals. Rapid adaptation is seen to goals composed of the same subgoals in novel combinations, and to goals where one of the subgoals was never seen in the history of the organism. The mechanisms for such enhanced generation of novelty (generalization are analyzed, as is the way that organisms store information in their genomes about their past environments. Elements of facilitated variation theory, such as weak regulatory linkage, modularity, and reduced pleiotropy of mutations, evolve spontaneously under these conditions. Thus, environments that change in a systematic, modular fashion seem to promote facilitated variation and allow evolution to generalize to novel conditions.

  1. Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus

    DEFF Research Database (Denmark)

    Casey, John R; Mardinoglu, Adil; Nielsen, Jens

    2016-01-01

    Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture and ...... and an extremely high proportion of essential metabolic genes (47%; defined as the percentage of lethal in silico gene knockouts). These strategies are examples of nutrient-controlled adaptive evolution and confer a dramatic growth rate advantage to MED4 in phosphorus-limited regions. ...

  2. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    Directory of Open Access Journals (Sweden)

    Jami L. Dixon

    2014-02-01

    Full Text Available Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1 similar trends in farming system evolution have had differential impacts on the diversity of farming systems; (2 trends have contributed to the erosion of informal social and cultural institutions and an increasing dependence on formal institutions; and (3 trade-offs between components of adaptive capacity are made at the farm-scale, thus influencing farming system adaptive capacity. To identify the actual impacts of future climate change and variability, it is important to recognize the dynamic nature of adaptation. In practice, areas identified for further adaptation support include: shift away from one-size-fits-all approach the identification and integration of appropriate modern farming method; a greater focus on building inclusive formal and informal institutions; and a more nuanced understanding regarding the roles and decision-making processes of influential, but external, actors. More research is needed to understand farm-scale trade-offs and the resulting impacts across spatial and temporal scales.

  3. Adapting Digital Libraries to Continual Evolution

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    Barkstrom, Bruce R.; Finch, Melinda; Ferebee, Michelle; Mackey, Calvin

    2002-01-01

    In this paper, we describe five investment streams (data storage infrastructure, knowledge management, data production control, data transport and security, and personnel skill mix) that need to be balanced against short-term operating demands in order to maximize the probability of long-term viability of a digital library. Because of the rapid pace of information technology change, a digital library cannot be a static institution. Rather, it has to become a flexible organization adapted to continuous evolution of its infrastructure.

  4. Adaptive Prediction Error Coding in the Human Midbrain and Striatum Facilitates Behavioral Adaptation and Learning Efficiency.

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    Diederen, Kelly M J; Spencer, Tom; Vestergaard, Martin D; Fletcher, Paul C; Schultz, Wolfram

    2016-06-01

    Effective error-driven learning benefits from scaling of prediction errors to reward variability. Such behavioral adaptation may be facilitated by neurons coding prediction errors relative to the standard deviation (SD) of reward distributions. To investigate this hypothesis, we required participants to predict the magnitude of upcoming reward drawn from distributions with different SDs. After each prediction, participants received a reward, yielding trial-by-trial prediction errors. In line with the notion of adaptive coding, BOLD response slopes in the Substantia Nigra/Ventral Tegmental Area (SN/VTA) and ventral striatum were steeper for prediction errors occurring in distributions with smaller SDs. SN/VTA adaptation was not instantaneous but developed across trials. Adaptive prediction error coding was paralleled by behavioral adaptation, as reflected by SD-dependent changes in learning rate. Crucially, increased SN/VTA and ventral striatal adaptation was related to improved task performance. These results suggest that adaptive coding facilitates behavioral adaptation and supports efficient learning. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution.

    Science.gov (United States)

    Schönknecht, Gerald; Weber, Andreas P M; Lercher, Martin J

    2014-01-01

    In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice-binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism. Editor's suggested further reading in BioEssays Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract. © 2014 WILEY Periodicals, Inc.

  6. Biodiversity, evolution and adaptation of cultivated crops.

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    Vigouroux, Yves; Barnaud, Adeline; Scarcelli, Nora; Thuillet, Anne-Céline

    2011-05-01

    The human diet depends on very few crops. Current diversity in these crops is the result of a long interaction between farmers and cultivated plants, and their environment. Man largely shaped crop biodiversity from the domestication period 12,000 B.P. to the development of improved varieties during the last century. We illustrate this process through a detailed analysis of the domestication and early diffusion of maize. In smallholder agricultural systems, farmers still have a major impact on crop diversity today. We review several examples of the major impact of man on current diversity. Finally, biodiversity is considered to be an asset for adaptation to current environmental changes. We describe the evolution of pearl millet in West Africa, where average rainfall has decreased over the last forty years. Diversity in cultivated varieties has certainly helped this crop to adapt to climate variation. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  7. Epistatic adaptive evolution of human color vision.

    Directory of Open Access Journals (Sweden)

    Shozo Yokoyama

    2014-12-01

    Full Text Available Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV-free retinal environment, the short wavelength-sensitive (SWS1 visual pigment in human (human S1 switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.

  8. Elongated polyproline motifs facilitate enamel evolution through matrix subunit compaction.

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    Tianquan Jin

    2009-12-01

    Full Text Available Vertebrate body designs rely on hydroxyapatite as the principal mineral component of relatively light-weight, articulated endoskeletons and sophisticated tooth-bearing jaws, facilitating rapid movement and efficient predation. Biological mineralization and skeletal growth are frequently accomplished through proteins containing polyproline repeat elements. Through their well-defined yet mobile and flexible structure polyproline-rich proteins control mineral shape and contribute many other biological functions including Alzheimer's amyloid aggregation and prolamine plant storage. In the present study we have hypothesized that polyproline repeat proteins exert their control over biological events such as mineral growth, plaque aggregation, or viscous adhesion by altering the length of their central repeat domain, resulting in dramatic changes in supramolecular assembly dimensions. In order to test our hypothesis, we have used the vertebrate mineralization protein amelogenin as an exemplar and determined the biological effect of the four-fold increased polyproline tandem repeat length in the amphibian/mammalian transition. To study the effect of polyproline repeat length on matrix assembly, protein structure, and apatite crystal growth, we have measured supramolecular assembly dimensions in various vertebrates using atomic force microscopy, tested the effect of protein assemblies on crystal growth by electron microscopy, generated a transgenic mouse model to examine the effect of an abbreviated polyproline sequence on crystal growth, and determined the structure of polyproline repeat elements using 3D NMR. Our study shows that an increase in PXX/PXQ tandem repeat motif length results (i in a compaction of protein matrix subunit dimensions, (ii reduced conformational variability, (iii an increase in polyproline II helices, and (iv promotion of apatite crystal length. Together, these findings establish a direct relationship between polyproline tandem

  9. Adaptive CGFs Based on Grammatical Evolution

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    Jian Yao

    2015-01-01

    Full Text Available Computer generated forces (CGFs play blue or red units in military simulations for personnel training and weapon systems evaluation. Traditionally, CGFs are controlled through rule-based scripts, despite the doctrine-driven behavior of CGFs being rigid and predictable. Furthermore, CGFs are often tricked by trainees or fail to adapt to new situations (e.g., changes in battle field or update in weapon systems, and, in most cases, the subject matter experts (SMEs review and redesign a large amount of CGF scripts for new scenarios or training tasks, which is both challenging and time-consuming. In an effort to overcome these limitations and move toward more true-to-life scenarios, a study using grammatical evolution (GE to generate adaptive CGFs for air combat simulations has been conducted. Expert knowledge is encoded with modular behavior trees (BTs for compatibility with the operators in genetic algorithm (GA. GE maps CGFs, represented with BTs to binary strings, and uses GA to evolve CGFs with performance feedback from the simulation. Beyond-visual-range air combat experiments between adaptive CGFs and nonadaptive baseline CGFs have been conducted to observe and study this evolutionary process. The experimental results show that the GE is an efficient framework to generate CGFs in BTs formalism and evolve CGFs via GA.

  10. WAKES: Wavelet Adaptive Kinetic Evolution Solvers

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    Mardirian, Marine; Afeyan, Bedros; Larson, David

    2016-10-01

    We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.

  11. A critical transition in leaf evolution facilitated the Cretaceous angiosperm revolution.

    Science.gov (United States)

    de Boer, Hugo Jan; Eppinga, Maarten B; Wassen, Martin J; Dekker, Stefan C

    2012-01-01

    The revolutionary rise of broad-leaved (flowering) angiosperm plant species during the Cretaceous initiated a global ecological transformation towards modern biodiversity. Still, the mechanisms involved in this angiosperm radiation remain enigmatic. Here we show that the period of rapid angiosperm evolution initiated after the leaf interior (post venous) transport path length for water was reduced beyond the leaf interior transport path length for CO2 at a critical leaf vein density of 2.5-5 mm mm(-2). Data and our modelling approaches indicate that surpassing this critical vein density was a pivotal moment in leaf evolution that enabled evolving angiosperms to profit from developing leaves with more and smaller stomata in terms of higher carbon returns from equal water loss. Surpassing the critical vein density may therefore have facilitated evolving angiosperms to develop leaves with higher gas exchange capacities required to adapt to the Cretaceous CO2 decline and outcompete previously dominant coniferous species in the upper canopy.

  12. Distributed representations accelerate evolution of adaptive behaviours.

    Directory of Open Access Journals (Sweden)

    James V Stone

    2007-08-01

    Full Text Available Animals with rudimentary innate abilities require substantial learning to transform those abilities into useful skills, where a skill can be considered as a set of sensory-motor associations. Using linear neural network models, it is proved that if skills are stored as distributed representations, then within-lifetime learning of part of a skill can induce automatic learning of the remaining parts of that skill. More importantly, it is shown that this "free-lunch" learning (FLL is responsible for accelerated evolution of skills, when compared with networks which either 1 cannot benefit from FLL or 2 cannot learn. Specifically, it is shown that FLL accelerates the appearance of adaptive behaviour, both in its innate form and as FLL-induced behaviour, and that FLL can accelerate the rate at which learned behaviours become innate.

  13. Non-adaptive speciation of snails by left-right reversal is facilitated on oceanic islands

    NARCIS (Netherlands)

    Hoso, M.

    2012-01-01

    The nearly neutral theory of molecular evolution predicts that small population size is essential for non-adaptive evolution. Evolution of whole-body left-right reversal in snails is generally a compelling example of non-adaptive speciation, because variants with reversed chirality would suffer from

  14. Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation.

    Science.gov (United States)

    Ford, Antonia G P; Rüber, Lukas; Newton, Jason; Dasmahapatra, Kanchon K; Balarin, John D; Bruun, Kristoffer; Day, Julia J

    2016-12-01

    Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype-environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large-scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  15. Pervasive Adaptive Evolution in Primate Seminal Proteins.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Seminal fluid proteins show striking effects on reproduction, involving manipulation of female behavior and physiology, mechanisms of sperm competition, and pathogen defense. Strong adaptive pressures are expected for such manifestations of sexual selection and host defense, but the extent of positive selection in seminal fluid proteins from divergent taxa is unknown. We identified adaptive evolution in primate seminal proteins using genomic resources in a tissue-specific study. We found extensive signatures of positive selection when comparing 161 human seminal fluid proteins and 2,858 prostate-expressed genes to those in chimpanzee. Seven of eight outstanding genes yielded statistically significant evidence of positive selection when analyzed in divergent primates. Functional clues were gained through divergent analysis, including several cases of species-specific loss of function in copulatory plug genes, and statistically significant spatial clustering of positively selected sites near the active site of kallikrein 2. This study reveals previously unidentified positive selection in seven primate seminal proteins, and when considered with findings in Drosophila, indicates that extensive positive selection is found in seminal fluid across divergent taxonomic groups.

  16. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes.

    Science.gov (United States)

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens .

  17. A proposal for amending administrative law to facilitate adaptive management

    Science.gov (United States)

    Craig, Robin K.; Ruhl, J.B.; Brown, Eleanor D.; Williams, Byron K.

    2017-01-01

    In this article we examine how federal agencies use adaptive management. In order for federal agencies to implement adaptive management more successfully, administrative law must adapt to adaptive management, and we propose changes in administrative law that will help to steer the current process out of a dead end. Adaptive management is a form of structured decision making that is widely used in natural resources management. It involves specific steps integrated in an iterative process for adjusting management actions as new information becomes available. Theoretical requirements for adaptive management notwithstanding, federal agency decision making is subject to the requirements of the federal Administrative Procedure Act, and state agencies are subject to the states' parallel statutes. We argue that conventional administrative law has unnecessarily shackled effective use of adaptive management. We show that through a specialized 'adaptive management track' of administrative procedures, the core values of administrative law—especially public participation, judicial review, and finality— can be implemented in ways that allow for more effective adaptive management. We present and explain draft model legislation (the Model Adaptive Management Procedure Act) that would create such a track for the specific types of agency decision making that could benefit from adaptive management.

  18. A proposal for amending administrative law to facilitate adaptive management

    Science.gov (United States)

    Craig, Robin K.; Ruhl, J. B.; Brown, Eleanor D.; Williams, Byron K.

    2017-07-01

    In this article we examine how federal agencies use adaptive management. In order for federal agencies to implement adaptive management more successfully, administrative law must adapt to adaptive management, and we propose changes in administrative law that will help to steer the current process out of a dead end. Adaptive management is a form of structured decision making that is widely used in natural resources management. It involves specific steps integrated in an iterative process for adjusting management actions as new information becomes available. Theoretical requirements for adaptive management notwithstanding, federal agency decision making is subject to the requirements of the federal Administrative Procedure Act, and state agencies are subject to the states’ parallel statutes. We argue that conventional administrative law has unnecessarily shackled effective use of adaptive management. We show that through a specialized ‘adaptive management track’ of administrative procedures, the core values of administrative law—especially public participation, judicial review, and finality— can be implemented in ways that allow for more effective adaptive management. We present and explain draft model legislation (the Model Adaptive Management Procedure Act) that would create such a track for the specific types of agency decision making that could benefit from adaptive management.

  19. Key issues review: evolution on rugged adaptive landscapes

    Science.gov (United States)

    Obolski, Uri; Ram, Yoav; Hadany, Lilach

    2018-01-01

    Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.

  20. La recherche-action participative facilite l'adaptation aux ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    15 mai 2012 ... Les travaux de recherche menés dans le cadre du programme Adaptation aux changements climatiques en Afrique (ACCA) ont exploré des moyens d'améliorer la capacité des pays ... Impacts of climate change and variability, and adaptation strategies on agriculture in semi-arid areas of Tanzania.

  1. Extensive X-linked adaptive evolution in central chimpanzees

    DEFF Research Database (Denmark)

    Hvilsom, Christina; Qian, Yu; Bataillon, Thomas

    2012-01-01

    on the dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much...... as 30% of all amino acid replacements being adaptive. Adaptive evolution is barely detectable on the autosomes except for a few striking cases of recent selective sweeps associated with immunity gene clusters. We also find much stronger purifying selection than observed in humans, and in contrast...

  2. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    National Research Council Canada - National Science Library

    Jami L Dixon; Lindsay C Stringer; Andrew J Challinor

    2014-01-01

    .... We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations...

  3. Evolution of adaptive phenotypic traits without positive Darwinian selection.

    Science.gov (United States)

    Hughes, A L

    2012-04-01

    Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

  4. Cellular adaptation facilitates sparse and reliable coding in sensory pathways.

    Science.gov (United States)

    Farkhooi, Farzad; Froese, Anja; Muller, Eilif; Menzel, Randolf; Nawrot, Martin P

    2013-01-01

    Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. It is unclear how this phenomenon affects stimulus coding in the later stages of sensory processing. Here, we show that a temporally sparse and reliable stimulus representation develops naturally in sequential stages of a sensory network with adapting neurons. As a modeling framework we employ a mean-field approach together with an adaptive population density treatment, accompanied by numerical simulations of spiking neural networks. We find that cellular adaptation plays a critical role in the dynamic reduction of the trial-by-trial variability of cortical spike responses by transiently suppressing self-generated fast fluctuations in the cortical balanced network. This provides an explanation for a widespread cortical phenomenon by a simple mechanism. We further show that in the insect olfactory system cellular adaptation is sufficient to explain the emergence of the temporally sparse and reliable stimulus representation in the mushroom body. Our results reveal a generic, biophysically plausible mechanism that can explain the emergence of a temporally sparse and reliable stimulus representation within a sequential processing architecture.

  5. Not different, Just Better: The Adaptive Evolution of an Enzyme

    Science.gov (United States)

    2015-12-20

    specialists and enzyme evolution . Beijing Normal University workshop on microbial ecology . Renwick Dobson (2014) Not different, just better: the... ecology . 15) Renwick Dobson (2014) Not different, just better: the adaptive evolution of a glycolytic enzyme. Canberra, Australia: COMBIO2014, 28...pyruvate kinase found in Richard Lenski’s E. coli long- term evolution experiment. We have demonstrated, for the first time, that all the pykF mutations

  6. How psychological resources facilitate adaptation to organizational change

    NARCIS (Netherlands)

    van den Heuvel, M.; Demerouti, E.; Bakker, A.B.

    2014-01-01

    The purpose of this 1-year follow-up study among 580 police officers is to investigate whether identity-related resources are positively related to adaptive behaviour during times of organizational change. Combining the social identity perspective with resources theories, we hypothesized that

  7. Differential Evolution for Many-Particle Adaptive Quantum Metrology

    NARCIS (Netherlands)

    Lovett, N.B.; Crosnier, C.; Perarnau- Llobet, M.; Sanders, B.

    2013-01-01

    We devise powerful algorithms based on differential evolution for adaptive many-particle quantum metrology. Our new approach delivers adaptive quantum metrology policies for feedback control that are orders-of-magnitude more efficient and surpass the few-dozen-particle limitation arising in methods

  8. Urban Evolution: The Role of Water and Adaptation

    Science.gov (United States)

    Kaushal, S.

    2015-12-01

    The structure, function, and services of urban ecosystems evolve over time scales from seconds to centuries as Earth's population grows, infrastructure ages, and management decisions alter them. The concept of "urban evolution" was proposed in order to study changes in urban ecosystems over time. Urban evolution has exerted a major influence on Earth's water and elemental cycles from local to global scales over human history. A current understanding of urban evolution allows urban planning, management, and restoration to move beyond reactive management to predictive management. We explore two key mechanisms of urban evolution, urban selective pressure and adaptation, and their relationship to the evolution of modern water and biogeochemical cycles. Urban selective pressure is an environmental or societal driver contributing to urban adaptation. Urban adaptation is the sequential process by which an urban structure, function, or services becomes more fitted to its changing environment or human choices. We show how hydrological and biogeochemical traits evolve across successive generations of urban ecosystems via shifts in selective pressures and adaptations. We also discuss how urban evolution can be divided into distinct stages and transition periods of growth and expansion and decay and repair during the Anthropocene epoch. We explore multiple examples and drivers of urban evolution and adaptations including the role of unintended consequences and societal drivers. We also present a conceptual model for the evolution of urban waters from the Industrial Revolution to the present day emphasizing the role of urban adaptations in response to selective pressures. Finally, we conclude by proposing new concepts and questions for future research related to the urban evolution of water, material, and energy cycles.

  9. Genetic correlations: transient truths of adaptive evolution

    Indian Academy of Sciences (India)

    Unknown

    remains as to whether, genetic correlations among traits are really consistent ... Keywords. genetic architecture; life history; experimental evolution; genetic correlations; genotype × environment interaction; stress resistance; Drosophila ... result from linkage disequilibrium, inbreeding depression, or selection. However, the ...

  10. A Model for Designing Adaptive Laboratory Evolution Experiments

    DEFF Research Database (Denmark)

    LaCroix, Ryan A.; Palsson, Bernhard O.; Feist, Adam M.

    2017-01-01

    The occurrence of mutations is a cornerstone of the evolutionary theory of adaptation, capitalizing on the rare chance that a mutation confers a fitness benefit. Natural selection is increasingly being leveraged in laboratory settings for industrial and basic science applications. Despite...... increasing deployment, there are no standardized procedures available for designing and performing adaptive laboratory evolution (ALE) experiments. Thus, there is a need to optimize the experimental design, specifically for determining when to consider an experiment complete and for balancing outcomes...... adaptive laboratory evolution can achieve....

  11. La recherche-action participative facilite l'adaptation aux ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    15 mai 2012 ... Ces travaux comprenaient un riche portefeuille de recherches sur l'adaptation aux changements climatiques dans le secteur de l'agriculture. La méthodologie privilégiée dans le cadre du programme, la recherche-action participative, s'est avérée fructueuse et a permis de mettre au point et de déployer des ...

  12. Fitness seascapes and adaptive evolution of the influenza virus

    Science.gov (United States)

    Lassig, Michael

    2014-03-01

    The seasonal human influenza A virus undergoes rapid genome evolution. This process is triggered by interactions with the host immune system and produces significant year-to-year sequence turnover in the population of circulating viral strains. We develop a dynamical fitness model that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a viral strain: adaptive changes, which are under positive selection, and deleterious mutations, which affect conserved viral functions such as protein stability. Combined with the influenza strain tree, this fitness model maps the adaptive history of influenza A. We discuss the implications of our results for the statistical theory of adaptive evolution in asexual populations. Based on this and related systems, we touch upon the fundamental question of when evolution can be predicted. Joint work with Marta Luksza, Columbia University.

  13. Evolution and adaptation of Pseudomonas aeruginosa in cystic fibrosis airways

    DEFF Research Database (Denmark)

    Madsen Sommer, Lea Mette

    adaptational patterns.However, the genetic overlap between CF and PCD isolates did not extend to a phenotypic overlap, which indicates that the mucus, which is different in CF patients compared to PCD patients, is a significant selective factor for the evolution and adaptation of P. aeruginosa...... of evolution to these observations, this thesis shows that collections of longitudinal P. aeruginosa isolates from CF patients provide a valuable basis for the study of adaptation and evolution in natural environments....... laboratory experiments, with a high degree of control and rigour. But to truly understand evolution and the complex mechanisms it deploys, it is necessary to combine the laboratory learnings with investigations of natural systems. –Though, this can be tricky. Because of the heterogeneity and constant change...

  14. Improving cellulase production by Aspergillus niger using adaptive evolution.

    Science.gov (United States)

    Patyshakuliyeva, Aleksandrina; Arentshorst, Mark; Allijn, Iris E; Ram, Arthur F J; de Vries, Ronald P; Gelber, Isabelle Benoit

    2016-06-01

    To evaluate the potential of adaptive evolution as a tool in generating strains with an improved production of plant biomass degrading enzymes. An Aspergillus niger cellulase mutant was obtained by adaptive evolution. Physiological properties of this mutant revealed a five times higher cellulose production than the parental strain. Transcriptomic analysis revealed that the expression of noxR, encoding the regulatory subunit of the NADPH oxidase complex, was reduced in the mutant compared to the parental strain. Subsequent analysis of a noxR knockout strain showed the same phenotypic effect as observed for the evolution mutant, confirming the role of NoxR in cellulose degradation. Adaptive evolution is an efficient approach to modify a strain and activate genes involved in polysaccharide degradation.

  15. Facilitating climate change adaptation through communication: Insights from the development of a visualization tool

    DEFF Research Database (Denmark)

    Glaas, Erik; Ballantyne, Anne Gammelgaard; Neset, Tina

    2015-01-01

    Climate change communication on anticipated impacts and adaptive responses is frequently presented as an effective means to facilitate implementation of adaptation to mitigate risks to residential buildings. However, it requires that communication is developed in a way that resonates with the con......Climate change communication on anticipated impacts and adaptive responses is frequently presented as an effective means to facilitate implementation of adaptation to mitigate risks to residential buildings. However, it requires that communication is developed in a way that resonates...... with the context of the target audience, provides intelligible information and addresses perceived barriers to adaptation. In this paper we reflect upon criteria for useful climate change communication gained over a three year development process of a web-based tool - VisAdaptTM – aimed at increasing the adaptive...

  16. Stochastic Evolution Equations with Adapted Drift

    NARCIS (Netherlands)

    Pronk, M.

    2013-01-01

    In this thesis we study stochastic evolution equations in Banach spaces. We restrict ourselves to the two following cases. First, we consider equations in which the drift is a closed linear operator that depends on time and is random. Such equations occur as mathematical models in for instance

  17. Adaptive laboratory evolution – principles and applications for biotechnology

    Science.gov (United States)

    2013-01-01

    Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

  18. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

    Science.gov (United States)

    Covert, Arthur W.; Lenski, Richard E.; Wilke, Claus O.; Ofria, Charles

    2013-01-01

    Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions. PMID:23918358

  19. When do adaptive plasticity and genetic evolution prevent extinction of a density-regulated population?

    Science.gov (United States)

    Chevin, Luis-Miguel; Lande, Russell

    2010-04-01

    We study the dynamics of evolutionary recovery after an abrupt environmental shift in a density-regulated population with evolving plasticity. Maladaptation to the new environment initially causes the population to decline, until adaptive phenotypic plasticity and genetic evolution restore positive population growth rate. We assume that selection on a quantitative trait is density-independent and that the initial cost of plasticity is much lower than the benefit of the initial plastic response. The initial partially adaptive plasticity reduces the effective magnitude of the environmental shift, whereas evolution of plasticity increases the rate of adaptation. Both effects greatly facilitate population persistence. In contrast, density dependence of population growth always hinders persistence. With theta-logistic population regulation, a lower value of theta produces a faster initial population decline and a higher extinction risk.

  20. An Adaptive Unified Differential Evolution Algorithm for Global Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Qiang, Ji; Mitchell, Chad

    2014-11-03

    In this paper, we propose a new adaptive unified differential evolution algorithm for single-objective global optimization. Instead of the multiple mutation strate- gies proposed in conventional differential evolution algorithms, this algorithm employs a single equation unifying multiple strategies into one expression. It has the virtue of mathematical simplicity and also provides users the flexibility for broader exploration of the space of mutation operators. By making all control parameters in the proposed algorithm self-adaptively evolve during the process of optimization, it frees the application users from the burden of choosing appro- priate control parameters and also improves the performance of the algorithm. In numerical tests using thirteen basic unimodal and multimodal functions, the proposed adaptive unified algorithm shows promising performance in compari- son to several conventional differential evolution algorithms.

  1. The stochastic edge in adaptive evolution

    OpenAIRE

    Brunet, Éric; Rouzine, Igor M.; Wilke, Claus O

    2007-01-01

    In a recent article, Desai and Fisher (2007) proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the population. Desai and Fisher perform an elaborate stochastic calculation of the mean time $\\tau$ until a new class of mutants has been established, and interpret $1/\\tau$ as the sp...

  2. Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods

    OpenAIRE

    Klug Christian; De Baets Kenneth; Monnet Claude

    2011-01-01

    Abstract Background A major goal in evolutionary biology is to understand the processes that shape the evolutionary trajectory of clades. The repeated and similar large-scale morphological evolutionary trends of distinct lineages suggest that adaptation by means of natural selection (functional constraints) is the major cause of parallel evolution, a very common phenomenon in extinct and extant lineages. However, parallel evolution can result from other processes, which are usually ignored or...

  3. Evolution of morphological and climatic adaptations in Veronica L. (Plantaginaceae

    Directory of Open Access Journals (Sweden)

    Jian-Cheng Wang

    2016-08-01

    Full Text Available Perennials and annuals apply different strategies to adapt to the adverse environment, based on ‘tolerance’ and ‘avoidance’, respectively. To understand lifespan evolution and its impact on plant adaptability, we carried out a comparative study of perennials and annuals in the genus Veronica from a phylogenetic perspective. The results showed that ancestors of the genus Veronicawere likely to be perennial plants. Annual life history of Veronica has evolved multiple times and subtrees with more annual species have a higher substitution rate. Annuals can adapt to more xeric habitats than perennials. This indicates that annuals are more drought-resistant than their perennial relatives. Due to adaptation to similar selective pressures, parallel evolution occurs in morphological characters among annual species of Veronica.

  4. Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

    Science.gov (United States)

    Marsh, Joseph A.; Teichmann, Sarah A.

    2014-01-01

    The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes. We find that flexibility appears to be particularly conducive to the formation of heterologous (i.e., asymmetric) intersubunit interfaces. This leads to a strong association between subunit flexibility and homomeric complexes with cyclic and asymmetric quaternary structure topologies. Similarly, we also observe that the more nonhomologous subunits that assemble together within a complex, the more flexible those subunits tend to be. Importantly, these findings suggest that subunit flexibility should be closely related to the evolutionary history of a complex. We confirm this by showing that evolutionarily more recent subunits are generally more flexible than evolutionarily older subunits. Finally, we investigate the very different explorations of quaternary structure space that have occurred in different evolutionary lineages. In particular, the increased flexibility of eukaryotic proteins appears to enable the assembly of heteromeric complexes with more unique components. PMID:24866000

  5. Identification of genes that have undergone adaptive evolution in ...

    African Journals Online (AJOL)

    Cassava (Manihot esculenta) is a vital food security crop and staple in Africa, yet cassava brown streak disease (CBSD) and cassava mosaic disease result in substantial yield losses. The aim of this study was to identify genes that have undergone positive selection during adaptive evolution, from CBSD resistant, tolerant ...

  6. An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism

    DEFF Research Database (Denmark)

    Zhang, Tian; Tremblay, Pier-Luc

    2018-01-01

    Adaptive laboratory evolution (ALE) is an approach enabling the development of novel characteristics in microbial strains via the application of a constant selection pressure. This method is also an efficient tool to acquire insights on molecular mechanisms responsible for specific phenotypes. ALE...

  7. The rule of declining adaptability in microbial evolution experiments

    Directory of Open Access Journals (Sweden)

    Alejandro eCouce

    2015-03-01

    Full Text Available One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss this possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research.

  8. The adaptive evolution of the mammalian mitochondrial genome

    Directory of Open Access Journals (Sweden)

    O'Brien Stephen J

    2008-03-01

    Full Text Available Abstract Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas. Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.

  9. Quantifying adaptive evolution in the Drosophila immune system.

    Directory of Open Access Journals (Sweden)

    Darren J Obbard

    2009-10-01

    Full Text Available It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host-parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host-parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution.

  10. High rate of adaptive evolution in two widespread European pines.

    Science.gov (United States)

    Grivet, Delphine; Avia, Komlan; Vaattovaara, Aleksia; Eckert, Andrew J; Neale, David B; Savolainen, Outi; González-Martínez, Santiago C

    2017-11-07

    Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the Distribution of Fitness Effects (DFE), were similar across species, and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not differentially affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  11. Adaptive evolution of conserved noncoding elements in mammals.

    Directory of Open Access Journals (Sweden)

    Su Yeon Kim

    2007-09-01

    Full Text Available Conserved noncoding elements (CNCs are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the "shared rates test" to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that approximately 68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining approximately 32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.

  12. What facilitates adaptation? An analysis of community-based adaptation to environmental change in the Andes

    Directory of Open Access Journals (Sweden)

    Felipe Murtinho

    2016-02-01

    Full Text Available This study analyses the environmental, socio-economic andinstitutional factors that influence community-based adaptation strategies in 16municipalities in the rural Andes of Colombia. The study focuses specifically onthe factors that influence whether communities decide to take measures to managetheir water and micro-watersheds in response to water scarcity caused by climatevariability and land-use changes. The research uses quantitative and qualitativemethods incorporating data from surveys to 104 water user associations,precipitation and land-use data, municipal socio-economic information, and semistructured interviews with key informants. The results reveal 1 the links betweenenvironmental change and the type of adaptation that communities implement,and 2 how, in face of water scarcity changes, external funding facilitatesadaptation. The findings of this study contributes to the common-pool resourceand adaptation literatures by highlighting the important role that external actorsmay have in shaping collective action to adapt to environmental change.

  13. Adaptive Game Level Creation through Rank-based Interactive Evolution

    DEFF Research Database (Denmark)

    Liapis, Antonios; Martínez, Héctor Pérez; Togelius, Julian

    2013-01-01

    This paper introduces Rank-based Interactive Evolution (RIE) which is an alternative to interactive evolution driven by computational models of user preferences to generate personalized content. In RIE, the computational models are adapted to the preferences of users which, in turn, are used...... as fitness functions for the optimization of the generated content. The preference models are built via ranking-based preference learning, while the content is generated via evolutionary search. The proposed method is evaluated on the creation of strategy game maps, and its performance is tested using...

  14. Chromosomal Translocations in Black Flies (Diptera: Simuliidae-Facilitators of Adaptive Radiation?

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    Peter H Adler

    Full Text Available A macrogenomic investigation of a Holarctic clade of black flies-the Simulium cholodkovskii lineage-provided a platform to explore the implications of a unique, synapomorphic whole-arm interchange in the evolution of black flies. Nearly 60 structural rearrangements were discovered in the polytene complement of the lineage, including 15 common to all 138 analyzed individuals, relative to the central sequence for the entire subgenus Simulium. Three species were represented, of which two Palearctic entities (Simulium cholodkovskii and S. decimatum were sympatric; an absence of hybrids confirmed their reproductive isolation. A third (Nearctic entity had nonhomologous sex chromosomes, relative to the other species, and is considered a separate species, for which the name Simulium nigricoxum is revalidated. A cytophylogeny is inferred and indicates that the two Palearctic taxa are sister species and these, in turn, are the sister group of the Nearctic species. The rise of the S. cholodkovskii lineage encompassed complex chromosomal and genomic restructuring phenomena associated with speciation in black flies, viz. expression of one and the same rearrangement as polymorphic, fixed, or sex linked in different species; taxon-specific differentiation of sex chromosomes; and reciprocal translocation of chromosome arms. The translocation is hypothesized to have occurred early in male spermatogonia, with the translocated chromosomal complement being transmitted to the X- and Y-bearing sperm during spermatogenesis, resulting in alternate disjunction of viable F1 translocation heterozygotes and the eventual formation of more viable and selectable F2 translocation homozygous progeny. Of 11 or 12 independently derived whole-arm interchanges known in the family Simuliidae, at least six are associated with subsequent speciation events, suggesting a facilitating role of translocations in adaptive radiations. The findings are discussed in the context of potential

  15. Evolution of plasticity and adaptive responses to climate change along climate gradients.

    Science.gov (United States)

    Kingsolver, Joel G; Buckley, Lauren B

    2017-08-16

    The relative contributions of phenotypic plasticity and adaptive evolution to the responses of species to recent and future climate change are poorly understood. We combine recent (1960-2010) climate and phenotypic data with microclimate, heat balance, demographic and evolutionary models to address this issue for a montane butterfly, Colias eriphyle , along an elevational gradient. Our focal phenotype, wing solar absorptivity, responds plastically to developmental (pupal) temperatures and plays a central role in thermoregulatory adaptation in adults. Here, we show that both the phenotypic and adaptive consequences of plasticity vary with elevation. Seasonal changes in weather generate seasonal variation in phenotypic selection on mean and plasticity of absorptivity, especially at lower elevations. In response to climate change in the past 60 years, our models predict evolutionary declines in mean absorptivity (but little change in plasticity) at high elevations, and evolutionary increases in plasticity (but little change in mean) at low elevation. The importance of plasticity depends on the magnitude of seasonal variation in climate relative to interannual variation. Our results suggest that selection and evolution of both trait means and plasticity can contribute to adaptive response to climate change in this system. They also illustrate how plasticity can facilitate rather than retard adaptive evolutionary responses to directional climate change in seasonal environments. © 2017 The Author(s).

  16. Evolution of Adaptive Immune Recognition in Jawless Vertebrates

    OpenAIRE

    Saha, Nil Ratan; Smith, Jeramiah; Amemiya, Chris T.

    2010-01-01

    All extant vertebrates possess an adaptive immune system wherein diverse immune receptors are created and deployed in specialized blood cell lineages. Recent advances in DNA sequencing and developmental resources for basal vertebrates have facilitated numerous comparative analyses that have shed new light on the molecular and cellular bases of immune defense and the mechanisms of immune receptor diversification in the “jawless” vertebrates. With data from these key species in hand, it is beco...

  17. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes

    OpenAIRE

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae t...

  18. Have superfetation and matrotrophy facilitated the evolution of larger offspring in poeciliid fishes?

    Science.gov (United States)

    Olivera-Tlahuel, Claudia; Ossip-Klein, Alison G.; Espinosa-Pérez, Héctor S.; Zúñiga-Vega, J. Jaime

    2015-01-01

    Superfetation is the ability of females to simultaneously carry multiple broods of embryos, with each brood at a different developmental stage. Matrotrophy is the post-fertilization maternal provisioning of nutrients to developing embryos throughout gestation. Several studies have demonstrated that, in viviparous fishes, superfetation and matrotrophy have evolved in a correlated way, such that species capable of bearing several simultaneous broods also exhibit advanced degrees of post-fertilization provisioning. The adaptive value of the concurrent presence of both reproductive modes may be associated with the production of larger newborns, which in turn may result in enhanced offspring fitness. In this study, we tested two hypotheses: (1) species with superfetation and moderate or extensive matrotrophy give birth to larger offspring compared to species without superfetation or matrotrophy; (2) species with higher degrees of superfetation and matrotrophy (i.e. more simultaneous broods and increased amounts of post-fertilization provisioning) give birth to larger offspring compared to species with relatively low degrees of superfetation and matrotrophy (i.e. fewer simultaneous broods and lesser amounts of post-fertilization provisioning). Using different phylogenetic comparative methods and data on 44 species of viviparous fishes of the family Poeciliidae, we found a lack of association between offspring size and the combination of superfetation and matrotrophy. Therefore, the concurrent presence of superfetation and moderate or extensive matrotrophy has not facilitated the evolution of larger offspring. In fact, these traits have evolved differently. Superfetation and matrotrophy have accumulated gradual changes that largely can be explained by Brownian motion, whereas offspring size has evolved fluidly, experiencing changes that likely resulted from selective responses to the local conditions. PMID:26617418

  19. Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

    Science.gov (United States)

    Colautti, Robert I; Lau, Jennifer A

    2015-05-01

    Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

  20. Episodic evolution and adaptation of chloroplast genomes in ancestral grasses.

    Directory of Open Access Journals (Sweden)

    Bojian Zhong

    Full Text Available BACKGROUND: It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution. METHODOLOGY/PRINCIPAL FINDINGS: By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches. CONCLUSIONS/SIGNIFICANCE: Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms.

  1. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.

    Science.gov (United States)

    Schönknecht, Gerald; Chen, Wei-Hua; Ternes, Chad M; Barbier, Guillaume G; Shrestha, Roshan P; Stanke, Mario; Bräutigam, Andrea; Baker, Brett J; Banfield, Jillian F; Garavito, R Michael; Carr, Kevin; Wilkerson, Curtis; Rensing, Stefan A; Gagneul, David; Dickenson, Nicholas E; Oesterhelt, Christine; Lercher, Martin J; Weber, Andreas P M

    2013-03-08

    Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.

  2. Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods

    Directory of Open Access Journals (Sweden)

    Klug Christian

    2011-04-01

    Full Text Available Abstract Background A major goal in evolutionary biology is to understand the processes that shape the evolutionary trajectory of clades. The repeated and similar large-scale morphological evolutionary trends of distinct lineages suggest that adaptation by means of natural selection (functional constraints is the major cause of parallel evolution, a very common phenomenon in extinct and extant lineages. However, parallel evolution can result from other processes, which are usually ignored or difficult to identify, such as developmental constraints. Hence, understanding the underlying processes of parallel evolution still requires further research. Results Herein, we present a possible case of parallel evolution between two ammonoid lineages (Auguritidae and Pinacitidae of Early-Middle Devonian age (405-395 Ma, which are extinct cephalopods with an external, chambered shell. In time and through phylogenetic order of appearance, both lineages display a morphological shift toward more involute coiling (i.e. more tightly coiled whorls, larger adult body size, more complex suture line (the folded walls separating the gas-filled buoyancy-chambers, and the development of an umbilical lid (a very peculiar extension of the lateral shell wall covering the umbilicus in the most derived taxa. Increased involution toward shells with closed umbilicus has been demonstrated to reflect improved hydrodynamic properties of the shell and thus likely results from similar natural selection pressures. The peculiar umbilical lid might have also added to the improvement of the hydrodynamic properties of the shell. Finally, increasing complexity of suture lines likely results from covariation induced by trends of increasing adult size and whorl overlap given the morphogenetic properties of the suture. Conclusions The morphological evolution of these two Devonian ammonoid lineages follows a near parallel evolutionary path for some important shell characters during several

  3. Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods.

    Science.gov (United States)

    Monnet, Claude; De Baets, Kenneth; Klug, Christian

    2011-04-29

    A major goal in evolutionary biology is to understand the processes that shape the evolutionary trajectory of clades. The repeated and similar large-scale morphological evolutionary trends of distinct lineages suggest that adaptation by means of natural selection (functional constraints) is the major cause of parallel evolution, a very common phenomenon in extinct and extant lineages. However, parallel evolution can result from other processes, which are usually ignored or difficult to identify, such as developmental constraints. Hence, understanding the underlying processes of parallel evolution still requires further research. Herein, we present a possible case of parallel evolution between two ammonoid lineages (Auguritidae and Pinacitidae) of Early-Middle Devonian age (405-395 Ma), which are extinct cephalopods with an external, chambered shell. In time and through phylogenetic order of appearance, both lineages display a morphological shift toward more involute coiling (i.e. more tightly coiled whorls), larger adult body size, more complex suture line (the folded walls separating the gas-filled buoyancy-chambers), and the development of an umbilical lid (a very peculiar extension of the lateral shell wall covering the umbilicus) in the most derived taxa. Increased involution toward shells with closed umbilicus has been demonstrated to reflect improved hydrodynamic properties of the shell and thus likely results from similar natural selection pressures. The peculiar umbilical lid might have also added to the improvement of the hydrodynamic properties of the shell. Finally, increasing complexity of suture lines likely results from covariation induced by trends of increasing adult size and whorl overlap given the morphogenetic properties of the suture. The morphological evolution of these two Devonian ammonoid lineages follows a near parallel evolutionary path for some important shell characters during several million years and through their phylogeny. Evolution

  4. Local adaptation of plant viruses: lessons from experimental evolution.

    Science.gov (United States)

    Elena, Santiago F

    2017-04-01

    For multihost pathogens, adaptation to multiple hosts has important implications for both applied and basic research. At the applied level, it is one of the main factors determining the probability and severity of emerging disease outbreaks. At the basic level, it is thought to be a key mechanism for the maintenance of genetic diversity both in host and pathogen species. In recent years, a number of evolution experiments have assessed the fate of plant virus populations replicating within and adapting to one single or to multiple hosts species. A first group of these experiments tackled the existence of trade-offs in fitness and virulence for viruses evolving either within a single hosts species or alternating between two different host species. A second set of experiments explored the role of genetic variability in susceptibility and resistance to infection among individuals from the same host species in the extent of virus local adaptation and of virulence. In general, when a single host species or genotype is available, these experiments show that local adaptation takes place, often but not always associated with a fitness trade-off. However, alternating between different host species or infecting resistant host genotypes may select for generalist viruses that experience no fitness cost. Therefore, the expected cost of generalism, arising from antagonistic pleiotropy and other genetic mechanisms generating fitness trade-offs between hosts, could not be generalized and strongly depend on the characteristics of each particular pathosystem. At the genomic level, these studies show pervasive convergent molecular evolution, suggesting that the number of accessible molecular pathways leading to adaptation to novel hosts is limited. © 2016 John Wiley & Sons Ltd.

  5. Functional constraints on adaptive evolution of protein ubiquitination sites.

    Science.gov (United States)

    Lu, Liang; Li, Yang; Liu, Zhongyang; Liang, Fengji; Guo, Feifei; Yang, Shuai; Wang, Dan; He, Yangzhige; Xiong, Jianghui; Li, Dong; He, Fuchu

    2017-01-05

    It is still unclear whether there exist functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. We tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated the evolutionary conservation of human ubiquitination sites in a broad evolutionary scale from G. gorilla to S. pombe, and we found that in organisms originated after the divergence of vertebrate, ubiquitination sites are more conserved than their flanking regions, while the opposite tendency is observed before this divergence time. By grouping the ubiquitination proteins into different functional categories, we confirm that many functional constraints like certain molecular functions, protein tissue expression specificity and protein connectivity in protein-protein interaction network enhance the evolutionary conservation of ubiquitination sites. Furthermore, by analyzing the gains of ubiquitination sites at different divergence time and their functional characters, we validate that the emergences of ubiquitination sites at different evolutionary time were also affected by the uncovered functional constraints. The above results suggest that functional constraints on the adaptive evolution of ubiquitination sites increase the opportunity for ubiquitination to synthetically regulate various cellular and developmental processes during evolution.

  6. Evolution of collective action in adaptive social structures.

    Science.gov (United States)

    Moreira, João A; Pacheco, Jorge M; Santos, Francisco C

    2013-01-01

    Many problems in nature can be conveniently framed as a problem of evolution of collective cooperative behaviour, often modelled resorting to the tools of evolutionary game theory in well-mixed populations, combined with an appropriate N-person dilemma. Yet, the well-mixed assumption fails to describe the population dynamics whenever individuals have a say in deciding which groups they will participate. Here we propose a simple model in which dynamical group formation is described as a result of a topological evolution of a social network of interactions. We show analytically how evolutionary dynamics under public goods games in finite adaptive networks can be effectively transformed into a N-Person dilemma involving both coordination and co-existence. Such dynamics would be impossible to foresee from more conventional 2-person interactions as well as from descriptions based on infinite, well-mixed populations. Finally, we show how stochastic effects help rendering cooperation viable, promoting polymorphic configurations in which cooperators prevail.

  7. Using REDD+ Policy to Facilitate Climate Adaptation at the Local Level: Synergies and Challenges in Vietnam

    Directory of Open Access Journals (Sweden)

    Pamela McElwee

    2016-12-01

    Full Text Available Attention has recently been paid to how REDD+ mitigation policies are integrated into other sectoral policies, particularly those dealing with climate adaptation at the national level. But there is less understanding of how subnational policy and local projects are able to incorporate attention to adaptation; therefore, we use a case study in Vietnam to discuss how REDD+ projects and policies address both concerns of mitigation and adaptation together at subnational levels. Through stakeholder interviews, focus groups, and household surveys in three provinces of Vietnam with REDD+ activities, our research sought to understand if REDD+ policies and projects on the ground acknowledge that climate change is likely to impact forests and forest users; if this knowledge is built into REDD+ policy and activities; how households in forested areas subject to REDD+ policy are vulnerable to climate change; and how REDD+ activities can help or hinder needed adaptations. Our findings indicate that there continues to be a lack of coordination between mitigation and adaptation policies in Vietnam, particularly with regard to REDD+. Policies for forest-based climate mitigation at the national and subnational level, as well as site-based projects, have paid little attention to the adaptation needs of local communities, many of whom are already suffering from noticeable weather changes in their localities, and there is insufficient discussion of how REDD+ activities could facilitate increased resilience. While there were some implicit and coincidental adaptation benefits of some REDD+ activities, most studied projects and policies did not explicitly target their activities to focus on adaptation or resilience, and in at least one case, negative livelihood impacts that have increased household vulnerability to climate change were documented. Key barriers to integration were identified, such as sectoral specialization; a lack of attention in REDD+ projects to

  8. Increased tolerance towards serine obtained by adaptive laboratory evolution

    DEFF Research Database (Denmark)

    Mundhada, Hemanshu; Seoane, Jose Miguel; Koza, Anna

    2014-01-01

    by glyA), the conversion of serine to pyruvate (encoded by sdaA, sdaB and tdcG) was also deleted. As expected, the resulting strain turned out to be susceptible to even low concentrations of serine in the media. In order to improve the tolerance of the strain towards serine, adaptive laboratory evolution...... was implemented using a state of the art robotics platform. The strain was grown under inhibiting concentrations of serine in minimal media and was periodically transferred to new media during mid log phase. After achieving a desired increase in growth rate, the concentration was serine was gradually increased...

  9. Competition and adaptation in an Internet evolution model.

    Science.gov (United States)

    Serrano, M Angeles; Boguñá, Marián; Díaz-Guilera, Albert

    2005-01-28

    We model the evolution of the Internet at the autonomous system level as a process of competition for users and adaptation of bandwidth capability. From a weighted network formalism, where both nodes and links are weighted, we find the exponent of the degree distribution as a simple function of the growth rates of the number of autonomous systems and connections in the Internet, both empirically measurable quantities. Our approach also accounts for a high level of clustering as well as degree-degree correlations, both with the same hierarchical structure present in the real Internet. Further, it also highlights the interplay between bandwidth, connectivity, and traffic of the network.

  10. Localizing recent adaptive evolution in the human genome

    DEFF Research Database (Denmark)

    Williamson, Scott H; Hubisz, Melissa J; Clark, Andrew G

    2007-01-01

    Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single......, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome......-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome...

  11. Adaptive Multiscale Modeling of Geochemical Impacts on Fracture Evolution

    Science.gov (United States)

    Molins, S.; Trebotich, D.; Steefel, C. I.; Deng, H.

    2016-12-01

    Understanding fracture evolution is essential for many subsurface energy applications, including subsurface storage, shale gas production, fracking, CO2 sequestration, and geothermal energy extraction. Geochemical processes in particular play a significant role in the evolution of fractures through dissolution-driven widening, fines migration, and/or fracture sealing due to precipitation. One obstacle to understanding and exploiting geochemical fracture evolution is that it is a multiscale process. However, current geochemical modeling of fractures cannot capture this multi-scale nature of geochemical and mechanical impacts on fracture evolution, and is limited to either a continuum or pore-scale representation. Conventional continuum-scale models treat fractures as preferential flow paths, with their permeability evolving as a function (often, a cubic law) of the fracture aperture. This approach has the limitation that it oversimplifies flow within the fracture in its omission of pore scale effects while also assuming well-mixed conditions. More recently, pore-scale models along with advanced characterization techniques have allowed for accurate simulations of flow and reactive transport within the pore space (Molins et al., 2014, 2015). However, these models, even with high performance computing, are currently limited in their ability to treat tractable domain sizes (Steefel et al., 2013). Thus, there is a critical need to develop an adaptive modeling capability that can account for separate properties and processes, emergent and otherwise, in the fracture and the rock matrix at different spatial scales. Here we present an adaptive modeling capability that treats geochemical impacts on fracture evolution within a single multiscale framework. Model development makes use of the high performance simulation capability, Chombo-Crunch, leveraged by high resolution characterization and experiments. The modeling framework is based on the adaptive capability in Chombo

  12. Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes).

    Science.gov (United States)

    Miwa, Hidetsugu; Odrzykoski, Ireneusz J; Matsui, Atsushi; Hasegawa, Masami; Akiyama, Hiroyuki; Jia, Yu; Sabirov, Renat; Takahashi, Hideki; Boufford, David E; Murakami, Noriaki

    2009-07-15

    An excess of nonsynonymous substitutions over synonymous ones has been regarded as an important indicator of adaptive evolution or positive selection at the molecular level. We now report such a case for rbcL sequences among cryptic species in Conocephalum (Hepaticae, Bryophytes). This finding can be regarded as evidence of adaptive evolution in several cryptic species (especially in F and JN types) within the genus. Bryophytes are small land plants with simple morphology. We can therefore expect the existence of several biologically distinct units or cryptic species within each morphological species. In our previous study, we found three rbcL types in Asian Conocephalum japonicum (Thunb.) Grolle and also found evidence strongly suggesting that the three types are reproductively isolated cryptic species. Additionally, we examined rbcL sequence variation in six cryptic species of C. conicum (L.) Dumort. previously recognized by allozyme analyses. As a result, we were able to discriminate the six cryptic species based only on their rbcL sequences. We were able to show that rbcL sequence variation is also useful in finding cryptic species of C. conicum.

  13. Adaptive evolution of the vertebrate skeletal muscle sodium channel

    Directory of Open Access Journals (Sweden)

    Jian Lu

    2011-01-01

    Full Text Available Tetrodotoxin (TTX is a highly potent neurotoxin that blocks the action potential by selectively binding to voltage-gated sodium channels (Na v. The skeletal muscle Na v (Na v1.4 channels in most pufferfish species and certain North American garter snakes are resistant to TTX, whereas in most mammals they are TTX-sensitive. It still remains unclear as to whether the difference in this sensitivity among the various vertebrate species can be associated with adaptive evolution. In this study, we investigated the adaptive evolution of the vertebrate Na v1.4 channels. By means of the CODEML program of the PAML 4.3 package, the lineages of both garter snakes and pufferfishes were denoted to be under positive selection. The positively selected sites identified in the p-loop regions indicated their involvement in Na v1.4 channel sensitivity to TTX. Most of these sites were located in the intracellular regions of the Na v1.4 channel, thereby implying the possible association of these regions with the regulation of voltage-sensor movement.

  14. Functional specialization in regulation and quality control in thermal adaptive evolution.

    Science.gov (United States)

    Yama, Kazuma; Matsumoto, Yuki; Murakami, Yoshie; Seno, Shigeto; Matsuda, Hideo; Gotoh, Kazuyoshi; Motooka, Daisuke; Nakamura, Shota; Ying, Bei-Wen; Yomo, Tetsuya

    2015-11-01

    Distinctive survival strategies, specialized in regulation and in quality control, were observed in thermal adaptive evolution with a laboratory Escherichia coli strain. The two specialists carried a single mutation either within rpoH or upstream of groESL, which led to the activated global regulation by sigma factor 32 or an increased amount of GroEL/ES chaperonins, respectively. Although both specialists succeeded in thermal adaptation, the common winner of the evolution was the specialist in quality control, that is, the strategy of chaperonin-mediated protein folding. To understand this evolutionary consequence, multilevel analyses of cellular status, for example, transcriptome, protein and growth fitness, were carried out. The specialist in quality control showed less change in transcriptional reorganization responding to temperature increase, which was consistent with the finding of that the two specialists showed the biased expression of molecular chaperones. Such repressed changes in gene expression seemed to be advantageous for long-term sustainability because a specific increase in chaperonins not only facilitated the folding of essential gene products but also saved cost in gene expression compared with the overall transcriptional increase induced by rpoH regulation. Functional specialization offered two strategies for successful thermal adaptation, whereas the evolutionary advantageous was more at the points of cost-saving in gene expression and the essentiality in protein folding. © 2015 The Authors. Genes to Cells published by Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  15. The evolution, maintenance and adaptive function of genetic colour polymorphism in birds.

    Science.gov (United States)

    Roulin, Alexandre

    2004-11-01

    The hypothesis that ornaments can honestly signal quality only if their expression is condition-dependent has dominated the study of the evolution and function of colour traits. Much less interest has been devoted to the adaptive function of colour traits for which the expression is not, or is to a low extent, sensitive to body condition and the environment in which individuals live. The aim of the present paper is to review the current theoretical and empirical knowledge of the evolution, maintenance and adaptive function of colour plumage traits for which the expression is mainly under genetic control. The finding that in many bird species the inheritance of colour morphs follows the laws of Mendel indicates that genetic colour polymorphism is frequent. Polymorphism may have evolved or be maintained because each colour morph facilitates the exploitation of alternative ecological niches as suggested by the observation that individuals are not randomly distributed among habitats with respect to coloration. Consistent with the hypothesis that different colour morphs are linked to alternative strategies is the finding that in a majority of species polymorphism is associated with reproductive parameters, and behavioural, life-history and physiological traits. Experimental studies showed that such covariations can have a genetic basis. These observations suggest that colour polymorphism has an adaptive function. Aviary and field experiments demonstrated that colour polymorphism is used as a criterion in mate-choice decisions and dominance interactions confirming the claim that conspecifics assess each other's colour morphs. The factors favouring the evolution and maintenance of genetic variation in coloration are reviewed, but empirical data are virtually lacking to assess their importance. Although current theory predicts that only condition-dependent traits can signal quality, the present review shows that genetically inherited morphs can reveal the same qualities

  16. Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae).

    Science.gov (United States)

    Schulenburg, Hinrich; Boehnisch, Claudia

    2008-04-19

    Lysozymes are important model enzymes in biomedical research with a ubiquitous taxonomic distribution ranging from phages up to plants and animals. Their main function appears to be defence against pathogens, although some of them have also been implicated in digestion. Whereas most organisms have only few lysozyme genes, nematodes of the genus Caenorhabditis possess a surprisingly large repertoire of up to 15 genes. We used phylogenetic inference and sequence analysis tools to assess the evolution of lysozymes from three congeneric nematode species, Caenorhabditis elegans, C. briggsae, and C. remanei. Their lysozymes fall into three distinct clades, one belonging to the invertebrate-type and the other two to the protist-type lysozymes. Their diversification is characterised by (i) ancestral gene duplications preceding species separation followed by maintenance of genes, (ii) ancestral duplications followed by gene loss in some of the species, and (iii) recent duplications after divergence of species. Both ancestral and recent gene duplications are associated in several cases with signatures of adaptive sequence evolution, indicating that diversifying selection contributed to lysozyme differentiation. Current data strongly suggests that genetic diversity translates into functional diversity. Gene duplications are a major source of evolutionary innovation. Our analysis provides an evolutionary framework for understanding the diversification of lysozymes through gene duplication and subsequent differentiation. This information is expected to be of major value in future analysis of lysozyme function and in studies of the dynamics of evolution by gene duplication.

  17. Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae

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    Boehnisch Claudia

    2008-04-01

    Full Text Available Abstract Background Lysozymes are important model enzymes in biomedical research with a ubiquitous taxonomic distribution ranging from phages up to plants and animals. Their main function appears to be defence against pathogens, although some of them have also been implicated in digestion. Whereas most organisms have only few lysozyme genes, nematodes of the genus Caenorhabditis possess a surprisingly large repertoire of up to 15 genes. Results We used phylogenetic inference and sequence analysis tools to assess the evolution of lysozymes from three congeneric nematode species, Caenorhabditis elegans, C. briggsae, and C. remanei. Their lysozymes fall into three distinct clades, one belonging to the invertebrate-type and the other two to the protist-type lysozymes. Their diversification is characterised by (i ancestral gene duplications preceding species separation followed by maintenance of genes, (ii ancestral duplications followed by gene loss in some of the species, and (iii recent duplications after divergence of species. Both ancestral and recent gene duplications are associated in several cases with signatures of adaptive sequence evolution, indicating that diversifying selection contributed to lysozyme differentiation. Current data strongly suggests that genetic diversity translates into functional diversity. Conclusion Gene duplications are a major source of evolutionary innovation. Our analysis provides an evolutionary framework for understanding the diversification of lysozymes through gene duplication and subsequent differentiation. This information is expected to be of major value in future analysis of lysozyme function and in studies of the dynamics of evolution by gene duplication.

  18. Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.

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    Minjun Yang

    Full Text Available Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC. Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

  19. Replicated evolution of integrated plastic responses during early adaptive divergence.

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    Parsons, Kevin J; Robinson, Beren W

    2006-04-01

    . Variation between ecomorphs and among lake populations in the covariance of plastic responses suggests the presence of genetic variation in plastic character responses. In three populations, open water ecomorphs also exhibited larger plastic responses to the environmental gradient than the local shallow water ecomorph. This could account for the greater integration of plastic responses in open water ecomorphs in two of the populations. This suggests that the plastic responses of local sunfish ecomorphs can diverge through changes in the magnitude and coordination of plastic responses. Although these results require further investigation, they suggest that early adaptive evolution in a novel environment can include changes to plastic character states. The genetic assimilation of coordinated plastic responses could result in the further, and possibly rapid, divergence of such populations and could also account for the evolution of genes of major effect that contribute to suites of phenotypic differences between divergent populations.

  20. Adaptive microclimatic evolution of the dehydrin 6 gene in wild barley at "Evolution Canyon", Israel.

    Science.gov (United States)

    Yang, Zujun; Zhang, Tao; Li, Guangrong; Nevo, Eviatar

    2011-12-01

    Dehydrins are one of the major stress-induced gene families, and the expression of dehydrin 6 (Dhn6) is strictly related to drought in barley. In order to investigate how the evolution of the Dhn6 gene is associated with adaptation to environmental changes, we examined 48 genotypes of wild barley, Hordeum spontaneum, from "Evolution Canyon" at Mount Carmel, Israel. The Dhn6 sequences of the 48 genotypes were identified, and a recent insertion of 342 bp at 5'UTR was found in the sequences of 11 genotypes. Both nucleotide and haplotype diversity of single nucleotide polymorphism in Dhn6 coding regions were higher on the AS ("African" slope or dry slope) than on the ES ("European" slope or humid slope), and the applied Tajima D and Fu-Li test rejected neutrality of SNP diversity. Expression analysis indicated that the 342 bp insertion at 5'UTR was associated with the earlier up-regulation of Dhn6 after dehydration. The genetic divergence of amino acids sequences indicated significant positive selection of Dhn6 among the wild barley populations. The diversity of Dhn6 in microclimatic divergence slopes suggested that Dhn6 has been subjected to natural selection and adaptively associated with drought resistance of wild barley at "Evolution Canyon".

  1. Comparative genomics reveals insights into avian genome evolution and adaptation

    Science.gov (United States)

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  2. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

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    Fei Shi

    2011-01-01

    Full Text Available Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions.

  3. A global analysis of adaptive evolution of operons in cyanobacteria.

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    Memon, Danish; Singh, Abhay K; Pakrasi, Himadri B; Wangikar, Pramod P

    2013-02-01

    Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.

  4. Adaptive Evolution of CENP-A in Percid Fishes

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    Harriet N. A. Abbey

    2015-07-01

    Full Text Available Centromeric protein A (CENP-A is the epigenetic determinant of centromeres. This protein has been shown to be adaptively evolving in a number of animal and plant species. In a previous communication we were able to demonstrate that signs of adaptive evolution were detected in the comparison of CENP-A sequences from three percid fish species. In this study we isolated the CENP-A gene from eight additional species from the Percidae family. With these sequences and those previously obtained, we carried out a more robust statistical analysis of codon specific positive selection in CENP-A coding sequences of eleven percid species. We were able to demonstrate that at least two amino acid positions within the N-terminal tail are under strong positive selection and that one of these positions is potentially a substrate for phosphorylation. While nonsynonymous substitutions were detected in the histone fold domain, these were not statistically supported as resulting from positive selection.

  5. Adaptive evolution of synthetic cooperating communities improves growth performance.

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    Xiaolin Zhang

    Full Text Available Symbiotic interactions between organisms are important for human health and biotechnological applications. Microbial mutualism is a widespread phenomenon and is important in maintaining natural microbial communities. Although cooperative interactions are prevalent in nature, little is known about the processes that allow their initial establishment, govern population dynamics and affect evolutionary processes. To investigate cooperative interactions between bacteria, we constructed, characterized, and adaptively evolved a synthetic community comprised of leucine and lysine Escherichia coli auxotrophs. The co-culture can grow in glucose minimal medium only if the two auxotrophs exchange essential metabolites - lysine and leucine (or its precursors. Our experiments showed that a viable co-culture using these two auxotrophs could be established and adaptively evolved to increase growth rates (by ∼3 fold and optical densities. While independently evolved co-cultures achieved similar improvements in growth, they took different evolutionary trajectories leading to different community compositions. Experiments with individual isolates from these evolved co-cultures showed that changes in both the leucine and lysine auxotrophs improved growth of the co-culture. Interestingly, while evolved isolates increased growth of co-cultures, they exhibited decreased growth in mono-culture (in the presence of leucine or lysine. A genome-scale metabolic model of the co-culture was also constructed and used to investigate the effects of amino acid (leucine or lysine release and uptake rates on growth and composition of the co-culture. When the metabolic model was constrained by the estimated leucine and lysine release rates, the model predictions agreed well with experimental growth rates and composition measurements. While this study and others have focused on cooperative interactions amongst community members, the adaptive evolution of communities with other

  6. Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

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    Machado João

    2011-11-01

    Full Text Available Abstract Background Matrix extracellular phosphoglycoprotein (MEPE belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia. The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates. Results Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree of evolutionary conservation of some coding and non-coding regions of the MEPE gene across mammals indicating a possible regulatory or functional role likely related with mineralization and/or phosphate regulation. However, the majority of the coding region had a fast evolutionary rate, particularly within the largest exon (1467 bp. Rodentia and Scandentia had distinct substitution rates with an increased accumulation of both synonymous and non-synonymous mutations compared with other mammalian lineages. Characteristics of the gene (e.g. biochemical, evolutionary rate, and intronic conservation differed greatly among lineages of the eight mammalian orders. We identified 20 sites with significant positive selection signatures (codon and protein level outside the main regulatory motifs (dentonin and ASARM suggestive of an adaptive role. Conversely, we find three sites under selection in the signal peptide and one in the ASARM motif that were supported by at least one selection model. The MEPE protein tends to accumulate amino acids promoting disorder and potential phosphorylation targets. Conclusion MEPE shows a high number of selection signatures, revealing the crucial role of positive selection in the

  7. Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes.

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    Masako Ogura

    2007-08-01

    Full Text Available Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such "Sel1-like repeat" (SLR genes ("slr genes". Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, dN/dS = omega > 1 were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117 from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (omegaJ > 25, whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.

  8. Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation.

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    Rane, Rahul V; Rako, Lea; Kapun, Martin; Lee, Siu F; Hoffmann, Ary A

    2015-05-01

    Chromosomal inversion polymorphisms are common in animals and plants, and recent models suggest that alternative arrangements spread by capturing different combinations of alleles acting additively or epistatically to favour local adaptation. It is also thought that inversions typically maintain favoured combinations for a long time by suppressing recombination between alternative chromosomal arrangements. Here, we consider patterns of linkage disequilibrium and genetic divergence in an old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known to be associated with climate change adaptation and a recent invasion event into Australia. We extracted, karyotyped and sequenced whole chromosomes from two Australian populations, so that changes in the arrangement of the alleles between geographically separated tropical and temperate areas could be compared. Chromosome-wide linkage disequilibrium (LD) analysis revealed strong LD within the region spanned by In(3R)Payne. This genomic region also showed strong differentiation between the tropical and the temperate populations, but no differentiation between different karyotypes from the same population, after controlling for chromosomal arrangement. Patterns of differentiation across the chromosome arm and in gene ontologies were enhanced by the presence of the inversion. These data support the notion that inversions are strongly selected by bringing together combinations of genes, but it is still not clear if such combinations act additively or epistatically. Our data suggest that climatic adaptation through inversions can be dynamic, reflecting changes in the relative abundance of different forms of an inversion and ongoing evolution of allelic content within an inversion. © 2015 John Wiley & Sons Ltd.

  9. Facilitating Adaptive Water Management Planning Using Scenarios That Illuminate Vulnerabilities (Invited)

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    Lempert, R. J.

    2013-12-01

    Fast changing and hard-to-predict future supply, demand, technology, regulatory, and other conditions present water managers with significant planning challenges. Adaptive plans, ones designed to evolve over time in response to new information, represent an obvious solution in principle, but are often to develop and implement in practice. This talk will describe the use analytic methods to facilitate the development of scenarios as part of a decision support process that leads to the development of adaptive water management plans. The scenarios are chosen to illuminate the vulnerabilities of proposed policies, that is, provide concise summaries of the future states of the world in which a proposed policy would fail to meet its goals. Such scenarios emerge from a decision support process that begins with a proposed policy, seeks to understand the conditions under which it would fail, and then uses this information to identify and evaluate potential alternative policies that are robust over a wide range of future conditions. Statistical cluster analyses applied to databases of simulation model results can help identify scenarios as part of this process. This talk will describe efforts to evaluate the ability of such scenarios to effectively communicate decision-relevant information, and describe how water management agencies have used them to develop robust, adaptive plans.

  10. Niche divergence facilitated by fine‐scale ecological partitioning in a recent cichlid fish adaptive radiation

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    Ford, Antonia G. P.; Rüber, Lukas; Newton, Jason; Dasmahapatra, Kanchon K.; Balarin, John D.; Bruun, Kristoffer; Day, Julia J.

    2016-01-01

    Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi. PMID:27659769

  11. Following a natural experiment of guideline adaptation and early implementation: a mixed-methods study of facilitation

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    Dogherty Elizabeth J

    2012-02-01

    Full Text Available Abstract Background Facilitation is emerging as an important strategy in the uptake of evidence. However, it is not entirely clear from a practical perspective how facilitation occurs to help move research evidence into nursing practice. The Canadian Partnership Against Cancer, also known as the 'Partnership,' is a Pan-Canadian initiative supporting knowledge translation activity for improved care through guideline use. In this case-series study, five self-identified groups volunteered to use a systematic methodology to adapt existing clinical practice guidelines for Canadian use. With 'Partnership' support, local and external facilitators provided assistance for groups to begin the process by adapting the guidelines and planning for implementation. Methods To gain a more comprehensive understanding of the nature of facilitation, we conducted a mixed-methods study. Specifically, we examined the role and skills of individuals actively engaged in facilitation as well as the actual facilitation activities occurring within the 'Partnership.' The study was driven by and builds upon a focused literature review published in 2010 that examined facilitation as a role and process in achieving evidence-based practice in nursing. An audit tool outlining 46 discrete facilitation activities based on results of this review was used to examine the facilitation noted in the documents (emails, meeting minutes, field notes of three nursing-related cases participating in the 'Partnership' case-series study. To further examine the concept, six facilitators were interviewed about their practical experiences. The case-audit data were analyzed through a simple content analysis and triangulated with participant responses from the focus group interview to understand what occurred as these cases undertook guideline adaptation. Results The analysis of the three cases revealed that almost all of the 46 discrete, practical facilitation activities from the literature were

  12. Cooperative Learning Groups and the Evolution of Human Adaptability : (Another Reason) Why Hermits Are Rare in Tonga and Elsewhere.

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    Bell, Adrian Viliami; Hernandez, Daniel

    2017-03-01

    Understanding the prevalence of adaptive culture in part requires understanding the dynamics of learning. Here we explore the adaptive value of social learning in groups and how formal social groups function as effective mediums of information exchange. We discuss the education literature on Cooperative Learning Groups (CLGs), which outlines the potential of group learning for enhancing learning outcomes. Four qualities appear essential for CLGs to enhance learning: (1) extended conversations, (2) regular interactions, (3) gathering of experts, and (4) incentives for sharing knowledge. We analyze these four qualities within the context of a small-scale agricultural society using data we collected in 2010 and 2012. Through an analysis of surveys, interviews, and observations in the Tongan islands, we describe the role CLGs likely plays in facilitating individuals' learning of adaptive information. Our analysis of group affiliation, membership, and topics of conversation suggest that the first three CLG qualities reflect conditions for adaptive learning in groups. We utilize ethnographic anecdotes to suggest the fourth quality is also conducive to adaptive group learning. Using an evolutionary model, we further explore the scope for CLGs outside the Tongan socioecological context. Model analysis shows that environmental volatility and migration rates among human groups mediate the scope for CLGs. We call for wider attention to how group structure facilitates learning in informal settings, which may be key to assessing the contribution of groups to the evolution of complex, adaptive culture.

  13. Cultural adaptation and validation of the Portuguese version of the Nursing Clinical Facilitators Questionnaire

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    Maria Manuela Frederico-Ferreira

    Full Text Available ABSTRACT Objective: to perform the cultural adaptation to Portuguese of the Nursing Clinical Facilitators Questionnaire (NCFQ, which was designed by the Centre for Learning and Teaching at the University of Technology of Sydney, and to validate this instrument. Methods: this methodological study involved the cultural adaptation of the questionnaire by using translation, back-translation, semantic comparison, idiomatic and conceptual equivalence, and validation through validity and reliability analyses and used a sample of 767 students in their second year of the Nursing Program. Results: construct validity had a two-factor solution according to the varimax rotation method. In addition, there was a high overall internal consistency for the questionnaire (Cronbach's alpha of 0.977 and for the factors found (0.966 and 0.952, respectively. Conclusion: the Portuguese version has good psychometric characteristics; therefore, it is adequate to obtain reliable information on the perception of nursing students concerning the type of supervision that is provided in clinical practice, and this version is adequate to improve teaching practices.

  14. The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons

    Science.gov (United States)

    Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison P.; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E. G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H.; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W. H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H.

    2016-01-01

    To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before the teleost genome duplication (TGD). The slowly evolving gar genome conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and miRNA genes). Numerous conserved non-coding elements (CNEs, often cis-regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles of such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses revealed that the sum of expression domains and levels from duplicated teleost genes often approximate patterns and levels of gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes, and the function of human regulatory sequences. PMID:26950095

  15. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

    Science.gov (United States)

    Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H

    2016-04-01

    To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

  16. The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

    Science.gov (United States)

    Reznick, D N; Ghalambor, C K

    2001-01-01

    Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

  17. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment

    Directory of Open Access Journals (Sweden)

    Hikaru eSuenaga

    2015-09-01

    Full Text Available Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and therefore enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

  18. Respiratory Evolution Facilitated the Origin of Pterosaur Flight and Aerial Gigantism

    Science.gov (United States)

    Claessens, Leon P. A. M.; O'Connor, Patrick M.; Unwin, David M.

    2009-01-01

    Pterosaurs, enigmatic extinct Mesozoic reptiles, were the first vertebrates to achieve true flapping flight. Various lines of evidence provide strong support for highly efficient wing design, control, and flight capabilities. However, little is known of the pulmonary system that powered flight in pterosaurs. We investigated the structure and function of the pterosaurian breathing apparatus through a broad scale comparative study of respiratory structure and function in living and extinct archosaurs, using computer-assisted tomographic (CT) scanning of pterosaur and bird skeletal remains, cineradiographic (X-ray film) studies of the skeletal breathing pump in extant birds and alligators, and study of skeletal structure in historic fossil specimens. In this report we present various lines of skeletal evidence that indicate that pterosaurs had a highly effective flow-through respiratory system, capable of sustaining powered flight, predating the appearance of an analogous breathing system in birds by approximately seventy million years. Convergent evolution of gigantism in several Cretaceous pterosaur lineages was made possible through body density reduction by expansion of the pulmonary air sac system throughout the trunk and the distal limb girdle skeleton, highlighting the importance of respiratory adaptations in pterosaur evolution, and the dramatic effect of the release of physical constraints on morphological diversification and evolutionary radiation. PMID:19223979

  19. Respiratory evolution facilitated the origin of pterosaur flight and aerial gigantism.

    Science.gov (United States)

    Claessens, Leon P A M; O'Connor, Patrick M; Unwin, David M

    2009-01-01

    Pterosaurs, enigmatic extinct Mesozoic reptiles, were the first vertebrates to achieve true flapping flight. Various lines of evidence provide strong support for highly efficient wing design, control, and flight capabilities. However, little is known of the pulmonary system that powered flight in pterosaurs. We investigated the structure and function of the pterosaurian breathing apparatus through a broad scale comparative study of respiratory structure and function in living and extinct archosaurs, using computer-assisted tomographic (CT) scanning of pterosaur and bird skeletal remains, cineradiographic (X-ray film) studies of the skeletal breathing pump in extant birds and alligators, and study of skeletal structure in historic fossil specimens. In this report we present various lines of skeletal evidence that indicate that pterosaurs had a highly effective flow-through respiratory system, capable of sustaining powered flight, predating the appearance of an analogous breathing system in birds by approximately seventy million years. Convergent evolution of gigantism in several Cretaceous pterosaur lineages was made possible through body density reduction by expansion of the pulmonary air sac system throughout the trunk and the distal limb girdle skeleton, highlighting the importance of respiratory adaptations in pterosaur evolution, and the dramatic effect of the release of physical constraints on morphological diversification and evolutionary radiation.

  20. Respiratory evolution facilitated the origin of pterosaur flight and aerial gigantism.

    Directory of Open Access Journals (Sweden)

    Leon P A M Claessens

    Full Text Available Pterosaurs, enigmatic extinct Mesozoic reptiles, were the first vertebrates to achieve true flapping flight. Various lines of evidence provide strong support for highly efficient wing design, control, and flight capabilities. However, little is known of the pulmonary system that powered flight in pterosaurs. We investigated the structure and function of the pterosaurian breathing apparatus through a broad scale comparative study of respiratory structure and function in living and extinct archosaurs, using computer-assisted tomographic (CT scanning of pterosaur and bird skeletal remains, cineradiographic (X-ray film studies of the skeletal breathing pump in extant birds and alligators, and study of skeletal structure in historic fossil specimens. In this report we present various lines of skeletal evidence that indicate that pterosaurs had a highly effective flow-through respiratory system, capable of sustaining powered flight, predating the appearance of an analogous breathing system in birds by approximately seventy million years. Convergent evolution of gigantism in several Cretaceous pterosaur lineages was made possible through body density reduction by expansion of the pulmonary air sac system throughout the trunk and the distal limb girdle skeleton, highlighting the importance of respiratory adaptations in pterosaur evolution, and the dramatic effect of the release of physical constraints on morphological diversification and evolutionary radiation.

  1. Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution.

    Science.gov (United States)

    Sharma, Poonam; Gupta, Sushim Kumar; Rolain, Jean-Marc

    2014-03-01

    Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs.

  2. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

    Directory of Open Access Journals (Sweden)

    James Vaughn Kohl

    2013-06-01

    Full Text Available Background: The prenatal migration of gonadotropin-releasing hormone (GnRH neurosecretory neurons allows nutrients and human pheromones to alter GnRH pulsatility, which modulates the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems, thus influencing the development of ingestive behavior, reproductive sexual behavior, and other behaviors. Methods: This model details how chemical ecology drives adaptive evolution via: (1 ecological niche construction, (2 social niche construction, (3 neurogenic niche construction, and (4 socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH and systems biology. Results: Nutrients are metabolized to pheromones that condition behavior in the same way that food odors condition behavior associated with food preferences. The epigenetic effects of olfactory/pheromonal input calibrate and standardize molecular mechanisms for genetically predisposed receptor-mediated changes in intracellular signaling and stochastic gene expression in GnRH neurosecretory neurons of brain tissue. For example, glucose and pheromones alter the hypothalamic secretion of GnRH and LH. A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for nutrient acquisition, movement, reproduction, and the diversification of species from microbes to man. Conclusion: An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively

  3. Intrasexual competition facilitates the evolution of alternative mating strategies in a colour polymorphic fish

    Directory of Open Access Journals (Sweden)

    Uy J Albert C

    2010-12-01

    Full Text Available Abstract Background Intense competition for access to females can lead to males exploiting different components of sexual selection, and result in the evolution of alternative mating strategies (AMSs. Males of Poecilia parae, a colour polymorphic fish, exhibit five distinct phenotypes: drab-coloured (immaculata, striped (parae, structural-coloured (blue and carotenoid-based red and yellow morphs. Previous work indicates that immaculata males employ a sneaker strategy, whereas the red and yellow morphs exploit female preferences for carotenoid-based colours. Mating strategies favouring the maintenance of the other morphs remain to be determined. Here, we report the role of agonistic male-male interactions in influencing female mating preferences and male mating success, and in facilitating the evolution of AMSs. Results Our study reveals variation in aggressiveness among P. parae morphs during indirect and direct interactions with sexually receptive females. Two morphs, parae and yellow, use aggression to enhance their mating success (i.e., number of copulations by 1 directly monopolizing access to females, and 2 modifying female preferences after winning agonistic encounters. Conversely, we found that the success of the drab-coloured immaculata morph, which specializes in a sneak copulation strategy, relies in its ability to circumvent both male aggression and female choice when facing all but yellow males. Conclusions Strong directional selection is expected to deplete genetic variation, yet many species show striking genetically-based polymorphisms. Most studies evoke frequency dependent selection to explain the persistence of such variation. Consistent with a growing body of evidence, our findings suggest that a complex form of balancing selection may alternatively explain the evolution and maintenance of AMSs in a colour polymorphic fish. In particular, this study demonstrates that intrasexual competition results in phenotypically distinct

  4. Reduced plantar sole sensitivity facilitates early adaptation to a visual rotation pointing task when standing upright

    Directory of Open Access Journals (Sweden)

    Maxime Billot

    2016-09-01

    Full Text Available Humans are capable of pointing to a target with accuracy. However, when vision is distorted through a visual rotation or mirror-reversed vision, the performance is initially degraded and thereafter improves with practice. There are suggestions this gradual improvement results from a sensorimotor recalibration involving initial gating of the somatosensory information from the pointing hand. In the present experiment, we examined if this process interfered with balance control by asking participants to point to targets with a visual rotation from a standing posture. This duality in processing sensory information (i.e., gating sensory signals from the hand while processing those arising from the control of balance could generate initial interference leading to a degraded pointing performance. We hypothesized that if this is the case, the attenuation of plantar sole somatosensory information through cooling could reduce the sensorimotor interference, and facilitate the early adaptation (i.e. improvement in the pointing task. Results supported this hypothesis. These observations suggest that processing sensory information for balance control interferes with the sensorimotor recalibration process imposed by a pointing task when vision is rotated.

  5. Facilitating joint chaos and fractal analysis of biosignals through nonlinear adaptive filtering.

    Directory of Open Access Journals (Sweden)

    Jianbo Gao

    Full Text Available BACKGROUND: Chaos and random fractal theories are among the most important for fully characterizing nonlinear dynamics of complicated multiscale biosignals. Chaos analysis requires that signals be relatively noise-free and stationary, while fractal analysis demands signals to be non-rhythmic and scale-free. METHODOLOGY/PRINCIPAL FINDINGS: To facilitate joint chaos and fractal analysis of biosignals, we present an adaptive algorithm, which: (1 can readily remove nonstationarities from the signal, (2 can more effectively reduce noise in the signals than linear filters, wavelet denoising, and chaos-based noise reduction techniques; (3 can readily decompose a multiscale biosignal into a series of intrinsically bandlimited functions; and (4 offers a new formulation of fractal and multifractal analysis that is better than existing methods when a biosignal contains a strong oscillatory component. CONCLUSIONS: The presented approach is a valuable, versatile tool for the analysis of various types of biological signals. Its effectiveness is demonstrated by offering new important insights into brainwave dynamics and the very high accuracy in automatically detecting epileptic seizures from EEG signals.

  6. Evolution and Adaptation in Pseudomonas aeruginosa Biofilms Driven by Mismatch Repair System-Deficient Mutators

    DEFF Research Database (Denmark)

    Luján, Adela M.; Maciá, María D.; Yang, Liang

    2011-01-01

    diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution...

  7. Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate-induced range shifts.

    Science.gov (United States)

    Hargreaves, A L; Bailey, S F; Laird, R A

    2015-08-01

    Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient. We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual-based model. We compare range-wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs), and for a single climate genotype vs. multiple genotypes locally adapted to temperature. During climate stability, dispersal decreased towards RLs when fitness was uniform, but increased when fitness declined towards RLs, due to highly dispersive genotypes maintaining sink populations at RLs, increased kin selection in smaller populations, and an emergent fitness asymmetry that favoured dispersal in low-quality habitat. However, this initial dispersal advantage at low-fitness RLs did not facilitate climate tracking, as it was outweighed by an increased probability of extinction. Locally adapted genotypes benefited from staying close to their climate optima; this selected against dispersal under stable climates but for increased dispersal throughout shifting ranges, compared to cases without local adaptation. Dispersal increased at expanding RLs in most scenarios, but only increased at the range centre and contracting RLs given local adaptation to climate. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary

  8. Evolution of time-keeping mechanisms: early emergence and adaptation to photoperiod.

    Science.gov (United States)

    Hut, R A; Beersma, D G M

    2011-07-27

    Virtually all species have developed cellular oscillations and mechanisms that synchronize these cellular oscillations to environmental cycles. Such environmental cycles in biotic (e.g. food availability and predation risk) or abiotic (e.g. temperature and light) factors may occur on a daily, annual or tidal time scale. Internal timing mechanisms may facilitate behavioural or physiological adaptation to such changes in environmental conditions. These timing mechanisms commonly involve an internal molecular oscillator (a 'clock') that is synchronized ('entrained') to the environmental cycle by receptor mechanisms responding to relevant environmental signals ('Zeitgeber', i.e. German for time-giver). To understand the evolution of such timing mechanisms, we have to understand the mechanisms leading to selective advantage. Although major advances have been made in our understanding of the physiological and molecular mechanisms driving internal cycles (proximate questions), studies identifying mechanisms of natural selection on clock systems (ultimate questions) are rather limited. Here, we discuss the selective advantage of a circadian system and how its adaptation to day length variation may have a functional role in optimizing seasonal timing. We discuss various cases where selective advantages of circadian timing mechanisms have been shown and cases where temporarily loss of circadian timing may cause selective advantage. We suggest an explanation for why a circadian timing system has emerged in primitive life forms like cyanobacteria and we evaluate a possible molecular mechanism that enabled these bacteria to adapt to seasonal variation in day length. We further discuss how the role of the circadian system in photoperiodic time measurement may explain differential selection pressures on circadian period when species are exposed to changing climatic conditions (e.g. global warming) or when they expand their geographical range to different latitudes or altitudes.

  9. The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

    NARCIS (Netherlands)

    Mekel-Bobrov, N.; Posthuma, D.; Gilbert, S.L.; Lind, P.; Gosso, M.F.; Luciano, M.; Harris, S.E.; Bates, T.C.; Polderman, T.J.C.; Whalley, L.J.; Fox, H.; Starr, J.M.; Evans, P.D.; Montgomery, GW; Fernandes, C.; Heutink, P.; Martin, N.G.; Boomsma, D.I.; Deary, I.J.; Wright, M.J.; de Geus, E.J.C.; Lahn, B.T.

    2007-01-01

    Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary

  10. Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30ºC

    DEFF Research Database (Denmark)

    Caspeta, Luis; Chen, Yun; Nielsen, Jens

    2016-01-01

    Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution ...

  11. Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts

    DEFF Research Database (Denmark)

    Hargreaves, Anna; Bailey, Susan; Laird, Robert

    2015-01-01

    Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at contrac......Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution...... at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient...

  12. Fisheries-induced neutral and adaptive evolution in exploited fish populations and consequences for their adaptive potential

    DEFF Research Database (Denmark)

    Marty, Lise; Dieckmann, Ulf; Ernande, Bruno

    2015-01-01

    . An individual-based eco-genetic model is devised that includes neutral and functional loci in a realistic ecological setting. In line with theoretical expectations, we find that fishing induces evolution towards slow growth, early maturation at small size and higher reproductive investment. We show, first......Fishing may induce neutral and adaptive evolution affecting life-history traits, and molecular evidence has shown that neutral genetic diversity has declined in some exploited populations. Here, we theoretically study the interplay between neutral and adaptive evolution caused by fishing......, that the choice of genetic model (based on either quantitative genetics or gametic inheritance) influences the evolutionary recovery of traits after fishing ceases. Second, we analyse the influence of three factors possibly involved in the lack of evolutionary recovery: the strength of selection, the effect...

  13. Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers

    OpenAIRE

    Tokita, Masayoshi; Yano, Wataru; James, Helen F.; Abzhanov, Arhat

    2017-01-01

    Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried ...

  14. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Molin, Søren

    2015-01-01

    fibrosis. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance and loss of extracellular virulence factors....... Furthermore, we find an ordered succession of mutations in key regulatory networks. Accordingly, mutations in downstream transcriptional regulators were contingent upon mutations in upstream regulators, suggesting that remodeling of regulatory networks might be important in adaptation. The characterization...... of genes involved in host adaptation may help in predicting bacterial evolution in patients with cystic fibrosis and in the design of future intervention strategies....

  15. Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex

    Directory of Open Access Journals (Sweden)

    McTaggart Seanna J

    2012-05-01

    Full Text Available Abstract Background Understanding which parts of the genome have been most influenced by adaptive evolution remains an unsolved puzzle. Some evidence suggests that selection has the greatest impact on regions of the genome that interact with other evolving genomes, including loci that are involved in host-parasite co-evolutionary processes. In this study, we used a population genetic approach to test this hypothesis by comparing DNA sequences of 30 putative immune system genes in the crustacean Daphnia pulex with 24 non-immune system genes. Results In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman (MK test indicate that immune system genes as a class have experienced more adaptive evolution than non-immune system genes. However, not all immune system genes show evidence of adaptive evolution. Additionally, we apply single locus MK tests and calculate population genetic parameters at all loci in order to characterize the mode of selection (directional versus balancing in the genes that show the greatest deviation from neutral evolution. Conclusions Our data are consistent with the hypothesis that immune system genes undergo more adaptive evolution than non-immune system genes, possibly as a result of host-parasite arms races. The results of these analyses highlight several candidate loci undergoing adaptive evolution that could be targeted in future studies.

  16. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.

    2017-01-01

    Adaptive laboratory evolution (ALE) experiments are often designed to maintain a static culturing environment to minimize confounding variables that could influence the adaptive process, but dynamic nutrient conditions occur frequently in natural and bioprocessing settings. To study the nature...... applications.IMPORTANCE Evolution and natural selection inexorably lead to an organism's improved fitness in a given environment, whether in a laboratory or natural setting. However, despite the frequent natural occurrence of complex and dynamic growth environments, laboratory evolution experiments typically...... maintain simple, static culturing environments so as to reduce selection pressure complexity. In this study, we investigated the adaptive strategies underlying evolution to fluctuating environments by evolving Escherichia coli to conditions of frequently switching growth substrate. Characterization...

  17. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

    DEFF Research Database (Denmark)

    Jahn, Leonie Johanna; Munck, Christian; Ellabaan, Mostafa M Hashim

    2017-01-01

    Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution....... However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes...... are simpler to implement and therefore allow higher throughput. The specific regimen of adaptive evolution may have a profound impact on the adapted cell state. Indeed, substantial effects of the selection regime on the resulting geno- and phenotypes have been reported in the literature. In this study we...

  18. Rapid adaptive evolution in novel environments acts as an architect of population range expansion.

    Science.gov (United States)

    Szűcs, M; Vahsen, M L; Melbourne, B A; Hoover, C; Weiss-Lehman, C; Hufbauer, R A

    2017-12-19

    Colonization and expansion into novel landscapes determine the distribution and abundance of species in our rapidly changing ecosystems worldwide. Colonization events are crucibles for rapid evolution, but it is not known whether evolutionary changes arise mainly after successful colonization has occurred, or if evolution plays an immediate role, governing the growth and expansion speed of colonizing populations. There is evidence that spatial evolutionary processes can speed range expansion within a few generations because dispersal tendencies may evolve upwards at range edges. Additionally, rapid adaptation to a novel environment can increase population growth rates, which also promotes spread. However, the role of adaptive evolution and the relative contributions of spatial evolution and adaptation to expansion are unclear. Using a model system, red flour beetles (Tribolium castaneum), we either allowed or constrained evolution of populations colonizing a novel environment and measured population growth and spread. At the end of the experiment we assessed the fitness and dispersal tendency of individuals originating either from the core or edge of evolving populations or from nonevolving populations in a common garden. Within six generations, evolving populations grew three times larger and spread 46% faster than populations in which evolution was constrained. Increased size and expansion speed were strongly driven by adaptation, whereas spatial evolutionary processes acting on edge subpopulations contributed less. This experimental evidence demonstrates that rapid evolution drives both population growth and expansion speed and is thus crucial to consider for managing biological invasions and successfully introducing or reintroducing species for management and conservation.

  19. Trichinella spiralis: the evolution of adaptation and parasitism

    Science.gov (United States)

    Parasitism among nematodes has occurred in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and a...

  20. Cultural adaptation and validation of the Portuguese version of the Nursing Clinical Facilitators Questionnaire.

    Science.gov (United States)

    Frederico-Ferreira, Maria Manuela; Camarneiro, Ana Paula Forte; Loureiro, Cândida Rosalinda Exposto da Costa; Ventura, Maria Clara Amado Apóstolo

    2016-08-15

    to perform the cultural adaptation to Portuguese of the Nursing Clinical Facilitators Questionnaire (NCFQ), which was designed by the Centre for Learning and Teaching at the University of Technology of Sydney, and to validate this instrument. this methodological study involved the cultural adaptation of the questionnaire by using translation, back-translation, semantic comparison, idiomatic and conceptual equivalence, and validation through validity and reliability analyses and used a sample of 767 students in their second year of the Nursing Program. construct validity had a two-factor solution according to the varimax rotation method. In addition, there was a high overall internal consistency for the questionnaire (Cronbach's alpha of 0.977) and for the factors found (0.966 and 0.952, respectively). the Portuguese version has good psychometric characteristics; therefore, it is adequate to obtain reliable information on the perception of nursing students concerning the type of supervision that is provided in clinical practice, and this version is adequate to improve teaching practices. realizar a adaptação cultural para a língua portuguesa do Nursing Clinical Facilitators Questionnaire (NCFQ) concebido pelo Centre for Learning and Teaching, University of Technology de Sydney e proceder à validação do instrumento. estudo metodológico de adaptação cultural do questionário através de tradução, retroversão, comparação semântica, idiomática e equivalência conceitual, seguido de validação em uma amostra de 767 estudantes do 2º ano do Curso de Licenciatura em Enfermagem, por meio de análise da validade e confiabilidade. a validade de constructo apresenta uma solução bifatorial após rotação varimax. A consistência interna global do questionário é elevada (alfa de Cronbach 0,977), assim como dos fatores encontrados (respectivamente, 0,966 e 0,952). a versão portuguesa apresenta boas características psicométricas, sendo um instrumento v

  1. Restoring of Glucose Metabolism of Engineered Yarrowia lipolytica for Succinic Acid Production via a Simple and Efficient Adaptive Evolution Strategy.

    Science.gov (United States)

    Yang, Xiaofeng; Wang, Huaimin; Li, Chong; Lin, Carol Sze Ki

    2017-05-24

    Succinate dehydrogenase inactivation in Yarrowia lipolytica has been demonstrated for robust succinic acid production, whereas the inefficient glucose metabolism has hindered its practical application. In this study, a simple and efficient adaptive evolution strategy via cell immobilization was conducted in shake flasks, with an aim to restore the glucose metabolism of Y. lipolytica mutant PGC01003. After 21 days with 14 generations evolution, glucose consumption rate increased to 0.30 g/L/h in YPD medium consisting of 150 g/L initial glucose concentration, while poor yeast growth was observed in the same medium using the initial strain without adaptive evolution. Succinic acid productivity of the evolved strain also increased by 2.3-fold, with stable cell growth in YPD medium with high initial glucose concentration. Batch fermentations resulted in final succinic acid concentrations of 65.7 g/L and 87.9 g/L succinic acid using YPD medium and food waste hydrolysate, respectively. The experimental results in this study show that a simple and efficient strategy could facilitate the glucose uptake rate in succinic acid fermentation using glucose-rich substrates.

  2. Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor.

    Science.gov (United States)

    Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben; Paina, Cristiana; Rudi, Heidi; Rognli, Odd-Arne; Fjellheim, Siri; Sandve, Simen R

    2013-09-01

    Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence (P temperate crops. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  3. Structure and evolution of the plant cation diffusion facilitator family of ion transporters

    Directory of Open Access Journals (Sweden)

    Zanis Michael J

    2011-03-01

    Full Text Available Abstract Background Members of the cation diffusion facilitator (CDF family are integral membrane divalent cation transporters that transport metal ions out of the cytoplasm either into the extracellular space or into internal compartments such as the vacuole. The spectrum of cations known to be transported by proteins of the CDF family include Zn, Fe, Co, Cd, and Mn. Members of this family have been identified in prokaryotes, eukaryotes, and archaea, and in sequenced plant genomes. CDF families range in size from nine members in Selaginella moellendorffii to 19 members in Populus trichocarpa. Phylogenetic analysis suggests that the CDF family has expanded within plants, but a definitive plant CDF family phylogeny has not been constructed. Results Representative CDF members were annotated from diverse genomes across the Viridiplantae and Rhodophyta lineages and used to identify phylogenetic relationships within the CDF family. Bayesian phylogenetic analysis of CDF amino acid sequence data supports organizing land plant CDF family sequences into 7 groups. The origin of the 7 groups predates the emergence of land plants. Among these, 5 of the 7 groups are likely to have originated at the base of the tree of life, and 2 of 7 groups appear to be derived from a duplication event prior to or coincident with land plant evolution. Within land plants, local expansion continues within select groups, while several groups are strictly maintained as one gene copy per genome. Conclusions Defining the CDF gene family phylogeny contributes to our understanding of this family in several ways. First, when embarking upon functional studies of the members, defining primary groups improves the predictive power of functional assignment of orthologous/paralogous genes and aids in hypothesis generation. Second, defining groups will allow a group-specific sequence motif to be generated that will help define future CDF family sequences and aid in functional motif

  4. The evolution of predictive adaptive responses in human life history

    NARCIS (Netherlands)

    Nettle, D.; Frankenhuis, W.E.; Rickard, I.J.

    2012-01-01

    Many studies in humans have shown that adverse experience in early life is associated with accelerated reproductive timing, and there is comparative evidence for similar effects in other animals. There are two different classes of adaptive explanation for associations between early-life adversity

  5. Adaptive evolution by spontaneous domain fusion and protein relocalization

    NARCIS (Netherlands)

    Farr, Andrew D.; Remigi, Philippe; Rainey, Paul B.

    2017-01-01

    Knowledge of adaptive processes encompasses understanding the emergence of new genes. Computational analyses of genomes suggest that new genes can arise by domain swapping; however, empirical evidence has been lacking. Here we describe a set of nine independent deletion mutations that arose during

  6. The bill of evolution : trophic adaptations in anseriform birds

    NARCIS (Netherlands)

    Kurk, Carolina Deborah

    2008-01-01

    Adaptive radiation involves the rapid divergence of a single ancestral species into a group of species each occupying a different ecological niche. Differences between species are the result of trade-offs in the ability to exploit different environments to avoid competitive interactions. The many

  7. Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation

    Science.gov (United States)

    Bullaughey, Kevin

    2016-01-01

    When multiple substitutions affect a trait in opposing ways, they are often assumed to be compensatory, not only with respect to the trait, but also with respect to fitness. This type of compensatory evolution has been suggested to underlie the evolution of protein structures and interactions, RNA secondary structures, and gene regulatory modules and networks. The possibility for compensatory evolution results from epistasis. Yet if epistasis is widespread, then it is also possible that the opposing substitutions are individually adaptive. I term this possibility an adaptive reversal. Although possible for arbitrary phenotype-fitness mappings, it has not yet been investigated whether such epistasis is prevalent in a biologically-realistic setting. I investigate a particular regulatory circuit, the type I coherent feed-forward loop, which is ubiquitous in natural systems and is accurately described by a simple mathematical model. I show that such reversals are common during adaptive evolution, can result solely from the topology of the fitness landscape, and can occur even when adaptation follows a modest environmental change and the network was well adapted to the original environment. The possibility of adaptive reversals warrants a systems perspective when interpreting substitution patterns in gene regulatory networks. PMID:23289561

  8. From lifetime to evolution: timescales of human gut microbiota adaptation

    Directory of Open Access Journals (Sweden)

    Sara eQuercia

    2014-11-01

    Full Text Available Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

  9. Adaptive Evolution and Demographic History of Norway Spruce (Picea Abies)

    OpenAIRE

    Källman, Thomas

    2009-01-01

    One of the major challenges in evolutionary biology is to determine the genetic basis of adaptive variation. In Norway spruce (Picea abies) the timing of bud set shows a very strong latitudinal cline despite a very low genetic differentiation between populations. The timing of bud set in Norway spruce is under strong genetic control and triggered by changes in photoperiod, but no genes controlling this response have so far been described. In this thesis we used a combination of functional stu...

  10. The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

    Science.gov (United States)

    Mekel-Bobrov, Nitzan; Posthuma, Danielle; Gilbert, Sandra L; Lind, Penelope; Gosso, M Florencia; Luciano, Michelle; Harris, Sarah E; Bates, Timothy C; Polderman, Tinca J C; Whalley, Lawrence J; Fox, Helen; Starr, John M; Evans, Patrick D; Montgomery, Grant W; Fernandes, Croydon; Heutink, Peter; Martin, Nicholas G; Boomsma, Dorret I; Deary, Ian J; Wright, Margaret J; de Geus, Eco J C; Lahn, Bruce T

    2007-03-15

    Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary microcephaly, a developmental disorder characterized by severe reduction in brain size and intelligence, reminiscent of the early hominid condition. This has led to the hypothesis that the adaptive evolution of these genes has contributed to the emergence of modern human cognition. As with other candidate loci, however, this hypothesis remains speculative due to the current lack of methodologies for characterizing the evolutionary function of these genes in humans. Two primary microcephaly genes, ASPM and Microcephalin, have been implicated not only in the adaptive evolution of the lineage leading to humans, but in ongoing selective sweeps in modern humans as well. The presence of both the putatively adaptive and neutral alleles at these loci provides a unique opportunity for using normal trait variation within humans to test the hypothesis that the recent selective sweeps are driven by an advantage in cognitive abilities. Here, we report a large-scale association study between the adaptive alleles of these genes and normal variation in several measures of IQ. Five independent samples were used, totaling 2393 subjects, including both family-based and population-based datasets. Our overall findings do not support a detectable association between the recent adaptive evolution of either ASPM or Microcephalin and changes in IQ. As we enter the post-genomic era, with the number of candidate loci underlying human evolution growing rapidly, our findings highlight the importance of direct experimental validation in elucidating their evolutionary role in shaping the human phenotype.

  11. Aging as Evolution-Facilitating Program and a Biochemical Approach to Switch It Off

    Science.gov (United States)

    Skulachev, Vladimir P.

    A concept is presented considering aging of living organisms as a final step of their ontogenetic program. It is assumed that such an aging program was invented by biological evolution to facilitate the evolutionary process. Indications are summarized suggesting that controlled production of toxic forms of oxygen (so called reactive oxygen species) by respiring intracellular organelles (mitochondria) is an obligatory component of the aging program. First results of a research project devoted to an attempt to interrupt aging program by antioxidants specifically addressed to mitochondria have been described. Within the framework of the project, antioxidants of a new type (SkQ) were synthesized. SkQs are composed of (i) plastoquinone (an antioxidant moiety), (ii) a penetrating cation, and (iii) a decane or pentane linker. Using planar bilayer phospholipid membranes, we selected SkQ derivatives of the highest penetrability, namely plastoquinonyl decyl triphenylphosphonium (SkQ1), plastoquinonyl decyl rhodamine 19 (SkQR1), and methylplastoquinonyl decyl triphenylphosphonium (SkQ3). Anti- and prooxidant properties of these substances and also of ubiquinonyl-decyl-triphenylphosphonium (MitoQ) were tested in isolated mitochondria. Micromolar concentrations of cationic quinones are found to be very strong prooxidants, but in the lower (sub-micromolar) concentrations they display antioxidant activity which decreases in the series SkQ1 = SkQR1 > SkQ3 > MitoQ. Thus, the window between the anti- and prooxidant effects is the smallest for MitoQ and the largest for SkQ1 and SkQR1. SkQ1 is rapidly reduced by complex III of the mitochondrial respiratory chain, i.e. it is a rechargeable antioxidant. Extremely low concentrations of SkQ1 and SkQR1 completely arrest the H2O2-induced apoptosis in human fibroblasts and HeLa cells (for SkQ1, C 1/2 = 8 · 10-9M). Higher concentrations of SkQ1 are required to block necrosis initiated by reactive oxygen species (ROS). In mice, SkQ1

  12. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens.

    Science.gov (United States)

    Mekel-Bobrov, Nitzan; Gilbert, Sandra L; Evans, Patrick D; Vallender, Eric J; Anderson, Jeffrey R; Hudson, Richard R; Tishkoff, Sarah A; Lahn, Bruce T

    2005-09-09

    The gene ASPM (abnormal spindle-like microcephaly associated) is a specific regulator of brain size, and its evolution in the lineage leading to Homo sapiens was driven by strong positive selection. Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong positive selection. These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution.

  13. The evolution of coexistence: Reciprocal adaptation promotes the assembly of a simple community.

    Science.gov (United States)

    Bassar, Ronald D; Simon, Troy; Roberts, William; Travis, Joseph; Reznick, David N

    2017-02-01

    Species coexistence may result by chance when co-occurring species do not strongly interact or it may be an evolutionary outcome of strongly interacting species adapting to each other. Although patterns like character displacement indicate that coexistence has often been an evolutionary outcome, it is unclear how often the evolution of coexistence represents adaptation in only one species or reciprocal adaptation among all interacting species. Here, we demonstrate a strong role for evolution in the coexistence of guppies and killifish in Trinidadian streams. We experimentally recreated the temporal stages in the invasion and establishment of guppies into communities that previously contained only killifish. We combined demographic responses of guppies and killifish with a size-based integral projection model to calculate the fitness of the phenotypes of each species in each of the stages of community assembly. We show that guppies from locally adapted populations that are sympatric with killifish have higher fitness when paired with killifish than guppies from allopatric populations. This elevated fitness involves effects traceable to both guppy and killifish evolution. We discuss the implications of our results to the study of species coexistence and how it may be mediated through eco-evolutionary feedbacks. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  14. How Adaptive Learning Affects Evolution: Reviewing Theory on the Baldwin Effect.

    Science.gov (United States)

    Sznajder, B; Sabelis, M W; Egas, M

    2012-09-01

    We review models of the Baldwin effect, i.e., the hypothesis that adaptive learning (i.e., learning to improve fitness) accelerates genetic evolution of the phenotype. Numerous theoretical studies scrutinized the hypothesis that a non-evolving ability of adaptive learning accelerates evolution of genetically determined behavior. However, their results are conflicting in that some studies predict an accelerating effect of learning on evolution, whereas others show a decelerating effect. We begin by describing the arguments underlying the hypothesis on the Baldwin effect and identify the core argument: adaptive learning influences the rate of evolution because it changes relative fitness of phenotypes. Then we analyze the theoretical studies of the Baldwin effect with respect to their model of adaptive learning and discuss how their contrasting results can be explained from differences in (1) the ways in which the effect of adaptive learning on the phenotype is modeled, (2) the assumptions underlying the function used to quantify fitness and (3) the time scale at which the evolutionary rate is measured. We finish by reviewing the specific assumptions used by the theoretical studies of the Baldwin effect and discuss the evolutionary implications for cases where these assumptions do not hold.

  15. Brain evolution and development: adaptation, allometry and constraint.

    Science.gov (United States)

    Montgomery, Stephen H; Mundy, Nicholas I; Barton, Robert A

    2016-09-14

    Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns. © 2016 The Author(s).

  16. The evolution of predictive adaptive responses in human life history.

    Science.gov (United States)

    Nettle, Daniel; Frankenhuis, Willem E; Rickard, Ian J

    2013-09-07

    Many studies in humans have shown that adverse experience in early life is associated with accelerated reproductive timing, and there is comparative evidence for similar effects in other animals. There are two different classes of adaptive explanation for associations between early-life adversity and accelerated reproduction, both based on the idea of predictive adaptive responses (PARs). According to external PAR hypotheses, early-life adversity provides a 'weather forecast' of the environmental conditions into which the individual will mature, and it is adaptive for the individual to develop an appropriate phenotype for this anticipated environment. In internal PAR hypotheses, early-life adversity has a lasting negative impact on the individual's somatic state, such that her health is likely to fail more rapidly as she gets older, and there is an advantage to adjusting her reproductive schedule accordingly. We use a model of fluctuating environments to derive evolveability conditions for acceleration of reproductive timing in response to early-life adversity in a long-lived organism. For acceleration to evolve via the external PAR process, early-life cues must have a high degree of validity and the level of annual autocorrelation in the individual's environment must be almost perfect. For acceleration to evolve via the internal PAR process requires that early-life experience must determine a significant fraction of the variance in survival prospects in adulthood. The two processes are not mutually exclusive, and mechanisms for calibrating reproductive timing on the basis of early experience could evolve through a combination of the predictive value of early-life adversity for the later environment and its negative impact on somatic state.

  17. Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic.

    Science.gov (United States)

    Chen, Song-Can; Sun, Guo-Xin; Rosen, Barry P; Zhang, Si-Yu; Deng, Ye; Zhu, Bo-Kai; Rensing, Christopher; Zhu, Yong-Guan

    2017-08-10

    The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase. Our results suggest that life successfully moved into arsenic-rich environments in the late Archean Eon and Proterozoic Eon, respectively, by the spread of arsM genes. The arsM genes of bacterial origin have been transferred to other kingdoms of life on at least six occasions, and the resulting domesticated arsM genes promoted adaptation to environmental arsenic. These results allow us to peer into the history of arsenic adaptation of life on our planet and imply that dissemination of genes encoding diverse adaptive functions to toxic chemicals permit adaptation to changes in concentrations of environmental toxins over evolutionary history.

  18. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

    DEFF Research Database (Denmark)

    Bailey, Susan; Bataillon, Thomas

    2015-01-01

    and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights......, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions – that is simple environments, a small range of usually asexual species, relatively short timescales – the question remains as to how applicable...

  19. Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

    Directory of Open Access Journals (Sweden)

    Shen Tong

    2012-03-01

    Full Text Available Abstract Background Cetaceans (whales, dolphins and porpoises are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs, which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω values along most (30 out of 33 examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS, and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This

  20. Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

    Science.gov (United States)

    Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

    2012-03-24

    Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR

  1. The genomic signatures of Shigella evolution, adaptation and geographical spread.

    Science.gov (United States)

    The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

    2016-04-01

    Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.

  2. Enhancement of Microbial Biodesulfurization via Genetic Engineering and Adaptive Evolution.

    Science.gov (United States)

    Wang, Jia; Butler, Robert R; Wu, Fan; Pombert, Jean-François; Kilbane, John J; Stark, Benjamin C

    2017-01-01

    In previous work from our laboratories a synthetic gene encoding a peptide ("Sulpeptide 1" or "S1") with a high proportion of methionine and cysteine residues had been designed to act as a sulfur sink and was inserted into the dsz (desulfurization) operon of Rhodococcus erythropolis IGTS8. In the work described here this construct (dszAS1BC) and the intact dsz operon (dszABC) cloned into vector pRESX under control of the (Rhodococcus) kstD promoter were transformed into the desulfurization-negative strain CW25 of Rhodococcus qingshengii. The resulting strains (CW25[pRESX-dszABC] and CW25[pRESX-dszAS1BC]) were subjected to adaptive selection by repeated passages at log phase (up to 100 times) in minimal medium with dibenzothiophene (DBT) as sole sulfur source. For both strains DBT metabolism peaked early in the selection process and then decreased, eventually averaging four times that of the initial transformed cells; the maximum specific activity achieved by CW25[pRESX-dszAS1BC] exceeded that of CW25[pRESX-dszABC]. Growth rates increased by 7-fold (CW25[pRESX-dszABC]) and 13-fold (CW25[pRESX-dszAS1BC]) and these increases were stable. The adaptations of CW25[pRESX-dszAS1BC] were correlated with a 3-5X increase in plasmid copy numbers from those of the initial transformed cells; whole genome sequencing indicated that during its selection processes no mutations occurred to any of the dsz, S1, or other genes and promoters involved in sulfur metabolism, stress response, or DNA methylation, and that the effect of the sulfur sink produced by S1 is likely very small compared to the cells' overall cysteine and methionine requirements. Nevertheless, a combination of genetic engineering using sulfur sinks and increasing Dsz capability with adaptive selection may be a viable strategy to increase biodesulfurization ability.

  3. Short-time evolution in the adaptive immune system.

    Science.gov (United States)

    Guttenberg, Nicholas; Tabei, S M Ali; Dinner, Aaron R

    2011-09-01

    We exploit a simple model to numerically and analytically investigate the effect of enforcing a time constraint for achieving a system-wide goal during an evolutionary dynamics. This situation is relevant to finding antibody specificities in the adaptive immune response as well as to artificial situations in which an evolutionary dynamics is used to generate a desired capability in a limited number of generations. When the likelihood of finding the target phenotype is low, we find that the optimal mutation rate can exceed the error threshold, in contrast to conventional evolutionary dynamics. We also show how a logarithmic correction to the usual inverse scaling of population size with mutation rate arises. Implications for natural and artificial evolutionary situations are discussed.

  4. Diversity and adaptive evolution of Saccharomyces wine yeast: a review.

    Science.gov (United States)

    Marsit, Souhir; Dequin, Sylvie

    2015-11-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. © FEMS 2015.

  5. Diversity and adaptive evolution of Saccharomyces wine yeast: a review

    Science.gov (United States)

    Marsit, Souhir; Dequin, Sylvie

    2015-01-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. PMID:26205244

  6. The evolution of female orgasm: adaptation or byproduct?

    Science.gov (United States)

    Puts, David Andrew; Dawood, Khytam

    2006-06-01

    Do women experience orgasm because this trait was shaped by natural selection to augment female fitness? Or are women merely the lucky recipients of developmental patterns favored by selection to produce orgasm in males? A recent and widely publicized book by Elisabeth Lloyd (2005a) contends that there is insufficient evidence to validate any of the adaptive explanations yet proposed for female orgasm. We agree. But our reading of the data differs from Lloyd's. In this essay, we outline why, unlike Caton (2006), whose review of Lloyd's book appeared previously in this journal, we are not persuaded by Lloyd's argument that female orgasm is a nonadaptive byproduct of orgasm in men. We hold this view because we disagree with the criteria Lloyd uses to evaluate evolutionary hypotheses, and because we believe Lloyd defines female orgasm too narrowly, ignoring critical information about its affective aspects.

  7. How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation

    National Research Council Canada - National Science Library

    Kouvaris, Kostas; Clune, Jeff; Kounios, Loizos; Brede, Markus; Watson, Richard A

    2017-01-01

    .... Such variability is crucial for evolvability, but poorly understood. In particular, how can natural selection favour developmental organisations that facilitate adaptive evolution in previously unseen environments...

  8. An Evolving Simulation/Gaming Process to Facilitate Adaptive Watershed Management in Northern Mountainous Thailand

    Science.gov (United States)

    Barnaud, Cecile; Promburom, Tanya; Trebuil, Guy; Bousquet, Francois

    2007-01-01

    The decentralization of natural resource management provides an opportunity for communities to increase their participation in related decision making. Research should propose adapted methodologies enabling the numerous stakeholders of these complex socioecological settings to define their problems and identify agreed-on solutions. This article…

  9. Studying the Genetics of Behavior and Evolution by Adaptation and Natural Selection.

    Science.gov (United States)

    Silverman, Jules

    1998-01-01

    Provides an exercise designed to give students an appreciation for the genetic basis of behavior. Employs the phenomenon of glucose aversion as an example of evolution by mutation and accelerated natural selection, thereby revealing one of the ways in which organisms adapt to human interference. (DDR)

  10. Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

    DEFF Research Database (Denmark)

    Mundhada, Hemanshu; Seoane, Jose Miguel; Schneider, Konstantin

    2017-01-01

    L-serine concentration from 3 to 100 g/L using adaptive laboratory evolution (ALE). Genome sequencing of isolated clones revealed multiplication of genetic regions, as well as mutations in thrA, thereby showing a potential mechanism of serine inhibition. Other mutations were evaluated by MAGE...... thereby highlighting the potential of ALE for industrial biotechnology....

  11. Adaptation, niche conservatism, and convergence: comparative studies of leaf evolution in the California chaparral.

    Science.gov (United States)

    Ackerly, David D

    2004-05-01

    Small leaves and low specific leaf area (SLA) have long been viewed as adaptations to Mediterranean-type climates in many species of evergreen woody plants. However, paleobotanical and floristic evidence suggests that in many cases these traits originated prior to the advent of the summer-drought climate regime. In this study, molecular phylogenies and ancestral state reconstructions were used to test the hypothesis of adaptive leaf evolution in 12 lineages of evergreen shrubs in the California chaparral. Across all lineages there was a small but significant shift toward lower SLA, but there were no trends in leaf size evolution. For individual lineages, adaptive changes were detected in only three cases for SLA and in one case for leaf size. Three of these cases of evolutionary change were observed in taxa derived from cool temperate ancestors (e.g., Heteromeles). In contrast, most lineages originating from subtropical ancestors exhibited relative stasis in leaf trait evolution (e.g., Ceanothus). The absence of change suggests that ancestors of chaparral taxa had already acquired appropriate traits that contributed to their success under Mediterranean-type climates. These results illustrate how biogeographic history may influence patterns of trait evolution and adaptation and highlight the contribution of ecological sorting processes to the assembly and functional ecology of regional biotas.

  12. Gradually Adaptive Frameworks: Reasonable Disagreement and the Evolution of Evaluative Systems in Music Education

    Science.gov (United States)

    Haskins, Stanley

    2013-01-01

    The concept of "gradually adaptive frameworks" is introduced as a model with the potential to describe the evolution of belief evaluative systems through the consideration of reasonable arguments and evidence. This concept is demonstrated through an analysis of specific points of disagreement between David Elliott's praxial…

  13. Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa

    2014-01-01

    BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used...

  14. A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?

    Science.gov (United States)

    Meier, Sebastian; Ozbek, Suat

    2007-11-01

    While Darwin pictured organismal evolution as "descent with modification" more than 150 years ago, a detailed reconstruction of the basic evolutionary transitions at the molecular level is only emerging now. In particular, the evolution of today's protein structures and their concurrent functions has remained largely mysterious, as the destruction of these structures by mutation seems far easier than their construction. While the accumulation of genomic and structural data has indicated that proteins are related via common ancestors, naturally occurring protein structures are often considered to be evolutionarily robust, thus leaving open the question of how protein structures can be remodelled while selective pressure forces them to function. New information on the proteome, however, increasingly explains the nature of local and global conformational diversity in protein evolution, which allows the acquisition of novel functions via molecular transition forms containing ancestral and novel structures in dynamic equilibrium. Such structural plasticity may permit the evolution of new protein folds and help account for both the origins of new biological functions and the nature of molecular defects. (c) 2007 Wiley Periodicals, Inc.

  15. Adaptive evolution of the FADS gene cluster within Africa.

    Directory of Open Access Journals (Sweden)

    Rasika A Mathias

    Full Text Available Long chain polyunsaturated fatty acids (LC-PUFAs are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA from plant-based medium chain (MC PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ∼85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60-80 kya.

  16. Adaptive evolution of the FADS gene cluster within Africa.

    Science.gov (United States)

    Mathias, Rasika A; Fu, Wenqing; Akey, Joshua M; Ainsworth, Hannah C; Torgerson, Dara G; Ruczinski, Ingo; Sergeant, Susan; Barnes, Kathleen C; Chilton, Floyd H

    2012-01-01

    Long chain polyunsaturated fatty acids (LC-PUFAs) are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA) from plant-based medium chain (MC) PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS) gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ∼85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60-80 kya.

  17. Modelling the effects of plant facilitation-competition mechanisms on semiarid landscape co-evolution

    Science.gov (United States)

    Saco, Patricia M.

    2015-04-01

    Semiarid landscapes function as tightly coupled systems with strong biogeomorphic feedbacks. Worldwide, a vast portion of these areas are covered by patchy vegetation consisting of mixed herbaceous and woody plant species that interact exhibiting both competition and facilitation effects. Though the role of facilitative interactions in plant communities has received considerable attention in the last two decades, their effects on the coevolution of landscapes are still not clearly understood. Here a modelling framework is used to investigate the effects of facilitative interactions among vegetation species, as well as their role on the coevolution of water redistribution, vegetation patterns, and landforms. The model simulates the dynamics of and interactions between coexisting grasses and shrubs under varying competition-facilitation conditions. We explore facilitation effects associated with changes in micro environmental conditions for water availability in dry environments focussing on the role of infiltration enhancement and shading effects. Field experiments have shown that in many semiarid environments vegetation enhances infiltration. However, herbaceous and woody plants seem to have varying hydrologic traits in different areas and it is therefore not clear which species has the greatest contribution to infiltration enhancement. This study tests alternative hypothesis, varying the relative contributions to total infiltration of both species, through a sensitivity analysis of the key parameters affecting infiltration. We analyze the results by examining the simulated spatial patterns of biomass density, soil moisture and erosion. Results indicate that final vegetation cover structure and hydrologic connectivity strongly depend on the facilitation mechanisms included in the model. We find that the removal of woody species can lead to alternative steady states, including an increase on herbaceous cover, which is the expected outcome of these management

  18. Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes.

    Science.gov (United States)

    Radzvilavicius, Arunas L

    2016-09-07

    Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of multi-copy mitochondrial genomes. Here I develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations under strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Adaptive bridge control strategy for opinion evolution on social networks.

    Science.gov (United States)

    Qian, Cheng; Cao, Jinde; Lu, Jianquan; Kurths, Jürgen

    2011-06-01

    In this paper, we present an efficient opinion control strategy for complex networks, in particular, for social networks. The proposed adaptive bridge control (ABC) strategy calls for controlling a special kind of nodes named bridge and requires no knowledge of the node degrees or any other global or local knowledge, which are necessary for some other immunization strategies including targeted immunization and acquaintance immunization. We study the efficiency of the proposed ABC strategy on random networks, small-world networks, scale-free networks, and the random networks adjusted by the edge exchanging method. Our results show that the proposed ABC strategy is efficient for all of these four kinds of networks. Through an adjusting clustering coefficient by the edge exchanging method, it is found out that the efficiency of our ABC strategy is closely related with the clustering coefficient. The main contributions of this paper can be listed as follows: (1) A new high-order social network is proposed to describe opinion dynamic. (2) An algorithm, which does not require the knowledge of the nodes' degree and other global∕local network structure information, is proposed to control the "bridges" more accurately and further control the opinion dynamics of the social networks. The efficiency of our ABC strategy is illustrated by numerical examples. (3) The numerical results indicate that our ABC strategy is more efficient for networks with higher clustering coefficient.

  20. Three-dimensional Adaptive Evolutions of Strong Gravitational Waves

    Science.gov (United States)

    Choi, Dae-Il; Centrella, Joan

    2001-04-01

    General relativistic research is entering a new era with the installation of several worldwide gravitational wave (GW) observatories based on laser interferometers. These include ground-based detectors such as LIGO, VIRGO, GEO, and TAMA and a space-based detector LISA. Theoretical challenges for numerical relativists include calculating accurate waveforms generated by the sources likely to be detected by these GW observatories. These waveforms will greatly enhance the successful detection and interpretation of the signals. The final goal of our research program is to calculate waveforms for one such candidate--inspiralling binary neutron star system. The full Einstein equations in 3-D must be solved to follow both the dynamics of the binaries from initial inspiral to final merger, and the generation and propagation of gravitational waves into the wave zone. One of the crucial requirements for this kind of simulation is AMR (Adaptive Mesh Refinement). My talk is based on work-in-progress that solves the vacuum Einstein equations with strong gravitational waves as initial data. This problem constitutes a first step towards full simulations and allows us to test our AMR code without involving the complexity of hydrodynamics. 2-level AMR runs show that the fine grid tracks the features of the gravitational waves well.

  1. Stress, adaptation, and speciation in the evolution of the blind mole rat, Spalax, in Israel.

    Science.gov (United States)

    Nevo, Eviatar

    2013-02-01

    Environmental stress played a major role in the evolution of the blind mole rat superspecies Spalax ehrenbergi, affecting its adaptive evolution and ecological speciation underground. Spalax is safeguarded all of its life underground from aboveground climatic fluctuations and predators. However, it encounters multiple stresses in its underground burrows including darkness, energetics, hypoxia, hypercapnia, food scarcity, and pathogenicity. Consequently, it evolved adaptive genomic, proteomic, and phenomic complexes to cope with those stresses. Here I describe some of these adaptive complexes, and their theoretical and applied perspectives. Spalax mosaic molecular and organismal evolution involves reductions or regressions coupled with expansions or progressions caused by evolutionary tinkering and natural genetic engineering. Speciation of Spalax in Israel occurred in the Pleistocene, during the last 2.00-2.35 Mya, generating four species associated intimately with four climatic regimes with increasing aridity stress southwards and eastwards representing an ecological speciational adaptive trend: (Spalax golani, 2n=54→S. galili, 2n=52→S. carmeli, 2n=58→S. judaei, 2n=60). Darwinian ecological speciation occurred gradually with relatively little genetic change by Robertsonian chromosomal and genic mutations. Spalax genome sequencing has just been completed. It involves multiple adaptive complexes to life underground and is an evolutionary model to a few hundred underground mammals. It involves great promise in the future for medicine, space flight, and deep-sea diving. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Adaptive evolution and functional redesign of core metabolic proteins in snakes.

    Science.gov (United States)

    Castoe, Todd A; Jiang, Zhi J; Gu, Wanjun; Wang, Zhengyuan O; Pollock, David D

    2008-05-21

    Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts. We conducted extensive molecular evolutionary analyses on snake mitochondrial proteins and discovered multiple lines of evidence suggesting that the proteins at the core of aerobic metabolism in snakes have undergone remarkably large episodic bursts of adaptive change. We show that snake mitochondrial proteins experienced unprecedented levels of positive selection, coevolution, convergence, and reversion at functionally critical residues. We examined Cytochrome C oxidase subunit I (COI) in detail, and show that it experienced extensive modification of normally conserved residues involved in proton transport and delivery of electrons and oxygen. Thus, adaptive changes likely altered the flow of protons and other aspects of function in CO, thereby influencing fundamental characteristics of aerobic metabolism. We refer to these processes as "evolutionary redesign" because of the magnitude of the episodic bursts and the degree to which they affected core functional residues. The evolutionary redesign of snake COI coincided with adaptive bursts in other mitochondrial proteins and substantial changes in mitochondrial genome structure. It also generally coincided with or preceded major shifts in ecological niche and the evolution of extensive physiological adaptations related to lung reduction, large prey consumption, and venom evolution. The parallel timing of these major evolutionary events suggests that evolutionary redesign of metabolic and mitochondrial function may be related to, or underlie, the extreme changes in physiological and metabolic efficiency, flexibility, and innovation observed in snake evolution.

  3. Adaptive evolution and functional redesign of core metabolic proteins in snakes.

    Directory of Open Access Journals (Sweden)

    Todd A Castoe

    Full Text Available BACKGROUND: Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts. METHODOLOGY/PRINCIPAL FINDINGS: We conducted extensive molecular evolutionary analyses on snake mitochondrial proteins and discovered multiple lines of evidence suggesting that the proteins at the core of aerobic metabolism in snakes have undergone remarkably large episodic bursts of adaptive change. We show that snake mitochondrial proteins experienced unprecedented levels of positive selection, coevolution, convergence, and reversion at functionally critical residues. We examined Cytochrome C oxidase subunit I (COI in detail, and show that it experienced extensive modification of normally conserved residues involved in proton transport and delivery of electrons and oxygen. Thus, adaptive changes likely altered the flow of protons and other aspects of function in CO, thereby influencing fundamental characteristics of aerobic metabolism. We refer to these processes as "evolutionary redesign" because of the magnitude of the episodic bursts and the degree to which they affected core functional residues. CONCLUSIONS/SIGNIFICANCE: The evolutionary redesign of snake COI coincided with adaptive bursts in other mitochondrial proteins and substantial changes in mitochondrial genome structure. It also generally coincided with or preceded major shifts in ecological niche and the evolution of extensive physiological adaptations related to lung reduction, large prey consumption, and venom evolution. The parallel timing of these major evolutionary events suggests that evolutionary redesign of metabolic and mitochondrial function may be related to, or underlie, the extreme changes in physiological and metabolic efficiency, flexibility, and innovation observed in snake evolution.

  4. Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes

    Science.gov (United States)

    Gu, Wanjun; Wang, Zhengyuan O.; Pollock, David D.

    2008-01-01

    Background Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts. Methodology/Principal Findings We conducted extensive molecular evolutionary analyses on snake mitochondrial proteins and discovered multiple lines of evidence suggesting that the proteins at the core of aerobic metabolism in snakes have undergone remarkably large episodic bursts of adaptive change. We show that snake mitochondrial proteins experienced unprecedented levels of positive selection, coevolution, convergence, and reversion at functionally critical residues. We examined Cytochrome C oxidase subunit I (COI) in detail, and show that it experienced extensive modification of normally conserved residues involved in proton transport and delivery of electrons and oxygen. Thus, adaptive changes likely altered the flow of protons and other aspects of function in CO, thereby influencing fundamental characteristics of aerobic metabolism. We refer to these processes as “evolutionary redesign” because of the magnitude of the episodic bursts and the degree to which they affected core functional residues. Conclusions/Significance The evolutionary redesign of snake COI coincided with adaptive bursts in other mitochondrial proteins and substantial changes in mitochondrial genome structure. It also generally coincided with or preceded major shifts in ecological niche and the evolution of extensive physiological adaptations related to lung reduction, large prey consumption, and venom evolution. The parallel timing of these major evolutionary events suggests that evolutionary redesign of metabolic and mitochondrial function may be related to, or underlie, the extreme changes in physiological and metabolic efficiency, flexibility, and innovation observed in snake evolution. PMID:18493604

  5. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    LENUS (Irish Health Repository)

    Sen, Lin

    2011-06-03

    Abstract Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase\\/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such

  6. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns.

    Science.gov (United States)

    Sen, Lin; Fares, Mario A; Liang, Bo; Gao, Lei; Wang, Bo; Wang, Ting; Su, Ying-Juan

    2011-06-03

    The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that

  7. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    Directory of Open Access Journals (Sweden)

    Gao Lei

    2011-06-01

    Full Text Available Abstract Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco, the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional

  8. Closed-loop adaptation of neurofeedback based on mental effort facilitates reinforcement learning of brain self-regulation.

    Science.gov (United States)

    Bauer, Robert; Fels, Meike; Royter, Vladislav; Raco, Valerio; Gharabaghi, Alireza

    2016-09-01

    Considering self-rated mental effort during neurofeedback may improve training of brain self-regulation. Twenty-one healthy, right-handed subjects performed kinesthetic motor imagery of opening their left hand, while threshold-based classification of beta-band desynchronization resulted in proprioceptive robotic feedback. The experiment consisted of two blocks in a cross-over design. The participants rated their perceived mental effort nine times per block. In the adaptive block, the threshold was adjusted on the basis of these ratings whereas adjustments were carried out at random in the other block. Electroencephalography was used to examine the cortical activation patterns during the training sessions. The perceived mental effort was correlated with the difficulty threshold of neurofeedback training. Adaptive threshold-setting reduced mental effort and increased the classification accuracy and positive predictive value. This was paralleled by an inter-hemispheric cortical activation pattern in low frequency bands connecting the right frontal and left parietal areas. Optimal balance of mental effort was achieved at thresholds significantly higher than maximum classification accuracy. Rating of mental effort is a feasible approach for effective threshold-adaptation during neurofeedback training. Closed-loop adaptation of the neurofeedback difficulty level facilitates reinforcement learning of brain self-regulation. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  9. APPLICATION OF RESTART COVARIANCE MATRIX ADAPTATION EVOLUTION STRATEGY (RCMA-ES TO GENERATION EXPANSION PLANNING PROBLEM

    Directory of Open Access Journals (Sweden)

    K. Karthikeyan

    2012-10-01

    Full Text Available This paper describes the application of an evolutionary algorithm, Restart Covariance Matrix Adaptation Evolution Strategy (RCMA-ES to the Generation Expansion Planning (GEP problem. RCMA-ES is a class of continuous Evolutionary Algorithm (EA derived from the concept of self-adaptation in evolution strategies, which adapts the covariance matrix of a multivariate normal search distribution. The original GEP problem is modified by incorporating Virtual Mapping Procedure (VMP. The GEP problem of a synthetic test systems for 6-year, 14-year and 24-year planning horizons having five types of candidate units is considered. Two different constraint-handling methods are incorporated and impact of each method has been compared. In addition, comparison and validation has also made with dynamic programming method.

  10. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.

    Directory of Open Access Journals (Sweden)

    Alisha K Holloway

    2007-10-01

    Full Text Available Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties.

  11. Boots on the Ground: Science-Management Partnerships Facilitate Climate Change Adaptation in National Forests

    Science.gov (United States)

    Peterson, D. L.; Halofsky, J. E.

    2013-12-01

    Effective climate change engagement on public lands is characterized by (1) an enduring science-management partnership, (2) involvement of key stakeholders, (3) consideration of broad landscapes with multiple landowners, (4) science-based, peer-reviewed assessments of sensitivity of natural resources to climate change, (5) adaptation strategies and tactics developed by resource managers, and (6) leadership and a workforce motivated to implement climate-smart practices in resource planning and project management. Using this sequence of steps, the U.S. Forest Service, in collaboration with other agencies and universities, has developed climate change vulnerability assessments and adaptation plans for national forests and other lands. Although implementation (step 6) has been slow in some cases, the success of this process has been documented in 25 national forests and is now being accelerated across the National Forest System (155 national forests). Although hundreds of meetings, strategies, plans, and panels have focused on climate change adaptation over the past decade, only direct engagement between scientists and resource managers (less planning, more doing) has resulted in substantive outcomes.

  12. Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

    Science.gov (United States)

    Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Antunes, Agostinho

    2015-10-06

    The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

  13. Supportive Communication to Facilitate Chinese Patients' Adaptation to a Permanent Colostomy: A Qualitative Case Study Approach.

    Science.gov (United States)

    Tao, Hui; Songwathana, Praneed; Isaramalai, Sang-Arun; Wang, Qingxi

    2016-01-01

    This study, which is a part of action research, aims to explore how supportive communication can impact individuals' adaptation to a permanent colostomy in a Chinese cultural context. Two Chinese rectal cancer patients with complexity and difficulty in living with a permanent colostomy were selected using a qualitative case study approach. The researcher (H.T.) interacted with the participants along their journey from the preoperative period until the third postoperative month after discharge via face-to-face or telephone interviews. Content analysis was applied. Supportive communication was characterized by "communication as a supportive tool," which consisted of 4 elements: respect, description, empathy, and empowerment. The nursing strategies included (1) developing a collaborative relationship with patients and families; (2) understanding patients' concerns and problems; (3) discussing potential solutions; (4) encouraging patients to take action; (5) bringing out emotional expression; (6) normalizing negative emotions; and (7) protecting hope. The findings of this study informed that supportive communication is a valuable tool for nurses to provide informational and emotional support to Chinese patients in order to enhance their adaptation to living with a permanent colostomy. Developing an operational manual to enhance supportive communication for patients with colostomy is suggested.

  14. Adaptation to different host plant ages facilitates insect divergence without a host shift.

    Science.gov (United States)

    Zhang, Bin; Segraves, Kari A; Xue, Huai-Jun; Nie, Rui-E; Li, Wen-Zhu; Yang, Xing-Ke

    2015-09-22

    Host shifts and subsequent adaption to novel host plants are important drivers of speciation among phytophagous insects. However, there is considerably less evidence for host plant-mediated speciation in the absence of a host shift. Here, we investigated divergence of two sympatric sister elm leaf beetles, Pyrrhalta maculicollis and P. aenescens, which feed on different age classes of the elm Ulmus pumila L. (seedling versus adult trees). Using a field survey coupled with preference and performance trials, we show that these beetle species are highly divergent in both feeding and oviposition preference and specialize on either seedling or adult stages of their host plant. An experiment using artificial leaf discs painted with leaf surface wax extracts showed that host plant chemistry is a critical element that shapes preference. Specialization appears to be driven by adaptive divergence as there was also evidence of divergent selection; beetles had significantly higher survival and fecundity when reared on their natal host plant age class. Together, the results identify the first probable example of divergence induced by host plant age, thus extending how phytophagous insects might diversify in the absence of host shifts. © 2015 The Author(s).

  15. Cerebellar, but not Motor or Parietal, High-Density Anodal Transcranial Direct Current Stimulation Facilitates Motor Adaptation.

    Science.gov (United States)

    Doppelmayr, Michael; Pixa, Nils Henrik; Steinberg, Fabian

    2016-10-01

    Although motor adaptation is a highly relevant process for both everyday life as well as rehabilitation many details of this process are still unresolved. To evaluate the contribution of primary motor (M1), parietal and cerebellar areas to motor adaptation processes transcranial direct current stimulation (tDCS) has been applied. We hypothesized that anodal stimulation of the cerebellum and the M1 improves the learning process in mirror drawing, a task involving fine grained and spatially well-organized hand movements. High definition tDCS (HD-tDCS) allows a focal stimulation to modulate brain processes. In a single-session double-blind study, we compared the effects of different anodal stimulation procedures. The groups received stimulation either at the cerebellum (CER), at right parietal (PAR), or at left M1, and a SHAM group was included. Participants (n=83) had to complete several mirror drawing tasks before, during, and after stimulation. They were instructed to re-trace a line in the shape of a pentagonal star as fast and accurate as possible. Tracing time (seconds) and accuracy (deviation in mm) have been evaluated. The results indicated that cerebellar HD-tDCS can facilitate motor adaptation in a single session. The stimulation at M1 showed only a tendency to increase motor adaptation and these effects were visible only during the first part of the stimulation. Stimulating the right parietal area, relevant for visuospatial processing did not lead to increased performance. Our results suggest that motor adaptation relies to a great extent on cerebellar functions and HD-tDCS can speed up this process. (JINS, 2016, 22, 928-936).

  16. Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

    Science.gov (United States)

    Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

    2016-01-01

    This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

  17. Visual Experience Facilitates BDNF-Dependent Adaptive Recruitment of New Neurons in the Postembryonic Optic Tectum.

    Science.gov (United States)

    Hall, Zachary J; Tropepe, Vincent

    2018-02-21

    Postembryonic brain development is sensitive to environmental input and sensory experience, but the mechanisms underlying healthy adaptive brain growth are poorly understood. Here, we tested the importance of visual experience on larval zebrafish ( Danio rerio ) postembryonic development of the optic tectum (OT), a midbrain structure involved in visually guided behavior. We first characterized postembryonic neurogenic growth in OT, in which new neurons are generated along the caudal tectal surface and contribute appositionally to anatomical growth. Restricting visual experience during development by rearing larvae in dim light impaired OT anatomical and neurogenic growth, specifically by reducing the survival of new neurons in the medial periventricular gray zone. Neuronal survival in the OT was reduced only when visual experience was restricted for the first 5 d following new neuron generation, suggesting that tectal neurons exhibit an early sensitive period in which visual experience protects these cells from subsequent neuronal loss. The effect of dim rearing on neuronal survival was mimicked by treatment with an NMDA receptor antagonist early, but not later, in a new neuron's life. Both dim rearing and antagonist treatment reduced BDNF production in the OT, and supplementing larvae with exogenous BDNF during dim rearing prevented neuronal loss, suggesting that visual experience protects new tectal neurons through neural activity-dependent BDNF expression. Collectively, we present evidence for a sensitive period of neurogenic adaptive growth in the larval zebrafish OT that relies on visual experience-dependent mechanisms. SIGNIFICANCE STATEMENT Early brain development is shaped by environmental factors via sensory input; however, this form of experience-dependent neuroplasticity is traditionally studied as structural and functional changes within preexisting neurons. Here, we found that restricting visual experience affects development of the larval zebrafish

  18. A Convergent Differential Evolution Algorithm with Hidden Adaptation Selection for Engineering Optimization

    Directory of Open Access Journals (Sweden)

    Zhongbo Hu

    2014-01-01

    Full Text Available Many improved differential Evolution (DE algorithms have emerged as a very competitive class of evolutionary computation more than a decade ago. However, few improved DE algorithms guarantee global convergence in theory. This paper developed a convergent DE algorithm in theory, which employs a self-adaptation scheme for the parameters and two operators, that is, uniform mutation and hidden adaptation selection (haS operators. The parameter self-adaptation and uniform mutation operator enhance the diversity of populations and guarantee ergodicity. The haS can automatically remove some inferior individuals in the process of the enhancing population diversity. The haS controls the proposed algorithm to break the loop of current generation with a small probability. The breaking probability is a hidden adaptation and proportional to the changes of the number of inferior individuals. The proposed algorithm is tested on ten engineering optimization problems taken from IEEE CEC2011.

  19. Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization.

    Science.gov (United States)

    Wang, Meng; Yu, Chenzhao; Zhao, Huimin

    2016-03-01

    A highly active xylose specific transporter without glucose inhibition is highly desirable in cost-effective production of biofuels from lignocellulosic biomass. However, currently available xylose specific transporters suffer from low overall activity and most are inhibited by glucose. In this study, we applied a directed evolution strategy to engineer the xylose specific transporter AN25 from Neurospora crassa with improved xylose transportation capacity. After four rounds of directed evolution using two different strategies, we obtained an AN25 mutant AN25-R4.18 with 43-fold improvement in terms of xylose transportation capacity while maintaining its high xylose specificity. In addition, glucose inhibition was almost completely eliminated in the final evolved mutant. We demonstrated that improved xylose transportation of AN25 mutants in the exponential growth phase led to significant improvement of xylose consumption in high cell-density fermentation. Finally, we showed that AN25 mutant AN25-R4.18 can enable relatively efficient glucose-xylose co-utilization in high concentrations of mixed sugars. © 2015 Wiley Periodicals, Inc.

  20. Go forth, evolve and prosper: the genetic basis of adaptive evolution in an invasive species.

    Science.gov (United States)

    Franks, Steven J; Munshi-South, Jason

    2014-05-01

    Invasive species stand accused of a familiar litany of offences, including displacing native species, disrupting ecological processes and causing billions of dollars in ecological damage (Cox 1999). Despite these transgressions, invasive species have at least one redeeming virtue--they offer us an unparalleled opportunity to investigate colonization and responses of populations to novel conditions in the invaded habitat (Elton 1958; Sakai et al. 2001). Invasive species are by definition colonists that have arrived and thrived in a new location. How they are able to thrive is of great interest, especially considering a paradox of invasion (Sax & Brown 2000): if many populations are locally adapted (Leimu & Fischer 2008), how could species introduced into new locations become so successful? One possibility is that populations adjust to the new conditions through plasticity--increasing production of allelopathic compounds (novel weapons), or taking advantage of new prey, for example. Alternatively, evolution could play a role, with the populations adapting to the novel conditions of the new habitat. There is increasing evidence, based on phenotypic data, for rapid adaptive evolution in invasive species (Franks et al. 2012; Colautti & Barrett 2013; Sultan et al. 2013). Prior studies have also demonstrated genetic changes in introduced populations using neutral markers, which generally do not provide information on adaptation. Thus, the genetic basis of adaptive evolution in invasive species has largely remained unknown. In this issue of Molecular Ecology, Vandepitte et al. (2014) provide some of the first evidence in invasive populations for molecular genetic changes directly linked to adaptation. © 2014 John Wiley & Sons Ltd.

  1. Rapid adaptive evolution of photoperiodic response during invasion and range expansion across a climatic gradient.

    Science.gov (United States)

    Urbanski, Jennifer; Mogi, Motoyoshi; O'Donnell, Deborah; DeCotiis, Mark; Toma, Takako; Armbruster, Peter

    2012-04-01

    Abstract Understanding the mechanisms of adaptation to spatiotemporal environmental variation is a fundamental goal of evolutionary biology. This issue also has important implications for anticipating biological responses to contemporary climate warming and determining the processes by which invasive species are able to spread rapidly across broad geographic ranges. Here, we compare data from a historical study of latitudinal variation in photoperiodic response among Japanese and U.S. populations of the invasive Asian tiger mosquito Aedes albopictus with contemporary data obtained using comparable methods. Our results demonstrated rapid adaptive evolution of the photoperiodic response during invasion and range expansion across ∼15° of latitude in the United States. In contrast to the photoperiodic response, size-based morphological traits implicated in climatic adaptation in a wide range of other insects did not show evidence of adaptive variation in Ae. albopictus across either the U.S. (invasive) or Japanese (native) range. These results show that photoperiodism has been an important adaptation to climatic variation across the U.S. range of Ae. albopictus and, in conjunction with previous studies, strongly implicate the photoperiodic control of seasonal development as a critical evolutionary response to ongoing contemporary climate change. These results also emphasize that photoperiodism warrants increased attention in studies of the evolution of invasive species.

  2. Local adaptation and the evolution of phenotypic plasticity in Trinidadian guppies (Poecilia reticulata).

    Science.gov (United States)

    Torres-Dowdall, Julián; Handelsman, Corey A; Reznick, David N; Ghalambor, Cameron K

    2012-11-01

    Divergent selection pressures across environments can result in phenotypic differentiation that is due to local adaptation, phenotypic plasticity, or both. Trinidadian guppies exhibit local adaptation to the presence or absence of predators, but the degree to which predator-induced plasticity contributes to population differentiation is less clear. We conducted common garden experiments on guppies obtained from two drainages containing populations adapted to high- and low-predation environments. We reared full-siblings from all populations in treatments simulating the presumed ancestral (predator cues present) and derived (predator cues absent) conditions and measured water column use, head morphology, and size at maturity. When reared in presence of predator cues, all populations had phenotypes that were typical of a high-predation ecotype. However, when reared in the absence of predator cues, guppies from high- and low-predation regimes differed in head morphology and size at maturity; the qualitative nature of these differences corresponded to those that characterize adaptive phenotypes in high- versus low-predation environments. Thus, divergence in plasticity is due to phenotypic differences between high- and low-predation populations when reared in the absence of predator cues. These results suggest that plasticity might initially play an important role during colonization of novel environments, and then evolve as a by-product of adaptation to the derived environment. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  3. Solving Problems, Ensuring Relevance and Facilitating Change: The Evolution of Needs Assessment Within Cooperative Extension

    Directory of Open Access Journals (Sweden)

    Barry A. Garst

    2015-06-01

    Full Text Available Helping people solve the practical problems of everyday life while maintaining contemporary relevance describes the mission of Cooperative Extension. To achieve that mission, Extension professionals have increasingly relied on information gathered from stakeholders to identify relevant problems and potential educational solutions. The methods, efforts, and activities to understand people and their problems are collectively referred to as needs assessment. This article explores the history and evolution of needs assessment in Cooperative Extension, as well as in a broader educational context. While tracing needs assessment through the decades, this article examines the needs assessment opportunities and challenges faced by Cooperative Extension. Emerging trends and implications for the future of Extension needs assessment are also discussed.

  4. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.

    Directory of Open Access Journals (Sweden)

    Richard A Goldstein

    2008-05-01

    Full Text Available Bacteria are able to sense and respond to a variety of external stimuli, with responses that vary from stimuli to stimuli and from species to species. The best-understood is chemotaxis in the model organism Escherichia coli, where the dynamics and the structure of the underlying pathway are well characterised. It is not clear, however, how well this detailed knowledge applies to mechanisms mediating responses to other stimuli or to pathways in other species. Furthermore, there is increasing experimental evidence that bacteria integrate responses from different stimuli to generate a coherent taxis response. We currently lack a full understanding of the different pathway structures and dynamics and how this integration is achieved. In order to explore different pathway structures and dynamics that can underlie taxis responses in bacteria, we perform a computational simulation of the evolution of taxis. This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria better able to localise with favourable conditions gain a selective advantage. We find that a certain dynamics evolves consistently under different model assumptions and environments. These dynamics, which we call non-adaptive dynamics, directly couple tumbling probability of the cell to increasing stimuli. Dynamics that are adaptive under a wide range of conditions, as seen in the chemotaxis pathway of E. coli, do not evolve in these evolutionary simulations. However, we find that stimulus scarcity and fluctuations during evolution results in complex pathway dynamics that result both in adaptive and non-adaptive dynamics depending on basal stimuli levels. Further analyses of evolved pathway structures show that effective taxis dynamics can be mediated with as few as two components. The non-adaptive dynamics

  5. Usability of clinical decision support system as a facilitator for learning the assistive technology adaptation process.

    Science.gov (United States)

    Danial-Saad, Alexandra; Kuflik, Tsvi; Weiss, Patrice L Tamar; Schreuer, Naomi

    2016-01-01

    The aim of this study was to evaluate the usability of Ontology Supported Computerized Assistive Technology Recommender (OSCAR), a Clinical Decision Support System (CDSS) for the assistive technology adaptation process, its impact on learning the matching process, and to determine the relationship between its usability and learnability. Two groups of expert and novice clinicians (total, n = 26) took part in this study. Each group filled out system usability scale (SUS) to evaluate OSCAR's usability. The novice group completed a learning questionnaire to assess OSCAR's effect on their ability to learn the matching process. Both groups rated OSCAR's usability as "very good", (M [SUS] = 80.7, SD = 11.6, median = 83.7) by the novices, and (M [SUS] = 81.2, SD = 6.8, median = 81.2) by the experts. The Mann-Whitney results indicated that no significant differences were found between the expert and novice groups in terms of OSCAR's usability. A significant positive correlation existed between the usability of OSCAR and the ability to learn the adaptation process (rs = 0.46, p = 0.04). Usability is an important factor in the acceptance of a system. The successful application of user-centered design principles during the development of OSCAR may serve as a case study that models the significant elements to be considered, theoretically and practically in developing other systems. Implications for Rehabilitation Creating a CDSS with a focus on its usability is an important factor for its acceptance by its users. Successful usability outcomes can impact the learning process of the subject matter in general, and the AT prescription process in particular. The successful application of User-Centered Design principles during the development of OSCAR may serve as a case study that models the significant elements to be considered, theoretically and practically. The study emphasizes the importance of close collaboration between the developers and

  6. The evolution of cultural adaptations: Fijian food taboos protect against dangerous marine toxins

    Science.gov (United States)

    Henrich, Joseph; Henrich, Natalie

    2010-01-01

    The application of evolutionary theory to understanding the origins of our species' capacities for social learning has generated key insights into cultural evolution. By focusing on how our psychology has evolved to adaptively extract beliefs and practices by observing others, theorists have hypothesized how social learning can, over generations, give rise to culturally evolved adaptations. While much field research documents the subtle ways in which culturally transmitted beliefs and practices adapt people to their local environments, and much experimental work reveals the predicted patterns of social learning, little research connects real-world adaptive cultural traits to the patterns of transmission predicted by these theories. Addressing this gap, we show how food taboos for pregnant and lactating women in Fiji selectively target the most toxic marine species, effectively reducing a woman's chances of fish poisoning by 30 per cent during pregnancy and 60 per cent during breastfeeding. We further analyse how these taboos are transmitted, showing support for cultural evolutionary models that combine familial transmission with selective learning from locally prestigious individuals. In addition, we explore how particular aspects of human cognitive processes increase the frequency of some non-adaptive taboos. This case demonstrates how evolutionary theory can be deployed to explain both adaptive and non-adaptive behavioural patterns. PMID:20667878

  7. Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda).

    Science.gov (United States)

    Liu, Weixin; Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

    2017-01-01

    Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life.

  8. Inflammatory Monocytes Facilitate Adaptive CD4 T Cell Responses during Respiratory Fungal Infection

    Science.gov (United States)

    Hohl, Tobias M.; Rivera, Amariliz; Lipuma, Lauren; Gallegos, Alena; Shi, Chao; Mack, Mathias; Pamer, Eric G.

    2009-01-01

    SUMMARY Aspergillus fumigatus, a ubiquitous fungus, causes invasive disease in immunocompromised humans. Although monocytes and antigen-specific CD4 T cells contribute to defense against inhaled fungal spores, how these cells interact during infection remains undefined. Investigating the role of inflammatory monocytes and monocyte-derived dendritic cells during fungal infection, we find that A. fumigatus infection induces an influx of chemokine receptor CCR2- and Ly6C-expressing inflammatory monocytes into lungs and draining lymph nodes. Depletion of CCR2+ cells reduced A. fumigatus conidial transport from lungs to draining lymph nodes, abolished CD4 T cell priming following respiratory challenge, and impaired pulmonary fungal clearance. In contrast, depletion of CCR2+Ly6Chi monocytes during systemic fungal infection did not prevent CD4 T cell priming in the spleen. Our findings demonstrate that pulmonary CD4 T cell responses to inhaled spores require CCR2+Ly6Chi monocytes and their derivatives, revealing a compartmentally restricted function for these cells in adaptive respiratory immune responses. PMID:19917501

  9. Adaptation of acaricide stress facilitates Tetranychus urticae expanding against Tetranychus cinnabarinus in China.

    Science.gov (United States)

    Lu, Wencai; Wang, Mengyao; Xu, Zhifeng; Shen, Guangmao; Wei, Peng; Li, Ming; Reid, William; He, Lin

    2017-02-01

    The two-spotted spider mite, Tetranychus urticae, and the carmine spider mite, Tetranychus cinnabarinus, are invasive and native species in China, respectively. Compared with T. cinnabarinus, T. urticae has expanded into most parts of China and has become the dominant species of spider mite since 1983, when it was first reported in China. However, the mechanism of the demographic conversion has not been illuminated. In this study, one T. urticae field population and one T. cinnabarinus field population were isolated from the same plant in the same field, and the toxicological characteristics were compared between these two species. Laboratory bioassays demonstrated that T. urticae was more tolerant to commonly used acaricides than T. cinnabarinus. The activities of detoxification enzymes were significantly greater in T. urticae, and the fold changes of enzymes activities in T. urticae were also greater following exposure to acaricides. Furthermore, more metabolism-related genes were upregulated at a basal level, and more genes were induced in T. urticae following exposure to acaricides. The comparison of proteins and genes between both species led credence to the hypothesis that T. urticae was more resistant to acaricides, which was the reason explaining the expansion of invasive T. urticae against native T. cinnabarinus. Laboratory simulation experiments demonstrated that following the application of acaricides, the composition of a mixed T. urticae/T. cinnabarinus population would change from a T. cinnabarinus-dominant to a T. urticae-dominant population. This study not only reveals that T. urticae possesses stronger detoxification capacity than its sibling species T. cinnabarinus, which facilitated its persistent expansion in China, but also points to the need to accurately identify Tetranychus species and to develop species-specific management strategies for these pests.

  10. Non-equilibrium physics and evolution--adaptation, extinction, and ecology: a key issues review.

    Science.gov (United States)

    Kussell, E; Vucelja, M

    2014-10-01

    Evolutionary dynamics in nature constitute an immensely complex non-equilibrium process. We review the application of physical models of evolution, by focusing on adaptation, extinction, and ecology. In each case, we examine key concepts by working through examples. Adaptation is discussed in the context of bacterial evolution, with a view toward the relationship between growth rates, mutation rates, selection strength, and environmental changes. Extinction dynamics for an isolated population are reviewed, with emphasis on the relation between timescales of extinction, population size, and temporally correlated noise. Ecological models are discussed by focusing on the effect of spatial interspecies interactions on diversity. Connections between physical processes--such as diffusion, turbulence, and localization--and evolutionary phenomena are highlighted.

  11. Adaptive evolution of an artificial RNA genome to a reduced ribosome environment.

    Science.gov (United States)

    Mizuuchi, Ryo; Ichihashi, Norikazu; Usui, Kimihito; Kazuta, Yasuaki; Yomo, Tetsuya

    2015-03-20

    The reconstitution of an artificial system that has the same evolutionary ability as a living thing is a major challenge in the in vitro synthetic biology. In this study, we tested the adaptive evolutionary ability of an artificial RNA genome replication system, termed the translation-coupled RNA replication (TcRR) system. In a previous work, we performed a study of the long-term evolution of the genome with an excess amount of ribosome. In this study, we continued the evolution experiment in a reduced-ribosome environment and observed that the mutant genome compensated for the reduced ribosome concentration. This result demonstrated the ability of the TcRR system to adapt and may be a step toward generating living things with evolutionary ability.

  12. Facilitating adaptation in montane plants to changing precipitation along an elevation gradient

    Science.gov (United States)

    Hess, Steve; Leopold, Christina

    2017-01-01

    Montane plant communities throughout the world have responded to changes in precipitation and temperature regimes by shifting ranges upward in elevation. Continued warmer, drier climate conditions have been documented and are projected to increase in high-elevation areas in Hawai‘i, consistent with climate change effects reported in other environments throughout the world. Organisms that cannot disperse or adapt biologically to projected climate scenarios in situ may decrease in distributional range and abundance over time. Restoration efforts will need to accommodate future climate change and account for the interactive effects of existing invasive species to ensure long-term persistence. As part of a larger, ongoing restoration effort, we hypothesized that plants from a lower-elevation forest ecotype would have higher rates of survival and growth compared to high-elevation forest conspecifics when grown in common plots along an elevation gradient. We monitored climate conditions at planting sites to identify whether temperature or rainfall influenced survival and growth after 20 weeks. We found that origin significantly affected survival in only one of three native montane species, Dodonaea viscosa. Contrary to our hypothesis, 75.2% of seedlings from high-elevation origin survived in comparison to 58.7% of seedlings from low elevation across the entire elevation gradient. Origin also influenced survival in linearized mixed models that controlled for temperature, precipitation, and elevation in D. viscosa and Chenopodium oahuense. Only C. oahuense seedlings had similar predictors of growth and survival. There were no common patterns of growth or survival between species, indicating that responses to changing precipitation and emperature regimes varied between montane plant species. Results also suggest that locally sourced seed is important to ensure highest survival at restoration sites. Further experimentation on larger spatial and temporal scales is necessary

  13. Anhydrobiosis and freezing-tolerance: adaptations that facilitate the establishment of Panagrolaimus nematodes in polar habitats.

    Science.gov (United States)

    McGill, Lorraine M; Shannon, Adam J; Pisani, Davide; Félix, Marie-Anne; Ramløv, Hans; Dix, Ilona; Wharton, David A; Burnell, Ann M

    2015-01-01

    Anhydrobiotic animals can survive the loss of both free and bound water from their cells. While in this state they are also resistant to freezing. This physiology adapts anhydrobiotes to harsh environments and it aids their dispersal. Panagrolaimus davidi, a bacterial feeding anhydrobiotic nematode isolated from Ross Island Antarctica, can survive intracellular ice formation when fully hydrated. A capacity to survive freezing while fully hydrated has also been observed in some other Antarctic nematodes. We experimentally determined the anhydrobiotic and freezing-tolerance phenotypes of 24 Panagrolaimus strains from tropical, temperate, continental and polar habitats and we analysed their phylogenetic relationships. We found that several other Panagrolaimus isolates can also survive freezing when fully hydrated and that tissue extracts from these freezing-tolerant nematodes can inhibit the growth of ice crystals. We show that P. davidi belongs to a clade of anhydrobiotic and freezing-tolerant panagrolaimids containing strains from temperate and continental regions and that P. superbus, an early colonizer at Surtsey island, Iceland after its volcanic formation, is closely related to a species from Pennsylvania, USA. Ancestral state reconstructions show that anhydrobiosis evolved deep in the phylogeny of Panagrolaimus. The early-diverging Panagrolaimus lineages are strongly anhydrobiotic but weakly freezing-tolerant, suggesting that freezing tolerance is most likely a derived trait. The common ancestors of the davidi and the superbus clades were anhydrobiotic and also possessed robust freezing tolerance, along with a capacity to inhibit the growth and recrystallization of ice crystals. Unlike other endemic Antarctic nematodes, the life history traits of P. davidi do not show evidence of an evolved response to polar conditions. Thus we suggest that the colonization of Antarctica by P. davidi and of Surtsey by P. superbus may be examples of recent "ecological fitting

  14. Comparison-based Adaptive Strategy Selection with Bandits in Differential Evolution

    OpenAIRE

    Fialho, Álvaro; Ros, Raymond; Schoenauer, Marc; Sebag, Michèle

    2010-01-01

    International audience; Differential Evolution is a popular powerful optimization algorithm for continuous problems. Part of its efficiency comes from the availability of several mutation strategies that can (and must) be chosen in a problem-dependent way. However, such flexibility also makes DE difficult to be automatically used in a new context. F-AUC-Bandit is a comparison-based Adaptive Operator Selection method that has been proposed in the GA framework. It is used here for the on-line c...

  15. Evolution of the Marginal Ice Zone: Adaptive Sampling with Autonomous Gliders

    Science.gov (United States)

    2015-09-30

    access marginal ice zone . When operating in ice-covered waters, gliders navigate by trilateration from acoustic sound sources (or dead reckoning should...release; distribution is unlimited. Evolution of the Marginal Ice Zone : Adaptive Sampling with Autonomous Gliders Craig M. Lee, Luc Rainville and Jason I...edge after one week. All for gliders did several sections from the open ocean, through the marginal ice zone , to the fully ice-covered ocean (Fig. 1

  16. Limited fitness costs of herbicide-resistance traits in Amaranthus tuberculatus facilitate resistance evolution.

    Science.gov (United States)

    Wu, Chenxi; Davis, Adam S; Tranel, Patrick J

    2018-02-01

    The fitness cost of herbicide resistance (HR) in the absence of herbicide selection plays a key role in HR evolution. Quantifying the fitness cost of resistance, however, is challenging, and there exists a knowledge gap in this area. A synthetic (artificially generated) Amaranthus tuberculatus population segregating for five types of HR was subjected to competitive growth conditions in the absence of herbicide selection for six generations. Fitness costs were quantified by using a combination of phenotyping and genotyping to monitor HR frequency changes over generations. In the absence of herbicide selection, a significant fitness cost was observed for resistance to acetolactate synthase-inhibiting herbicides, but not for resistances to atrazine (non-target-site resistance mechanism), protoporphyrinogen oxidase inhibitors, 4-hydroxyphenylpryuvate dioxygenase inhibitors or glyphosate. Glyphosate resistance was conferred by multiple mechanisms in the synthetic population, and further analysis revealed that one mechanism, amplification of the 5-enolypyruvylshikimate-3-phosphate synthase gene, did decrease in frequency. Our results indicate that herbicide-resistance mitigation strategies (e.g. herbicide rotation) that rely on the existence of fitness costs in the absence of herbicide selection likely will be largely ineffective in many cases. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  17. Function, Structure, and Evolution of the Major Facilitator Superfamily: The LacY Manifesto

    Directory of Open Access Journals (Sweden)

    M. Gregor Madej

    2014-01-01

    Full Text Available The major facilitator superfamily (MFS is a diverse group of secondary transporters with members found in all kingdoms of life. A paradigm for MFS is the lactose permease (LacY of Escherichia coli, which couples the stoichiometric translocation of a galactopyranoside and an H+ across the cytoplasmic membrane. LacY has been the test bed for the development of many methods applied for the analysis of transport proteins. X-ray structures of an inward-facing conformation and the most recent structure of an almost occluded conformation confirm many conclusions from previous studies. Although structure models are critical, they are insufficient to explain the catalysis of transport. The clues to understanding transport are based on the principles of enzyme kinetics. Secondary transport is a dynamic process—static snapshots of X-ray crystallography describe it only partially. However, without structural information, the underlying chemistry is virtually impossible to conclude. A large body of biochemical/biophysical data derived from systematic studies of site-directed mutants in LacY suggests residues critically involved in the catalysis, and a working model for the symport mechanism that involves alternating access of the binding site is presented. The general concepts derived from the bacterial LacY are examined for their relevance to other MFS transporters.

  18. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation

    Science.gov (United States)

    2012-01-01

    Background The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei. PMID:23035691

  19. Microbial community succession mechanism coupling with adaptive evolution of adsorption performance in chalcopyrite bioleaching.

    Science.gov (United States)

    Feng, Shoushuai; Yang, Hailin; Wang, Wu

    2015-09-01

    The community succession mechanism of Acidithiobacillus sp. coupling with adaptive evolution of adsorption performance were systematically investigated. Specifically, the μmax of attached and free cells was increased and peak time was moved ahead, indicating both cell growth of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans was promoted. In the mixed strains system, the domination courses of A. thiooxidans was dramatically shortened from 22th day to 15th day, although community structure finally approached to the normal system. Compared to A. ferrooxidans, more positive effects of adaptive evolution on cell growth of A. thiooxidans were shown in either single or mixed strains system. Moreover, higher concentrations of sulfate and ferric ions indicated that both sulfur and iron metabolism was enhanced, especially of A. thiooxidans. Consistently, copper ion production was improved from 65.5 to 88.5 mg/L. This new adaptive evolution and community succession mechanism may be useful for guiding similar bioleaching processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.

    Science.gov (United States)

    Sandberg, Troy E; Lloyd, Colton J; Palsson, Bernhard O; Feist, Adam M

    2017-07-01

    Adaptive laboratory evolution (ALE) experiments are often designed to maintain a static culturing environment to minimize confounding variables that could influence the adaptive process, but dynamic nutrient conditions occur frequently in natural and bioprocessing settings. To study the nature of carbon substrate fitness tradeoffs, we evolved batch cultures of Escherichia coli via serial propagation into tubes alternating between glucose and either xylose, glycerol, or acetate. Genome sequencing of evolved cultures revealed several genetic changes preferentially selected for under dynamic conditions and different adaptation strategies depending on the substrates being switched between; in some environments, a persistent "generalist" strain developed, while in another, two "specialist" subpopulations arose that alternated dominance. Diauxic lag phenotype varied across the generalists and specialists, in one case being completely abolished, while gene expression data distinguished the transcriptional strategies implemented by strains in pursuit of growth optimality. Genome-scale metabolic modeling techniques were then used to help explain the inherent substrate differences giving rise to the observed distinct adaptive strategies. This study gives insight into the population dynamics of adaptation in an alternating environment and into the underlying metabolic and genetic mechanisms. Furthermore, ALE-generated optimized strains have phenotypes with potential industrial bioprocessing applications.IMPORTANCE Evolution and natural selection inexorably lead to an organism's improved fitness in a given environment, whether in a laboratory or natural setting. However, despite the frequent natural occurrence of complex and dynamic growth environments, laboratory evolution experiments typically maintain simple, static culturing environments so as to reduce selection pressure complexity. In this study, we investigated the adaptive strategies underlying evolution to fluctuating

  1. Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution.

    Science.gov (United States)

    Flegr, Jaroslav

    2013-01-16

    Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation--while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.

  2. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

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    Carolina M. Voloch

    2014-11-01

    Full Text Available Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G, RNA-dependent RNA polymerase (L and polymerase (P genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

  3. Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

    Science.gov (United States)

    Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

    2014-01-01

    Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

  4. Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts.

    Directory of Open Access Journals (Sweden)

    Erin S Kelleher

    2007-08-01

    Full Text Available It frequently has been postulated that intersexual coevolution between the male ejaculate and the female reproductive tract is a driving force in the rapid evolution of reproductive proteins. The dearth of research on female tracts, however, presents a major obstacle to empirical tests of this hypothesis. Here, we employ a comparative EST approach to identify 241 candidate female reproductive proteins in Drosophila arizonae, a repleta group species in which physiological ejaculate-female coevolution has been documented. Thirty-one of these proteins exhibit elevated amino acid substitution rates, making them candidates for molecular coevolution with the male ejaculate. Strikingly, we also discovered 12 unique digestive proteases whose expression is specific to the D. arizonae lower female reproductive tract. These enzymes belong to classes most commonly found in the gastrointestinal tracts of a diverse array of organisms. We show that these proteases are associated with recent, lineage-specific gene duplications in the Drosophila repleta species group, and exhibit strong signatures of positive selection. Observation of adaptive evolution in several female reproductive tract proteins indicates they are active players in the evolution of reproductive tract interactions. Additionally, pervasive gene duplication, adaptive evolution, and rapid acquisition of a novel digestive function by the female reproductive tract points to a novel coevolutionary mechanism of ejaculate-female interaction.

  5. Within-host co-evolution of chronic viruses and the adaptive immune system

    Science.gov (United States)

    Nourmohammad, Armita

    We normally think of evolution occurring in a population of organisms, in response to their external environment. Rapid evolution of cellular populations also occurs within our bodies, as the adaptive immune system works to eliminate infection. Some pathogens, such as HIV, are able to persist in a host for extended periods of time, during which they also evolve to evade the immune response. In this talk I will introduce an analytical framework for the rapid co-evolution of B-cell and viral populations, based on the molecular interactions between them. Since the co-evolution of antibodies and viruses is perpetually out of equilibrium, I will show how to quantify the amount of adaptation in each of the two populations by analysis of their co-evolutionary history. I will discuss the consequences of competition between lineages of antibodies, and characterize the fate of a given lineage dependent on the state of the antibody and viral populations. In particular, I will discuss the conditions for emergence of highly potent broadly neutralizing antibodies, which are now recognized as critical for designing an effective vaccine against HIV.

  6. Contribution of Multiple Inter-kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-killing Chytrid, Batrachochytrium dendrobatidis

    Directory of Open Access Journals (Sweden)

    Baofa Sun

    2016-08-01

    Full Text Available Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd. Although horizontal gene transfer (HGT facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.

  7. Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis.

    Science.gov (United States)

    Sun, Baofa; Li, Tong; Xiao, Jinhua; Liu, Li; Zhang, Peng; Murphy, Robert W; He, Shunmin; Huang, Dawei

    2016-01-01

    Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.

  8. Rapid implementation of the repair-misrepair-fixation (RMF) model facilitating online adaption of radiosensitivity parameters in ion therapy

    Science.gov (United States)

    Kamp, F.; Carlson, D. J.; Wilkens, J. J.

    2017-07-01

    Introduction: Treatment planning for ion therapy must account for physical properties of the beam as well as differences in the relative biological effectiveness (RBE) of ions compared to photons. In this work, we present a fast RBE calculation approach, based on the decoupling of physical properties and the αx / βx ratio commonly used to describe the radiosensitivity of irradiated cells or organs. Material and methods: In the framework of the mechanistic repair-misrepair-fixation (RMF) model, the biological modeling can be decoupled from the physical dose. This was implemented into a research treatment planning system for carbon ion therapy. Results: The presented implementation of the RMF model is very fast, allowing online changes of αx / βx . For example, a change of αx / βx including a complete biological modeling and a recalculation of RBE for 2.9\\cdot 105 voxel takes 4 ms on a 4 CPU, 3.2 GHz workstation. Discussion and conclusion: The derived decoupling within the RMF model allows fast changes in αx / βx , facilitating online adaption by the user. This provides new options for radiation oncologists, facilitating online variations of the radiobiological input parameters during the treatment plan evaluation process as well as uncertainty and sensitivity analyses.

  9. Evolution of adaptive diversity and genetic connectivity in Arctic charr (Salvelinus alpinus) in Iceland

    Science.gov (United States)

    Kapralova, K H; Morrissey, M B; Kristjánsson, B K; Ólafsdóttir, G Á; Snorrason, S S; Ferguson, M M

    2011-01-01

    The ecological theory of adaptive radiation predicts that the evolution of phenotypic diversity within species is generated by divergent natural selection arising from different environments and competition between species. Genetic connectivity among populations is likely also to have an important role in both the origin and maintenance of adaptive genetic diversity. Our goal was to evaluate the potential roles of genetic connectivity and natural selection in the maintenance of adaptive phenotypic differences among morphs of Arctic charr, Salvelinus alpinus, in Iceland. At a large spatial scale, we tested the predictive power of geographic structure and phenotypic variation for patterns of neutral genetic variation among populations throughout Iceland. At a smaller scale, we evaluated the genetic differentiation between two morphs in Lake Thingvallavatn relative to historically explicit, coalescent-based null models of the evolutionary history of these lineages. At the large spatial scale, populations are highly differentiated, but weakly structured, both geographically and with respect to patterns of phenotypic variation. At the intralacustrine scale, we observe modest genetic differentiation between two morphs, but this level of differentiation is nonetheless consistent with strong reproductive isolation throughout the Holocene. Rather than a result of the homogenizing effect of gene flow in a system at migration-drift equilibrium, the modest level of genetic differentiation could equally be a result of slow neutral divergence by drift in large populations. We conclude that contemporary and recent patterns of restricted gene flow have been highly conducive to the evolution and maintenance of adaptive genetic variation in Icelandic Arctic charr. PMID:21224880

  10. Adaptation and evolution in marine environments. Vol. 2. The impacts of global change on biodiversity

    Energy Technology Data Exchange (ETDEWEB)

    Verde, Cinzia; Di Prisco, Guido (eds.) [CNR, Napoli (Italy). Inst. of Protein Biochemistry

    2013-02-01

    Offers a regionally focussed approach. Describes research on adaptive evolution. State-of-the-art content. The second volume of ''Adaptation and Evolution in Marine Environments - The Impacts of Global Change on Biodiversity'' from the series ''From Pole to Pole'' integrates the marine biology contribution of the first tome to the IPY 2007-2009, presenting overviews of organisms (from bacteria and ciliates to higher vertebrates) thriving on polar continental shelves, slopes and deep sea. The speed and extent of warming in the Arctic and in regions of Antarctica (the Peninsula, at the present) are greater than elsewhere. Changes impact several parameters, in particular the extent of sea ice; organisms, ecosystems and communities that became finely adapted to increasing cold in the course of millions of years are now becoming vulnerable, and biodiversity is threatened. Investigating evolutionary adaptations helps to foresee the impact of changes in temperate areas, highlighting the invaluable contribution of polar marine research to present and future outcomes of the IPY in the Earth system scenario.

  11. The red queen in the corn: agricultural weeds as models of rapid adaptive evolution.

    Science.gov (United States)

    Vigueira, C C; Olsen, K M; Caicedo, A L

    2013-04-01

    Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world.

  12. Within-host evolution of Pseudomonas aeruginosa reveals adaptation toward iron acquisition from hemoglobin

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Pedersen, Søren Damkiær; Khademi, Seyed Mohammad Hossein

    2014-01-01

    advantage in the presence of hemoglobin, thus suggesting that P. aeruginosa evolves toward iron acquisition from hemoglobin. To rule out that this adaptive trait is specific to the DK2 lineage, we inspected the genomes of additional P. aeruginosa lineages isolated from CF airways and found similar adaptive...... pressures act on the pathogens' ability to acquire iron. Here, we investigated the within-host evolution of P. aeruginosa, and we found evidence that P. aeruginosa during long-term infections evolves toward iron acquisition from hemoglobin. This adaptive strategy might be due to a selective loss of other...... iron-scavenging mechanisms and/or an increase in the availability of hemoglobin at the site of infection. This information is relevant to the design of novel CF therapeutics and the development of models of chronic CF infections....

  13. Evolution of chemical-specific adjustment factors (CSAF) based on recent international experience; increasing utility and facilitating regulatory acceptance.

    Science.gov (United States)

    Bhat, Virunya S; Meek, M E Bette; Valcke, Mathieu; English, Caroline; Boobis, Alan; Brown, Richard

    2017-10-01

    The application of chemical-specific toxicokinetic or toxicodynamic data to address interspecies differences and human variability in the quantification of hazard has potential to reduce uncertainty and better characterize variability compared with the use of traditional default or categorically-based uncertainty factors. The present review summarizes the state-of-the-science since the introduction of the World Health Organization/International Programme on Chemical Safety (WHO/IPCS) guidance on chemical-specific adjustment factors (CSAF) in 2005 and the availability of recent applicable guidance including the WHO/IPCS guidance on physiologically-based pharmacokinetic (PBPK) modeling in 2010 as well as the U.S. EPA guidance on data-derived extrapolation factors in 2014. A summary of lessons learned from an analysis of more than 100 case studies from global regulators or published literature illustrates the utility and evolution of CSAF in regulatory decisions. Challenges in CSAF development related to the adequacy of, or confidence in, the supporting data, including verification or validation of PBPK models. The analysis also identified issues related to adequacy of CSAF documentation, such as inconsistent terminology and often limited and/or inconsistent reporting, of both supporting data and/or risk assessment context. Based on this analysis, recommendations for standardized terminology, documentation and relevant interdisciplinary research and engagement are included to facilitate the continuing evolution of CSAF development and guidance.

  14. Functional evolution of leptin of Ochotona curzoniae in adaptive thermogenesis driven by cold environmental stress.

    Directory of Open Access Journals (Sweden)

    Jie Yang

    Full Text Available BACKGROUND: Environmental stress can accelerate the directional selection and evolutionary rate of specific stress-response proteins to bring about new or altered functions, enhancing an organism's fitness to challenging environments. Plateau pika (Ochotona curzoniae, an endemic and keystone species on Qinghai-Tibetan Plateau, is a high hypoxia and low temperature tolerant mammal with high resting metabolic rate and non-shivering thermogenesis to cope in this harsh plateau environment. Leptin is a key hormone related to how these animals regulate energy homeostasis. Previous molecular evolutionary analysis helped to generate the hypothesis that adaptive evolution of plateau pika leptin may be driven by cold stress. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis, recombinant pika leptin was first purified. The thermogenic characteristics of C57BL/6J mice injected with pika leptin under warm (23±1°C and cold (5±1°C acclimation is investigated. Expression levels of genes regulating adaptive thermogenesis in brown adipose tissue and the hypothalamus are compared between pika leptin and human leptin treatment, suggesting that pika leptin has adaptively and functionally evolved. Our results show that pika leptin regulates energy homeostasis via reduced food intake and increased energy expenditure under both warm and cold conditions. Compared with human leptin, pika leptin demonstrates a superior induced capacity for adaptive thermogenesis, which is reflected in a more enhanced β-oxidation, mitochondrial biogenesis and heat production. Moreover, leptin treatment combined with cold stimulation has a significant synergistic effect on adaptive thermogenesis, more so than is observed with a single cold exposure or single leptin treatment. CONCLUSIONS/SIGNIFICANCE: These findings support the hypothesis that cold stress has driven the functional evolution of plateau pika leptin as an ecological adaptation to the Qinghai-Tibetan Plateau.

  15. Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitates expression of diverse tissue-specific isoforms

    Energy Technology Data Exchange (ETDEWEB)

    Parra, Marilyn; Gee, Sherry; Chan, Nadine; Ryaboy, Dmitriy; Dubchak, Inna; Narla, Mohandas; Gascard, Philippe D.; Conboy, John G.

    2004-07-15

    The EPB41 (protein 4.1) genes epitomize the resourcefulness of the mammalian genome to encode a complex proteome from a small number of genes. By utilizing alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing, EPB41, EPB41L2, EPB41L3, and EPB41L1 encode a diverse array of structural adapter proteins. Comparative genomic and transcript analysis of these 140kb-240kb genes indicates several unusual features: differential evolution of highly conserved exons encoding known functional domains, interspersed with unique exons whose size and sequence variations contribute substantially to intergenic diversity: alternative first exons, most of which map far upstream of the coding regions; and complex tissue-specific alternative pre-mRNA splicing that facilitates synthesis of functionally different complements of 4.1 proteins in various cells. Understanding the splicing regulatory networks that control protein 4.1 expression will be critical to a full appreciation of the many roles of 4.1 proteins in normal cell biology and their proposed roles in human cancer.

  16. Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1 in cetaceans

    Directory of Open Access Journals (Sweden)

    Montgomery Stephen H

    2011-04-01

    Full Text Available Abstract Background Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans. Results We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1 in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea. Conclusion In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.

  17. Niche evolution and adaptive radiation: testing the order of trait divergence.

    Science.gov (United States)

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

    2006-07-01

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

  18. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

    DEFF Research Database (Denmark)

    Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.

    2017-01-01

    Adaptive laboratory evolution (ALE) is a widely-used method for improving the fitness of microorganisms in selected environmental conditions. It has been applied previously to Escherichia coli K-12 MG1655 during aerobic exponential growth on glucose minimal media, a frequently used model organism...... principal components. The distance between measured and flux balance analysis predicted fluxes was also investigated. It suggested a relatively wide range of similar stoichiometric optima, which opens new questions about the path-dependency of adaptive evolution....

  19. Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers.

    Science.gov (United States)

    Tokita, Masayoshi; Yano, Wataru; James, Helen F; Abzhanov, Arhat

    2017-02-05

    Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried cranial skeletons. We show that cranial shapes in both Hawaiian honeycreepers and Coerebinae (Darwin's finches and their close relatives) are much more diverse than in their respective outgroups, but Hawaiian honeycreepers as a group display the highest diversity and disparity of all other bird groups studied. We also report a significant contribution of allometry to skull shape variation, and distinct patterns of evolutionary change in skull morphology in the two lineages of songbirds that underwent adaptive radiation on oceanic islands. These findings help to better understand the nature of adaptive radiations in general and provide a foundation for future investigations on the developmental and molecular mechanisms underlying diversification of these morphologically distinguished groups of birds.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Authors.

  20. The adaptive evolution of plasticity: phytochrome-mediated shade avoidance responses.

    Science.gov (United States)

    Schmitt, Johanna; Stinchcombe, John R; Heschel, M Shane; Huber, Heidrun

    2003-07-01

    Many plants display a characteristic suite of developmental "shade avoidance" responses, such as stem elongation and accelerated reproduction, to the low ratio of red to far-red wavelengths (R:FR) reflected or transmitted from green vegetation. This R:FR cue of crowding and vegetation shade is perceived by the phytochrome family of photoreceptors. Phytochrome-mediated responses provide an ideal system for investigating the adaptive evolution of phenotypic plasticity in natural environments. The molecular and developmental mechanisms underlying shade avoidance responses are well studied, and testable ecological hypotheses exist for their adaptive significance. Experimental manipulation of phenotypes demonstrates that shade avoidance responses may be adaptive, resulting in phenotypes with high relative fitness in the environments that induce those phenotypes. The adaptive value of shade avoidance depends upon the competitive environment, resource availability, and the reliability of the R:FR cue for predicting the selective environment experienced by an induced phenotype. Comparative studies and a reciprocal transplant experiment with Impatiens capensis provide evidence of adaptive divergence in shade avoidance responses between woodland and clearing habitats, which may result from population differences in the frequency of selection on shade avoidance traits, as well as differences in the reliability of the R:FR cue. Recent rapid progress in elucidating phytochrome signaling pathways in the genetic model Arabidopsis thaliana and other species now provides the opportunity for studying how selection on shade avoidance traits in natural environments acts upon the molecular mechanisms underlying natural phenotypic variation.

  1. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

    Science.gov (United States)

    Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J

    2015-07-28

    The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.

  2. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery.

    Science.gov (United States)

    Parhad, Swapnil S; Tu, Shikui; Weng, Zhiping; Theurkauf, William E

    2017-10-09

    Reproductive isolation defines species divergence and is linked to adaptive evolution of hybrid incompatibility genes. Hybrids between Drosophila melanogaster and Drosophila simulans are sterile, and phenocopy mutations in the PIWI interacting RNA (piRNA) pathway, which silences transposons and shows pervasive adaptive evolution, and Drosophila rhino and deadlock encode rapidly evolving components of a complex that binds to piRNA clusters. We show that Rhino and Deadlock interact and co-localize in simulans and melanogaster, but simulans Rhino does not bind melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Significantly, a chimera expressing the simulans Shadow domain in a melanogaster Rhino backbone fails to support piRNA production, disrupts binding to piRNA clusters, and leads to ectopic localization to bulk heterochromatin. Fusing melanogaster Deadlock to simulans Rhino, by contrast, restores localization to clusters. Deadlock binding thus directs Rhino to piRNA clusters, and Rhino-Deadlock co-evolution has produced cross-species incompatibilities, which may contribute to reproductive isolation. Copyright © 2017. Published by Elsevier Inc.

  3. Hybridization of Adaptive Differential Evolution with an Expensive Local Search Method

    Directory of Open Access Journals (Sweden)

    Rashida Adeeb Khanum

    2016-01-01

    Full Text Available Differential evolution (DE is an effective and efficient heuristic for global optimization problems. However, it faces difficulty in exploiting the local region around the approximate solution. To handle this issue, local search (LS techniques could be hybridized with DE to improve its local search capability. In this work, we hybridize an updated version of DE, adaptive differential evolution with optional external archive (JADE with an expensive LS method, Broydon-Fletcher-Goldfarb-Shano (BFGS for solving continuous unconstrained global optimization problems. The new hybrid algorithm is denoted by DEELS. To validate the performance of DEELS, we carried out extensive experiments on well known test problems suits, CEC2005 and CEC2010. The experimental results, in terms of function error values, success rate, and some other statistics, are compared with some of the state-of-the-art algorithms, self-adaptive control parameters in differential evolution (jDE, sequential DE enhanced by neighborhood search for large-scale global optimization (SDENS, and differential ant-stigmergy algorithm (DASA. These comparisons reveal that DEELS outperforms jDE and SDENS except DASA on the majority of test instances.

  4. Rates of phenotypic evolution of ecological characters and sexual traits during the Tanganyikan cichlid adaptive radiation.

    Science.gov (United States)

    Gonzalez-Voyer, A; Kolm, N

    2011-11-01

    Theory suggests that sexual traits evolve faster than ecological characters. However, characteristics of a species niche may also influence evolution of sexual traits. Hence, a pending question is whether ecological characters and sexual traits present similar tempo and mode of evolution during periods of rapid ecological divergence, such as adaptive radiation. Here, we use recently developed phylogenetic comparative methods to analyse the temporal dynamics of evolution for ecological and sexual traits in Tanganyikan cichlids. Our results indicate that whereas disparity in ecological characters was concentrated early in the radiation, disparity in sexual traits remained high throughout the radiation. Thus, closely related Tanganyikan cichlids presented higher disparity in sexual traits than ecological characters. Sexual traits were also under stronger selection than ecological characters. In sum, our results suggest that ecological characters and sexual traits present distinct evolutionary patterns, and that sexual traits can evolve faster than ecological characters, even during adaptive radiation. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  5. Identifying innovation in laboratory studies of cultural evolution: rates of retention and measures of adaptation.

    Science.gov (United States)

    Caldwell, Christine A; Cornish, Hannah; Kandler, Anne

    2016-03-19

    In recent years, laboratory studies of cultural evolution have become increasingly prevalent as a means of identifying and understanding the effects of cultural transmission on the form and functionality of transmitted material. The datasets generated by these studies may provide insights into the conditions encouraging, or inhibiting, high rates of innovation, as well as the effect that this has on measures of adaptive cultural change. Here we review recent experimental studies of cultural evolution with a view to elucidating the role of innovation in generating observed trends. We first consider how tasks are presented to participants, and how the corresponding conceptualization of task success is likely to influence the degree of intent underlying any deviations from perfect reproduction. We then consider the measures of interest used by the researchers to track the changes that occur as a result of transmission, and how these are likely to be affected by differing rates of retention. We conclude that considering studies of cultural evolution from the perspective of innovation provides us with valuable insights that help to clarify important differences in research designs, which have implications for the likely effects of variation in retention rates on measures of cultural adaptation. © 2016 The Author(s).

  6. The evolution of annelids reveals two adaptive routes to the interstitial realm.

    Science.gov (United States)

    Struck, Torsten Hugo; Golombek, Anja; Weigert, Anne; Franke, Franziska Anni; Westheide, Wilfried; Purschke, Günter; Bleidorn, Christoph; Halanych, Kenneth Michael

    2015-08-03

    Many animals permanently inhabit the marine interstitium, the space between sand grains [1, 2]. Different evolutionary scenarios may explain the existence of interstitial animals [3, 4]. These scenarios include (1) that the interstitial realm is the ancestral habitat of bilaterians [5, 6], (2) that interstitial taxa evolved from larger ancestors by miniaturization, or (3) progenesis [3]. The first view mirrors the former hypothesis that interstitial annelids, called archiannelids, were at the base of the annelid radiation [7]. Based on morphological data, however, progenesis is generally favored for interstitial annelids today [3, 4, 8]. Herein, our phylogenomic approach revealed that interstitial archiannelids are robustly placed into two groups nested within the annelid tree. Evolution of the first group comprising among others Dinophilidae is best explained by progenesis. In contrast, the second group comprising Protodrilida and Polygordiidae appears to have evolved by stepwise miniaturization adapting from coarser to finer sediments. Thus, in addition to progenesis [3, 4], miniaturization, thought to be too slow for an adaptation to the interstitium [3], is an important second route allowing adaptation to interstitial environments. Both progenesis and miniaturization should be considered when investigating evolution of interstitial taxa [1, 3]. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution

    Science.gov (United States)

    Suzuki, Haruo; Lefébure, Tristan; Hubisz, Melissa Jane; Pavinski Bitar, Paulina; Lang, Ping; Siepel, Adam; Stanhope, Michael J.

    2011-01-01

    Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters. PMID:21282711

  8. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    Energy Technology Data Exchange (ETDEWEB)

    Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM

    2008-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

  9. Adaptive evolution of Saccharomyces cerevisiae with enhanced ethanol tolerance for Chinese rice wine fermentation.

    Science.gov (United States)

    Chen, Shuang; Xu, Yan

    2014-08-01

    High tolerance towards ethanol is a desirable property for the Saccharomyces cerevisiae strains used in the alcoholic beverage industry. To improve the ethanol tolerance of an industrial Chinese rice wine yeast, a sequential batch fermentation strategy was used to adaptively evolve a chemically mutagenized Chinese rice wine G85 strain. The high level of ethanol produced under Chinese rice wine-like fermentation conditions was used as the selective pressure. After adaptive evolution of approximately 200 generations, mutant G85X-8 was isolated and shown to have markedly increased ethanol tolerance. The evolved strain also showed higher osmotic and temperature tolerances than the parental strain. Laboratory Chinese rice wine fermentation showed that the evolved G85X-8 strain was able to catabolize sugars more completely than the parental G85 strain. A higher level of yeast cell activity was found in the fermentation mash produced by the evolved strain, but the aroma profiles were similar between the evolved and parental strains. The improved ethanol tolerance in the evolved strain might be ascribed to the altered fatty acids composition of the cell membrane and higher intracellular trehalose concentrations. These results suggest that adaptive evolution is an efficient approach for the non-recombinant modification of industrial yeast strains.

  10. Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes

    Directory of Open Access Journals (Sweden)

    Lynch Vincent J

    2007-01-01

    Full Text Available Abstract Background Gene duplication followed by functional divergence has long been hypothesized to be the main source of molecular novelty. Convincing examples of neofunctionalization, however, remain rare. Snake venom phospholipase A2 genes are members of large multigene families with many diverse functions, thus they are excellent models to study the emergence of novel functions after gene duplications. Results Here, I show that positive Darwinian selection and neofunctionalization is common in snake venom phospholipase A2 genes. The pattern of gene duplication and positive selection indicates that adaptive molecular evolution occurs immediately after duplication events as novel functions emerge and continues as gene families diversify and are refined. Surprisingly, adaptive evolution of group-I phospholipases in elapids is also associated with speciation events, suggesting adaptation of the phospholipase arsenal to novel prey species after niche shifts. Mapping the location of sites under positive selection onto the crystal structure of phospholipase A2 identified regions evolving under diversifying selection are located on the molecular surface and are likely protein-protein interactions sites essential for toxin functions. Conclusion These data show that increases in genomic complexity (through gene duplications can lead to phenotypic complexity (venom composition and that positive Darwinian selection is a common evolutionary force in snake venoms. Finally, regions identified under selection on the surface of phospholipase A2 enzymes are potential candidate sites for structure based antivenin design.

  11. Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes.

    Science.gov (United States)

    Lynch, Vincent J

    2007-01-18

    Gene duplication followed by functional divergence has long been hypothesized to be the main source of molecular novelty. Convincing examples of neofunctionalization, however, remain rare. Snake venom phospholipase A2 genes are members of large multigene families with many diverse functions, thus they are excellent models to study the emergence of novel functions after gene duplications. Here, I show that positive Darwinian selection and neofunctionalization is common in snake venom phospholipase A2 genes. The pattern of gene duplication and positive selection indicates that adaptive molecular evolution occurs immediately after duplication events as novel functions emerge and continues as gene families diversify and are refined. Surprisingly, adaptive evolution of group-I phospholipases in elapids is also associated with speciation events, suggesting adaptation of the phospholipase arsenal to novel prey species after niche shifts. Mapping the location of sites under positive selection onto the crystal structure of phospholipase A2 identified regions evolving under diversifying selection are located on the molecular surface and are likely protein-protein interactions sites essential for toxin functions. These data show that increases in genomic complexity (through gene duplications) can lead to phenotypic complexity (venom composition) and that positive Darwinian selection is a common evolutionary force in snake venoms. Finally, regions identified under selection on the surface of phospholipase A2 enzymes are potential candidate sites for structure based antivenin design.

  12. Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers.

    Directory of Open Access Journals (Sweden)

    Sharon A Jansa

    Full Text Available The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae and pitvipers (Serpentes: Crotalinae. In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF, a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role.

  13. Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation

    Science.gov (United States)

    Burbrink, Frank T.; Chen, Xin; Myers, Edward A.; Brandley, Matthew C.; Pyron, R. Alexander

    2012-01-01

    Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification. PMID:23034709

  14. Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans.

    Science.gov (United States)

    Evans, Patrick D; Anderson, Jeffrey R; Vallender, Eric J; Gilbert, Sandra L; Malcom, Christine M; Dorus, Steve; Lahn, Bruce T

    2004-03-01

    A prominent trend in the evolution of humans is the progressive enlargement of the cerebral cortex. The ASPM (Abnormal spindle-like microcephaly associated) gene has the potential to play a role in this evolutionary process, because mutations in this gene cause severe reductions in the cerebral cortical size of affected humans. Here, we show that the evolution of ASPM is significantly accelerated in great apes, especially along the ape lineages leading to humans. Additionally, the lineage from the last human/chimpanzee ancestor to humans shows an excess of non-synonymous over synonymous substitutions, which is a signature of positive Darwinian selection. A comparison of polymorphism and divergence using the McDonald-Kreitman test confirms that ASPM has indeed experienced intense positive selection during recent human evolution. This test also reveals that, on average, ASPM fixed one advantageous amino acid change in every 300,000-400,000 years since the human lineage diverged from chimpanzees some 5-6 million years ago. We therefore conclude that ASPM underwent strong adaptive evolution in the descent of Homo sapiens, which is consistent with its putative role in the evolutionary enlargement of the human brain.

  15. Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host.

    Science.gov (United States)

    Wang, Shuai; Wang, Sen; Luo, Yingfeng; Xiao, Lihua; Luo, Xuenong; Gao, Shenghan; Dou, Yongxi; Zhang, Huangkai; Guo, Aijiang; Meng, Qingshu; Hou, Junling; Zhang, Bing; Zhang, Shaohua; Yang, Meng; Meng, Xuelian; Mei, Hailiang; Li, Hui; He, Zilong; Zhu, Xueliang; Tan, Xinyu; Zhu, Xing-Quan; Yu, Jun; Cai, Jianping; Zhu, Guan; Hu, Songnian; Cai, Xuepeng

    2016-09-22

    Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica.

  16. Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

    Science.gov (United States)

    Wang, Shuai; Wang, Sen; Luo, Yingfeng; Xiao, Lihua; Luo, Xuenong; Gao, Shenghan; Dou, Yongxi; Zhang, Huangkai; Guo, Aijiang; Meng, Qingshu; Hou, Junling; Zhang, Bing; Zhang, Shaohua; Yang, Meng; Meng, Xuelian; Mei, Hailiang; Li, Hui; He, Zilong; Zhu, Xueliang; Tan, Xinyu; Zhu, Xing-quan; Yu, Jun; Cai, Jianping; Zhu, Guan; Hu, Songnian; Cai, Xuepeng

    2016-01-01

    Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica. PMID:27653464

  17. Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss.

    Science.gov (United States)

    Zhang, Xian; Liu, Xueduan; Liang, Yili; Guo, Xue; Xiao, Yunhua; Ma, Liyuan; Miao, Bo; Liu, Hongwei; Peng, Deliang; Huang, Wenkun; Zhang, Yuguang; Yin, Huaqun

    2017-04-01

    Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillus thermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains. IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT

  18. Phylogenetic patterns and the adaptive evolution of osmoregulation in fiddler crabs (Brachyura, Uca)

    Science.gov (United States)

    Faria, Samuel Coelho; Provete, Diogo Borges; Thurman, Carl Leo

    2017-01-01

    Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyper-osmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher intertidal habitats than Indo-west Pacific species mainly found in the low intertidal zone. Here, we characterize numerous osmoregulatory traits in all ten fiddler crabs found along the Atlantic coast of Brazil, and we employ phylogenetic comparative methods using 24 species to test for: (i) similarities of osmoregulatory ability among closely related species; (ii) salinity as a driver of osmoregulatory evolution; (iii) correlation between salt uptake and secretion; and (iv) adaptive peaks in osmoregulatory ability in the high intertidal American lineages. Our findings reveal that osmoregulation in Uca exhibits strong phylogenetic patterns in salt uptake traits. Salinity does not correlate with hyper/hypo-regulatory abilities, but drives hemolymph osmolality at ambient salinities. Osmoregulatory traits have evolved towards three adaptive peaks, revealing a significant contribution of hyper/hypo-regulatory ability in the American clades. Thus, during the evolutionary history of fiddler crabs, salinity has driven some of the osmoregulatory transformations that underpin habitat diversification, although others are apparently constrained phylogenetically. PMID:28182764

  19. Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

    Directory of Open Access Journals (Sweden)

    Flegr Jaroslav

    2013-01-01

    Full Text Available Abstract Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ. Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III, genetic revolution model of Mayr (class IV or the frozen plasticity theory of Flegr (class V, suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation – while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III or elastic (class IV and V on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation. The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories. Reviewers This article was reviewed by Claus Wilke, Pierre Pantarotti and David Penny (nominated by Anthony Poole.

  20. Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates

    DEFF Research Database (Denmark)

    Pereira, Joana; Johnson, Warren E.; O'Brien, Stephen J.

    2014-01-01

    . In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive...... the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints...

  1. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants.

    Science.gov (United States)

    Alix, Karine; Gérard, Pierre R; Schwarzacher, Trude; Heslop-Harrison, J S Pat

    2017-08-01

    Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation

  2. The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

    DEFF Research Database (Denmark)

    Melo-Ferreira, Jose; Vilela, Joana; Fonseca, Miguel M.

    2014-01-01

    understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread......Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from...... selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may...

  3. The evolution of sex is favoured during adaptation to new environments.

    Science.gov (United States)

    Becks, Lutz; Agrawal, Aneil F

    2012-01-01

    Both theory and experiments have demonstrated that sex can facilitate adaptation, potentially yielding a group-level advantage to sex. However, it is unclear whether this process can help solve the more difficult problem of the maintenance of sex within populations. Using experimental populations of the facultatively sexual rotifer Brachionus calyciflorus, we show that rates of sex evolve to higher levels during adaptation but then decline as fitness plateaus. To assess the fitness consequences of genetic mixing, we directly compare the fitnesses of sexually and asexually derived genotypes that naturally occur in our experimental populations. Sexually derived genotypes are more fit than asexually derived genotypes when adaptive pressures are strong, but this pattern reverses as the pace of adaptation slows, matching the pattern of evolutionary change in the rate of sex. These fitness assays test the net effect of sex but cannot be used to disentangle whether selection on sex arises because highly sexual lineages become associated with different allele combinations or with different allele frequencies than less sexual lineages (i.e., "short-" or "long-term" effects, respectively). We infer which of these mechanisms provides an advantage to sex by performing additional manipulations to obtain fitness distributions of sexual and asexual progeny arrays from unbiased parents (rather than from naturally occurring, and thereby evolutionarily biased, parents). We find evidence that sex breaks down adaptive gene combinations, resulting in lower average fitness of sexual progeny (i.e., a short-term disadvantage to sex). As predicted by theory, the advantage to sex arises because sexually derived progeny are more variable in fitness, allowing for faster adaptation. This "long-term advantage" builds over multiple generations, eventually resulting in higher fitness of sexual types.

  4. Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Pedersen, Margit; LaCroix, Ryan A.

    2014-01-01

    Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental...... reaffirmed the impact of the key mutations on the growth rate at 42 °C. Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype...

  5. Post-translocational adaptation drives evolution through genetic selection and transcriptional shift in Saccharomyces cerevisiae.

    Science.gov (United States)

    Tosato, Valentina; Sims, Jason; West, Nicole; Colombin, Martina; Bruschi, Carlo V

    2017-05-01

    Adaptation by natural selection might improve the fitness of an organism and its probability to survive in unfavorable environmental conditions. Decoding the genetic basis of adaptive evolution is one of the great challenges to deal with. To this purpose, Saccharomyces cerevisiae has been largely investigated because of its short division time, excellent aneuploidy tolerance and the availability of the complete sequence of its genome with a thorough genome database. In the past, we developed a system, named bridge-induced translocation, to trigger specific, non-reciprocal translocations, exploiting the endogenous recombination system of budding yeast. This technique allows users to generate a heterogeneous population of cells with different aneuploidies and increased phenotypic variation. In this work, we demonstrate that ad hoc chromosomal translocations might induce adaptation, fostering selection of thermo-tolerant yeast strains with improved phenotypic fitness. This "yeast eugenomics" correlates with a shift to enhanced expression of genes involved in stress response, heat shock as well as carbohydrate metabolism. We propose that the bridge-induced translocation is a suitable approach to generate adapted, physiologically boosted strains for biotechnological applications.

  6. Adaptive potential of genomic structural variation in human and mammalian evolution.

    Science.gov (United States)

    Radke, David W; Lee, Charles

    2015-09-01

    Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  7. Evolution and adaptation in Pseudomonas aeruginosa biofilms driven by mismatch repair system-deficient mutators.

    Directory of Open Access Journals (Sweden)

    Adela M Luján

    Full Text Available Pseudomonas aeruginosa is an important opportunistic pathogen causing chronic airway infections, especially in cystic fibrosis (CF patients. The majority of the CF patients acquire P. aeruginosa during early childhood, and most of them develop chronic infections resulting in severe lung disease, which are rarely eradicated despite intensive antibiotic therapy. Current knowledge indicates that three major adaptive strategies, biofilm development, phenotypic diversification, and mutator phenotypes [driven by a defective mismatch repair system (MRS], play important roles in P. aeruginosa chronic infections, but the relationship between these strategies is still poorly understood. We have used the flow-cell biofilm model system to investigate the impact of the mutS associated mutator phenotype on development, dynamics, diversification and adaptation of P. aeruginosa biofilms. Through competition experiments we demonstrate for the first time that P. aeruginosa MRS-deficient mutators had enhanced adaptability over wild-type strains when grown in structured biofilms but not as planktonic cells. This advantage was associated with enhanced micro-colony development and increased rates of phenotypic diversification, evidenced by biofilm architecture features and by a wider range and proportion of morphotypic colony variants, respectively. Additionally, morphotypic variants generated in mutator biofilms showed increased competitiveness, providing further evidence for mutator-driven adaptive evolution in the biofilm mode of growth. This work helps to understand the basis for the specific high proportion and role of mutators in chronic infections, where P. aeruginosa develops in biofilm communities.

  8. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Aifen; Hillesland, Kristina; He, Zhili; Joachimiak, Marcin; Zane, Grant; Dehal, Paramvir; Arkin, Adam; Stahl, David; Wall, Judy; Hazen, Terry; Zhou, Jizhong; Baidoo, Edward; Benke, Peter; Mukhopadhyay, Aindrila

    2010-05-17

    High salinity is one of the most common environmental stressors. In order to understand how environmental organisms adapt to salty environment, an experiment evolution with sulfate reducing bacteria Desulfovibrio vugaris Hildenborough was conducted. Control lines and salt-stressed lines (6 lines each) grown in minimal medium LS4D or LS4D + 100 mM NaCl were transferred for 1200 generations. The salt tolerance was tested with LS4D supplemented with 250 mM NaCl. Statistical analysis of the growth data suggested that all lines adapted to their evolutionary environment. In addition, the control lines performed better than the ancestor with faster growth rate, higher biomass yield and shorter lag phase under salty environment they did not evolve in. However, the salt-adapted lines performed better than the control lines on measures of growth rate and yield under salty environment, suggesting that the salt?evolved lines acquired mutations specific to having extra salt in LS4D. Growth data and gene transcription data suggested that populations tended to improve till 1000 generations and active mutations tended to be fixed at the stage of 1000 generations. Point mutations and insertion/deletions were identified in isolated colonies from salt-adapted and control lines via whole genome sequencing. Glu, Gln and Ala appears to be the major osmoprotectant in evolved salt-stressed line. Ongoing studies are now characterizing the contribution of specific mutations identified in the salt-evolved D. vulgaris.

  9. Response to Puts and Dawood's 'the evolution of female orgasm: adaptation or byproduct?'--Been there.

    Science.gov (United States)

    Lloyd, Elisabeth A

    2006-08-01

    David Puts and Khytam Dawood's recent critique of my book, The Case of the Female Orgasm: Bias in the Science of Evolution, attempts to make plausible an adaptive account of female orgasm based on a hypothesized mechanism of uterine upsuck and sperm competition. Yet the authors fail to respond to the criticisms of such accounts that I detailed previously in my book. They raise a further concern about my definition of adaptation--a red herring--and manufacture a conceptual error regarding heritability that they then attribute to me. Most seriously, they fail to address the glaring failure of sperm competition accounts to accord with evidence from sexology. Specifically, the distribution curve of orgasm-with-intercourse--according to Dawood et al.'s own data, as well as others'--is relatively flat across the various classes. This curve needs to be tested against a well-formed multistrategy adaptive hypothesis; it cannot be explained by the adaptive account defended by Puts and Dawood in their critique.

  10. An adaptive left-right eigenvector evolution algorithm for vibration isolation control

    Science.gov (United States)

    Wu, T. Y.

    2009-11-01

    The purpose of this research is to investigate the feasibility of utilizing an adaptive left and right eigenvector evolution (ALREE) algorithm for active vibration isolation. As depicted in the previous paper presented by Wu and Wang (2008 Smart Mater. Struct. 17 015048), the structural vibration behavior depends on both the disturbance rejection capability and mode shape distributions, which correspond to the left and right eigenvector distributions of the system, respectively. In this paper, a novel adaptive evolution algorithm is developed for finding the optimal combination of left-right eigenvectors of the vibration isolator, which is an improvement over the simultaneous left-right eigenvector assignment (SLREA) method proposed by Wu and Wang (2008 Smart Mater. Struct. 17 015048). The isolation performance index used in the proposed algorithm is defined by combining the orthogonality index of left eigenvectors and the modal energy ratio index of right eigenvectors. Through the proposed ALREE algorithm, both the left and right eigenvectors evolve such that the isolation performance index decreases, and therefore one can find the optimal combination of left-right eigenvectors of the closed-loop system for vibration isolation purposes. The optimal combination of left-right eigenvectors is then synthesized to determine the feedback gain matrix of the closed-loop system. The result of the active isolation control shows that the proposed method can be utilized to improve the vibration isolation performance compared with the previous approaches.

  11. Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals.

    Science.gov (United States)

    Tian, Ran; Yin, Daiqing; Liu, Yanzhi; Seim, Inge; Xu, Shixia; Yang, Guang

    2017-01-01

    Animals that are able to sustain life under hypoxic conditions have long captured the imagination of biologists and medical practitioners alike. Although the associated morphological modifications have been extensively described, the mechanisms underlying the evolution of hypoxia tolerance are not well understood. To provide such insights, we investigated genes in four major energy metabolism pathways, and provide evidence of distinct evolutionary paths to mammalian hypoxia-tolerance. Positive selection of genes in the oxidative phosphorylation pathway mainly occurred in terrestrial hypoxia-tolerant species; possible adaptations to chronically hypoxic environments. The strongest candidate for positive selection along cetacean lineages was the citrate cycle signaling pathway, suggestive of enhanced aerobic metabolism during and after a dive. Six genes with cetacean-specific amino acid changes are rate-limiting enzymes involved in the gluconeogenesis pathway, which would be expected to enhance the lactate removal after diving. Intriguingly, 38 parallel amino acid substitutions in 29 genes were observed between hypoxia-tolerant mammals. Of these, 76.3% were radical amino acid changes, suggesting that convergent molecular evolution drives the adaptation to hypoxic stress and similar phenotypic changes. This study provides further insights into life under low oxygen conditions and the evolutionary trajectories of hypoxia-tolerant species.

  12. Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals

    Directory of Open Access Journals (Sweden)

    Ran Tian

    2017-12-01

    Full Text Available Animals that are able to sustain life under hypoxic conditions have long captured the imagination of biologists and medical practitioners alike. Although the associated morphological modifications have been extensively described, the mechanisms underlying the evolution of hypoxia tolerance are not well understood. To provide such insights, we investigated genes in four major energy metabolism pathways, and provide evidence of distinct evolutionary paths to mammalian hypoxia-tolerance. Positive selection of genes in the oxidative phosphorylation pathway mainly occurred in terrestrial hypoxia-tolerant species; possible adaptations to chronically hypoxic environments. The strongest candidate for positive selection along cetacean lineages was the citrate cycle signaling pathway, suggestive of enhanced aerobic metabolism during and after a dive. Six genes with cetacean-specific amino acid changes are rate-limiting enzymes involved in the gluconeogenesis pathway, which would be expected to enhance the lactate removal after diving. Intriguingly, 38 parallel amino acid substitutions in 29 genes were observed between hypoxia-tolerant mammals. Of these, 76.3% were radical amino acid changes, suggesting that convergent molecular evolution drives the adaptation to hypoxic stress and similar phenotypic changes. This study provides further insights into life under low oxygen conditions and the evolutionary trajectories of hypoxia-tolerant species.

  13. GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution?

    Science.gov (United States)

    Bridi, L C; Rafael, M S

    2016-02-01

    Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi.

  14. An adapted yield criterion for the evolution of subsequent yield surfaces

    Science.gov (United States)

    Küsters, N.; Brosius, A.

    2017-09-01

    In numerical analysis of sheet metal forming processes, the anisotropic material behaviour is often modelled with isotropic work hardening and an average Lankford coefficient. In contrast, experimental observations show an evolution of the Lankford coefficients, which can be associated with a yield surface change due to kinematic and distortional hardening. Commonly, extensive efforts are carried out to describe these phenomena. In this paper an isotropic material model based on the Yld2000-2d criterion is adapted with an evolving yield exponent in order to change the yield surface shape. The yield exponent is linked to the accumulative plastic strain. This change has the effect of a rotating yield surface normal. As the normal is directly related to the Lankford coefficient, the change can be used to model the evolution of the Lankford coefficient during yielding. The paper will focus on the numerical implementation of the adapted material model for the FE-code LS-Dyna, mpi-version R7.1.2-d. A recently introduced identification scheme [1] is used to obtain the parameters for the evolving yield surface and will be briefly described for the proposed model. The suitability for numerical analysis will be discussed for deep drawing processes in general. Efforts for material characterization and modelling will be compared to other common yield surface descriptions. Besides experimental efforts and achieved accuracy, the potential of flexibility in material models and the risk of ambiguity during identification are of major interest in this paper.

  15. Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.

    Science.gov (United States)

    Richards, Vincent P; Lang, Ping; Bitar, Paulina D Pavinski; Lefébure, Tristan; Schukken, Ynte H; Zadoks, Ruth N; Stanhope, Michael J

    2011-08-01

    In addition to causing severe invasive infections in humans, Streptococcus agalactiae, or group B Streptococcus (GBS), is also a major cause of bovine mastitis. Here we provide the first genome sequence for S. agalactiae isolated from a cow diagnosed with clinical mastitis (strain FSL S3-026). Comparison to eight S. agalactiae genomes obtained from human disease isolates revealed 183 genes specific to the bovine strain. Subsequent polymerase chain reaction (PCR) screening for the presence/absence of a subset of these loci in additional bovine and human strains revealed strong differentiation between the two groups (Fisher exact test: pother mastitis-causing species of bacteria provided strong evidence for two cases of interspecies LGT within the shared bovine environment: bovine S. agalactiae with Streptococcus uberis (nisin U operon) and Streptococcus dysgalactiae subsp. dysgalactiae (lactose operon). We also found evidence for LGT, involving the salivaricin operon, between the bovine S. agalactiae strain and either Streptococcus pyogenes or Streptococcus salivarius. Our findings provide insight into mechanisms facilitating environmental adaptation and acquisition of potential virulence factors, while highlighting both the key role LGT has played in the recent evolution of the bovine S. agalactiae strain, and the importance of LGT among pathogens within a shared environment. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Implications of prion adaptation and evolution paradigm for human neurodegenerative diseases.

    Science.gov (United States)

    Kabir, M Enamul; Safar, Jiri G

    2014-01-01

    There is a growing body of evidence indicating that number of human neurodegenerative diseases, including Alzheimer disease, Parkinson disease, fronto-temporal dementias, and amyotrophic lateral sclerosis, propagate in the brain via prion-like intercellular induction of protein misfolding. Prions cause lethal neurodegenerative diseases in humans, the most prevalent being sporadic Creutzfeldt-Jakob disease (sCJD); they self-replicate and spread by converting the cellular form of prion protein (PrP(C)) to a misfolded pathogenic conformer (PrP(Sc)). The extensive phenotypic heterogeneity of human prion diseases is determined by polymorphisms in the prion protein gene, and by prion strain-specific conformation of PrP(Sc). Remarkably, even though informative nucleic acid is absent, prions may undergo rapid adaptation and evolution in cloned cells and upon crossing the species barrier. In the course of our investigation of this process, we isolated distinct populations of PrP(Sc) particles that frequently co-exist in sCJD. The human prion particles replicate independently and undergo competitive selection of those with lower initial conformational stability. Exposed to mutant substrate, the winning PrP(Sc) conformers are subject to further evolution by natural selection of the subpopulation with the highest replication rate due to the lowest stability. Thus, the evolution and adaptation of human prions is enabled by a dynamic collection of distinct populations of particles, whose evolution is governed by the selection of progressively less stable, faster replicating PrP(Sc) conformers. This fundamental biological mechanism may explain the drug resistance that some prions gained after exposure to compounds targeting PrP(Sc). Whether the phenotypic heterogeneity of other neurodegenerative diseases caused by protein misfolding is determined by the spectrum of misfolded conformers (strains) remains to be established. However, the prospect that these conformers may evolve and

  17. Long-term adaptive evolution of Leuconostoc mesenteroides for enhancement of lactic acid tolerance and production.

    Science.gov (United States)

    Ju, Si Yeon; Kim, Jin Ho; Lee, Pyung Cheon

    2016-01-01

    Lactic acid has been approved by the United States Food and Drug Administration as Generally Regarded As Safe (GRAS) and is commonly used in the cosmetics, pharmaceutical, and food industries. Applications of lactic acid have also emerged in the plastics industry. Lactic acid bacteria (LAB), such as Leuconostoc and Lactobacillus, are widely used as lactic acid producers for food-related and biotechnological applications. Nonetheless, industrial mass production of lactic acid in LAB is a challenge mainly because of growth inhibition caused by the end product, lactic acid. Thus, it is important to improve acid tolerance of LAB to achieve balanced cell growth and a high titer of lactic acid. Recently, adaptive evolution has been employed as one of the strategies to improve the fitness and to induce adaptive changes in bacteria under specific growth conditions, such as acid stress. Wild-type Leuconostoc mesenteroides was challenged long term with exogenously supplied lactic acid, whose concentration was increased stepwise (for enhancement of lactic acid tolerance) during 1 year. In the course of the adaptive evolution at 70 g/L lactic acid, three mutants (LMS50, LMS60, and LMS70) showing high specific growth rates and lactic acid production were isolated and characterized. Mutant LMS70, isolated at 70 g/L lactic acid, increased d-lactic acid production up to 76.8 g/L, which was twice that in the wild type (37.8 g/L). Proteomic, genomic, and physiological analyses revealed that several possible factors affected acid tolerance, among which a mutation of ATPase ε subunit (involved in the regulation of intracellular pH) and upregulation of intracellular ammonia, as a buffering system, were confirmed to contribute to the observed enhancement of tolerance and production of d-lactic acid. During adaptive evolution under lethal stress conditions, the fitness of L. mesenteroides gradually increased to accumulate beneficial mutations according to the stress level. The

  18. Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.

    Directory of Open Access Journals (Sweden)

    A Faddeeva

    Full Text Available Collembola (springtails represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor.We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade.Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response, ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development.We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.

  19. Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny

    Science.gov (United States)

    Martínez-Castilla, León Patricio; Alvarez-Buylla, Elena R.

    2003-01-01

    Gene duplication is a substrate of evolution. However, the relative importance of positive selection versus relaxation of constraints in the functional divergence of gene copies is still under debate. Plant MADS-box genes encode transcriptional regulators key in various aspects of development and have undergone extensive duplications to form a large family. We recovered 104 MADS sequences from the Arabidopsis genome. Bayesian phylogenetic trees recover type II lineage as a monophyletic group and resolve a branching sequence of monophyletic groups within this lineage. The type I lineage is comprised of several divergent groups. However, contrasting gene structure and patterns of chromosomal distribution between type I and II sequences suggest that they had different evolutionary histories and support the placement of the root of the gene family between these two groups. Site-specific and site-branch analyses of positive Darwinian selection (PDS) suggest that different selection regimes could have affected the evolution of these lineages. We found evidence for PDS along the branch leading to flowering time genes that have a direct impact on plant fitness. Sites with high probabilities of having been under PDS were found in the MADS and K domains, suggesting that these played important roles in the acquisition of novel functions during MADS-box diversification. Detected sites are targets for further experimental analyses. We argue that adaptive changes in MADS-domain protein sequences have been important for their functional divergence, suggesting that changes within coding regions of transcriptional regulators have influenced phenotypic evolution of plants. PMID:14597714

  20. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

    Science.gov (United States)

    Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

    2013-12-17

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

  1. Evolution of cooperation through adaptive interaction in a spatial prisoner's dilemma game

    Science.gov (United States)

    Pan, Qiuhui; Liu, Xuesong; Bao, Honglin; Su, Yu; He, Mingfeng

    2018-02-01

    In this paper, we study the effect of adaptive interaction on the evolution of cooperation in a spatial prisoner's dilemma game. The connections of players are co-evolutionary with cooperation; whether adjacent players can play the prisoner's dilemma game is associated with the strategies they took in the preceding round. If a player defected in the preceding round, his neighbors will refuse to play the prisoner's dilemma game with him in accordance with a certain probability distribution. We use the disconnecting strength to represent this probability. We discuss the evolution of cooperation with different values of temptation to defect, sucker's payoff and disconnecting strength. The simulation results show that cooperation can be significantly enhanced through increasing the value of the disconnecting strength. In addition, the increase in disconnecting strength can improve the cooperators' ability to resist the increase in temptation and the decrease in reward. We study the parameter ranges for three different evolutionary results: cooperators extinction, defectors extinction, cooperator and defector co-existence. Meanwhile, we recruited volunteers and designed a human behavioral experiment to verify the theoretical simulation results. The punishment of disconnection has a positive effect on cooperation. A higher disconnecting strength will enhance cooperation more significantly. Our research findings reveal some significant insights into efficient mechanisms of the evolution of cooperation.

  2. The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment.

    Directory of Open Access Journals (Sweden)

    Gerda Saxer

    Full Text Available Adaptive radiations occur when a species diversifies into different ecological specialists due to competition for resources and trade-offs associated with the specialization. The evolutionary outcome of an instance of adaptive radiation cannot generally be predicted because chance (stochastic events and necessity (deterministic events contribute to the evolution of diversity. With increasing contributions of chance, the degree of parallelism among different instances of adaptive radiations and the predictability of an outcome will decrease. To assess the relative contributions of chance and necessity during adaptive radiation, we performed a selection experiment by evolving twelve independent microcosms of Escherichia coli for 1000 generations in an environment that contained two distinct resources. Specialization to either of these resources involves strong trade-offs in the ability to use the other resource. After selection, we measured three phenotypic traits: 1 fitness, 2 mean colony size, and 3 colony size diversity. We used fitness relative to the ancestor as a measure of adaptation to the selective environment; changes in colony size as a measure of the evolution of new resource specialists because colony size has been shown to correlate with resource specialization; and colony size diversity as a measure of the evolved ecological diversity. Resource competition led to the rapid evolution of phenotypic diversity within microcosms. Measurements of fitness, colony size, and colony size diversity within and among microcosms showed that the repeatability of adaptive radiation was high, despite the evolution of genetic variation within microcosms. Consistent with the observation of parallel evolution, we show that the relative contributions of chance are far smaller and less important than effects due to adaptation for the traits investigated. The two-resource environment imposed similar selection pressures in independent populations and

  3. Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution.

    Science.gov (United States)

    Esteban, David J; Hutchinson, Anne P

    2011-05-23

    Orthopoxviruses are dsDNA viruses with large genomes, some encoding over 200 genes. Genes essential for viral replication are located in the center of the linear genome and genes encoding host response modifiers and other host interacting proteins are located in the terminal regions. The central portion of the genome is highly conserved, both in gene content and sequence, while the terminal regions are more diverse. In this study, we investigated the role of adaptive molecular evolution in poxvirus genes and the selective pressures that act on the different regions of the genome. The relative fixation rates of synonymous and non-synonymous mutations (the d(N)/d(S) ratio) are an indicator of the mechanism of evolution of sequences, and can be used to identify purifying, neutral, or diversifying selection acting on a gene. Like highly conserved residues, amino acids under diversifying selection may be functionally important. Many genes experiencing diversifying selection are involved in host-pathogen interactions, such as antigen-antibody interactions, or the "host-pathogen arms race." We analyzed 175 gene families from orthopoxviruses for evidence of diversifying selection. 79 genes were identified as experiencing diversifying selection, 25 with high confidence. Many of these genes are located in the terminal regions of the genome and function to modify the host response to infection or are virion-associated, indicating a greater role for diversifying selection in host-interacting genes. Of the 79 genes, 20 are of unknown function, and implicating diversifying selection as an important mechanism in their evolution may help characterize their function or identify important functional residues. We conclude that diversifying selection is an important mechanism of orthopoxvirus evolution. Diversifying selection in poxviruses may be the result of interaction with host defense mechanisms.

  4. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

    Science.gov (United States)

    Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël; Willison, John C; Lenski, Richard E; Soyer, Orkun S; Schneider, Dominique

    2016-08-20

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.

  5. Multifunctional adaptive NS1 mutations are selected upon human influenza virus evolution in the mouse.

    Directory of Open Access Journals (Sweden)

    Nicole E Forbes

    Full Text Available The role of the NS1 protein in modulating influenza A virulence and host range was assessed by adapting A/Hong Kong/1/1968 (H3N2 (HK-wt to increased virulence in the mouse. Sequencing the NS genome segment of mouse-adapted variants revealed 11 mutations in the NS1 gene and 4 in the overlapping NEP gene. Using the HK-wt virus and reverse genetics to incorporate mutant NS gene segments, we demonstrated that all NS1 mutations were adaptive and enhanced virus replication (up to 100 fold in mouse cells and/or lungs. All but one NS1 mutant was associated with increased virulence measured by survival and weight loss in the mouse. Ten of twelve NS1 mutants significantly enhanced IFN-β antagonism to reduce the level of IFN β production relative to HK-wt in infected mouse lungs at 1 day post infection, where 9 mutants induced viral yields in the lung that were equivalent to or significantly greater than HK-wt (up to 16 fold increase. Eight of 12 NS1 mutants had reduced or lost the ability to bind the 30 kDa cleavage and polyadenylation specificity factor (CPSF30 thus demonstrating a lack of correlation with reduced IFN β production. Mutant NS1 genes resulted in increased viral mRNA transcription (10 of 12 mutants, and protein production (6 of 12 mutants in mouse cells. Increased transcription activity was demonstrated in the influenza mini-genome assay for 7 of 11 NS1 mutants. Although we have shown gain-of-function properties for all mutant NS genes, the contribution of the NEP mutations to phenotypic changes remains to be assessed. This study demonstrates that NS1 is a multifunctional virulence factor subject to adaptive evolution.

  6. Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

    Science.gov (United States)

    Pilote, Alex J; Donovan, Lisa A

    2016-12-01

    Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

  7. Design Of Multivariable Fractional Order Pid Controller Using Covariance Matrix Adaptation Evolution Strategy

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    Sivananaithaperumal Sudalaiandi

    2014-06-01

    Full Text Available This paper presents an automatic tuning of multivariable Fractional-Order Proportional, Integral and Derivative controller (FO-PID parameters using Covariance Matrix Adaptation Evolution Strategy (CMAES algorithm. Decoupled multivariable FO-PI and FO-PID controller structures are considered. Oustaloup integer order approximation is used for the fractional integrals and derivatives. For validation, two Multi-Input Multi- Output (MIMO distillation columns described byWood and Berry and Ogunnaike and Ray are considered for the design of multivariable FO-PID controller. Optimal FO-PID controller is designed by minimizing Integral Absolute Error (IAE as objective function. The results of previously reported PI/PID controller are considered for comparison purposes. Simulation results reveal that the performance of FOPI and FO-PID controller is better than integer order PI/PID controller in terms of IAE. Also, CMAES algorithm is suitable for the design of FO-PI / FO-PID controller.

  8. Adaptive Differential Evolution Approach for Constrained Economic Power Dispatch with Prohibited Operating Zones

    Directory of Open Access Journals (Sweden)

    Abdellatif HAMOUDA

    2011-12-01

    Full Text Available Economic power dispatch (EPD is one of the main tools for optimal operation and planning of modern power systems. To solve effectively the EPD problem, most of the conventional calculus methods rely on the assumption that the fuel cost characteristic of a generating unit is a continuous and convex function, resulting in inaccurate dispatch. This paper presents the design and application of efficient adaptive differential evolution (ADE algorithm for the solution of the economic power dispatch problem, where the non-convex characteristics of the generators, such us prohibited operating zones and ramp rate limits of the practical generator operation are considered. The 26 bus benchmark test system with 6 units having prohibited operating zones and ramp rate limits was used for testing and validation purposes. The results obtained demonstrate the effectiveness of the proposed method for solving the non-convex economic dispatch problem.

  9. The evolution and adaptation of A-to-I RNA editing.

    Directory of Open Access Journals (Sweden)

    Arielle L Yablonovitch

    2017-11-01

    Full Text Available Adenosine-to-inosine (A-to-I RNA editing is an important post-transcriptional modification that affects the information encoded from DNA to RNA to protein. RNA editing can generate a multitude of transcript isoforms and can potentially be used to optimize protein function in response to varying conditions. In light of this and the fact that millions of editing sites have been identified in many different species, it is interesting to examine the extent to which these sites have evolved to be functionally important. In this review, we discuss results pertaining to the evolution of RNA editing, specifically in humans, cephalopods, and Drosophila. We focus on how comparative genomics approaches have aided in the identification of sites that are likely to be advantageous. The use of RNA editing as a mechanism to adapt to varying environmental conditions will also be reviewed.

  10. Development Of An Efficient Glycerol Utilizing Saccharomyces Cerevisiae Strain Via Adaptive Laboratory Evolution

    DEFF Research Database (Denmark)

    Strucko, Tomas; Zirngibl, Katharina; Tharwat Tolba Mohamed, Elsayed

    2015-01-01

    fermentation processes. The most commonly known microbial cell factory, the yeast Saccharomyces cerevisiae, has been extensively applied for the production of a wide range of scientifically and industrially relevant products using saccharides (mainly glucose) as carbon source. However, it was shown...... that popular wild-type laboratory yeast strains, commonly applied in metabolic engineering studies, did not grow or grew very slowly in glycerol medium.In this work, an adaptive laboratory evolution approach to obtain S. cerevisiae strains with an improved ability to grow on glycerol was applied. A broad array...... catabolism in yeast. The knowledge acquired in this study may be further applied for rational S. cerevisiae strain improvement for using glycerol as a carbon source in industrial biotechnology processes. This work is a part of the DeYeastLibrary consortium financed by ERA-IB DeYeastLibrary - Designer yeast...

  11. Explaining the evolution of European Union foreign climate policy: A case of bounded adaptiveness

    Directory of Open Access Journals (Sweden)

    Simon Schunz

    2012-02-01

    Full Text Available Ever since the inception of the United Nations climate regime in the early 1990s, the European Union has aspired to play a leading part in the global combat against climate change. Based on an analysis of how the Union has developed its foreign climate policy to fulfil this role over the past two decades, the paper sets out to identify the driving factors behind this evolution. It demonstrates that the EU’s development in this area was co-determined by adaptations to shifting international dynamics strongly bounded by purely domestic concerns. Providing a concise understanding and explanation of how the Union designs its foreign policy with regard to one emblematic issue of its international activity, the contribution provides insights into the remarkably rapid, but not always effective maturation of this unique actor’s involvement in global politics.

  12. DiffeRential Evolution Adaptive Metropolis with Sampling From Past States

    Science.gov (United States)

    Vrugt, J. A.; Laloy, E.; Ter Braak, C.

    2010-12-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. In a previous paper te{vrugt_1} we have presented the {D}iffe{R}ential {E}volution {A}daptive {M}etropolis (DREAM) MCMC scheme that automatically tunes the scale and orientation of the proposal distribution during evolution to the posterior target distribution. In the same paper, detailed balance and ergodicity of DREAM have been proved, and various examples involving nonlinearity, high-dimensionality, and multimodality have shown that DREAM is generally superior to other adaptive MCMC sampling approaches. Standard DREAM requires at least N = d chains to be run in parallel, where d is the dimensionality of the posterior. Unfortunately, running many parallel chains is a potential source of inefficiency, as each individual chain must travel to high density region of the posterior. The lower the number of parallel chains required, the greater the practical applicability of DREAM for computationally demanding problems. This paper extends DREAM with a snooker updater and shows by simulation and real examples that DREAM can work for d up to 50-100 with far fewer parallel chains (e.g. N = 3) by generating jumps using differences of pairs of past states

  13. Adaptive reptile color variation and the evolution of the Mc1r gene.

    Science.gov (United States)

    Rosenblum, Erica Bree; Hoekstra, Hopi E; Nachman, Michael W

    2004-08-01

    The wealth of information on the genetics of pigmentation and the clear fitness consequences of many pigmentation phenotypes provide an opportunity to study the molecular basis of an ecologically important trait. The melanocortin-1 receptor (Mc1r) is responsible for intraspecific color variation in mammals and birds. Here, we study the molecular evolution of Mc1r and investigate its role in adaptive intraspecific color differences in reptiles. We sequenced the complete Mc1r locus in seven phylogenetically diverse squamate species with melanic or blanched forms associated with different colored substrates or thermal environments. We found that patterns of amino acid substitution across different regions of the receptor are similar to the patterns seen in mammals, suggesting comparable levels of constraint and probably a conserved function for Mc1r in mammals and reptiles. We also found high levels of silent-site heterozygosity in all species, consistent with a high mutation rate or large long-term effective population size. Mc1r polymorphisms were strongly associated with color differences in Holbrookia maculata and Aspidoscelis inornata. In A. inornata, several observations suggest that Mc1r mutations may contribute to differences in color: (1) a strong association is observed between one Mc1r amino acid substitution and dorsal color; (2) no significant population structure was detected among individuals from these populations at the mitochondrial ND4 gene; (3) the distribution of allele frequencies at Mc1r deviates from neutral expectations; and (4) patterns of linkage disequilibrium at Mc1r are consistent with recent selection. This study provides comparative data on a nuclear gene in reptiles and highlights the utility of a candidate-gene approach for understanding the evolution of genes involved in vertebrate adaptation.

  14. Pre-adaptations and the evolution of pollination by sexual deception: Cope's rule of specialization revisited.

    Science.gov (United States)

    Vereecken, Nicolas J; Wilson, Carol A; Hötling, Susann; Schulz, Stefan; Banketov, Sergey A; Mardulyn, Patrick

    2012-12-07

    Pollination by sexual deception is arguably one of the most unusual liaisons linking plants and insects, and perhaps the most illustrative example of extreme floral specialization in angiosperms. While considerable progress has been made in understanding the floral traits involved in sexual deception, less is known about how this remarkable mimicry system might have arisen, the role of pre-adaptations in promoting its evolution and its extent as a pollination mechanism outside the few groups of plants (primarily orchids) where it has been described to date. In the Euro-Mediterranean region, pollination by sexual deception is traditionally considered to be the hallmark of the orchid genus Ophrys. Here, we introduce two new cases outside of Ophrys, in plant groups dominated by generalized, shelter-mimicking species. On the basis of phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants, and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry. These findings, along with comparative analyses of floral traits (colours and scents), shed light on particular phenotypic changes that might have fuelled the parallel evolution of these extraordinary pollination strategies. Collectively, our results provide the first substantive insights into how pollination sexual deception might have evolved in the Euro-Mediterranean region, and demonstrate that even the most extreme cases of pollinator specialization can reverse to more generalized interactions, breaking 'Cope's rule of specialization'.

  15. Adaptive evolution of social traits: origin, trajectories, and correlations of altruism and mobility.

    Science.gov (United States)

    Le Galliard, Jean-François; Ferrière, Régis; Dieckmann, Ulf

    2005-02-01

    Social behavior involves "staying and helping," two individual attributes that vary considerably among organisms. Investigating the ultimate causes of such variation, this study integrates previously separate lines of research by analyzing the joint evolution of altruism and mobility. We unfold the network of selective pressures and derive how these depend on physiological costs, eco-evolutionary feedbacks, and a complex interaction between the evolving traits. Our analysis highlights habitat saturation, both around individuals (local aggregation) and around unoccupied space (local contention), as the key mediator of altruism and mobility evolution. Once altruism and mobility are allowed to evolve jointly, three general insights emerge. First, the cost of mobility affects the origin of altruism, determining whether and how quickly selfishness is overcome. Second, the cost of altruism determines which of two qualitatively different routes to sociality are taken: an evolutionary reduction of mobility, resulting in higher habitat saturation, is either preceded or followed by the adaptive rise of altruism. Third, contrary to conventional expectations, a positive correlation between evolutionarily stable levels of altruism and mobility can arise; this is expected when comparing populations that evolved under different constraints on mobility or that differ in other life-history traits.

  16. Optimization of reactor network design problem using Jumping Gene Adaptation of Differential Evolution

    Science.gov (United States)

    Gujarathi, Ashish M.; Purohit, S.; Srikanth, B.

    2015-06-01

    Detailed working principle of jumping gene adaptation of differential evolution (DE-JGa) is presented. The performance of the DE-JGa algorithm is compared with the performance of differential evolution (DE) and modified DE (MDE) by applying these algorithms on industrial problems. In this study Reactor network design (RND) problem is solved using DE, MDE, and DE-JGa algorithms: These industrial processes are highly nonlinear and complex with reference to optimal operating conditions with many equality and inequality constraints. Extensive computational comparisons have been made for all the chemical engineering problems considered. The results obtained in the present study show that DE-JGa algorithm outperforms the other algorithms (DE and MDE). Several comparisons are made among the algorithms with regard to the number of function evaluations (NFE)/CPU- time required to find the global optimum. The standard deviation and the variance values obtained using DE-JGa, DE and MDE algorithms also show that the DE-JGa algorithm gives consistent set of results for the majority of the test problems and the industrial real world problems.

  17. Adaptations to sexual selection and sexual conflict: insights from experimental evolution and artificial selection.

    Science.gov (United States)

    Edward, Dominic A; Fricke, Claudia; Chapman, Tracey

    2010-08-27

    Artificial selection and experimental evolution document natural selection under controlled conditions. Collectively, these techniques are continuing to provide fresh and important insights into the genetic basis of evolutionary change, and are now being employed to investigate mating behaviour. Here, we focus on how selection techniques can reveal the genetic basis of post-mating adaptations to sexual selection and sexual conflict. Alteration of the operational sex ratio of adult Drosophila over just a few tens of generations can lead to altered ejaculate allocation patterns and the evolution of resistance in females to the costly effects of elevated mating rates. We provide new data to show how male responses to the presence of rivals can evolve. For several traits, the way in which males responded to rivals was opposite in lines selected for male-biased, as opposed to female-biased, adult sex ratio. This shows that the manipulation of the relative intensity of intra- and inter-sexual selection can lead to replicable and repeatable effects on mating systems, and reveals the potential for significant contemporary evolutionary change. Such studies, with important safeguards, have potential utility for understanding sexual selection and sexual conflict across many taxa. We discuss how artificial selection studies combined with genomics will continue to deepen our knowledge of the evolutionary principles first laid down by Darwin 150 years ago.

  18. Differential Evolution with Novel Mutation and Adaptive Crossover Strategies for Solving Large Scale Global Optimization Problems

    Directory of Open Access Journals (Sweden)

    Ali Wagdy Mohamed

    2017-01-01

    Full Text Available This paper presents Differential Evolution algorithm for solving high-dimensional optimization problems over continuous space. The proposed algorithm, namely, ANDE, introduces a new triangular mutation rule based on the convex combination vector of the triplet defined by the three randomly chosen vectors and the difference vectors between the best, better, and the worst individuals among the three randomly selected vectors. The mutation rule is combined with the basic mutation strategy DE/rand/1/bin, where the new triangular mutation rule is applied with the probability of 2/3 since it has both exploration ability and exploitation tendency. Furthermore, we propose a novel self-adaptive scheme for gradual change of the values of the crossover rate that can excellently benefit from the past experience of the individuals in the search space during evolution process which in turn can considerably balance the common trade-off between the population diversity and convergence speed. The proposed algorithm has been evaluated on the 20 standard high-dimensional benchmark numerical optimization problems for the IEEE CEC-2010 Special Session and Competition on Large Scale Global Optimization. The comparison results between ANDE and its versions and the other seven state-of-the-art evolutionary algorithms that were all tested on this test suite indicate that the proposed algorithm and its two versions are highly competitive algorithms for solving large scale global optimization problems.

  19. Enhanced Differential Evolution Based on Adaptive Mutation and Wrapper Local Search Strategies for Global Optimization Problems

    Directory of Open Access Journals (Sweden)

    Chun-Liang Lu

    2014-12-01

    Full Text Available Differential evolution (DE is a simple, powerful optimization algorithm, which has been widely used in many areas. However, the choices of the best mutation and search strategies are difficult for the specific issues. To alleviate these drawbacks and enhance the performance of DE, in this paper, the hybrid framework based on the adaptive mutation and Wrapper Local Search (WLS schemes, is proposed to improve searching ability to efficiently guide the evolution of the population toward the global optimum. Furthermore, the effective particle encoding representation named Particle Segment Operation-Machine Assignment (PSOMA that we previously published is applied to always produce feasible candidate solutions for solving the Flexible Job-shop Scheduling Problem (FJSP. Experiments were conducted on comprehensive set of complex benchmarks including the unimodal, multimodal and hybrid composition function, to validate performance of the proposed method and to compare with other state-of-the art DE variants such as jDE, JADE, MDE_pBX etc. Meanwhile, the hybrid DE model incorporating PSOMA is used to solve different representative instances based on practical data for multi-objective FJSP verifications. Simulation results indicate that the proposed method performs better for the majority of the single-objective scalable benchmark functions in terms of the solution accuracy and convergence rate. In addition, the wide range of Pareto-optimal solutions and more Gantt chart decision-makings can be provided for the multi-objective FJSP combinatorial optimizations.

  20. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.

    Science.gov (United States)

    Lee, Dae-Hee; Feist, Adam M; Barrett, Christian L; Palsson, Bernhard Ø

    2011-01-01

    Adaptive laboratory evolution (ALE) under controlled conditions has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a given selection pressure. Conventionally, the timescale in ALE experiments has been set in terms of number of generations. As mutations are believed to occur primarily during cell division in growing cultures, the cumulative number of cell divisions (CCD) would be an alternative way to set the timescale for ALE. Here we show that in short-term ALE (up to 40-50 days), Escherichia coli, under growth rate selection pressure, was found to undergo approximately 10(11.2) total cumulative cell divisions in the population to produce a new stable growth phenotype that results from 2 to 8 mutations. Continuous exposure to a low level of the mutagen N-methyl-N'-nitro-N-nitrosoguanidine was found to accelerate this timescale and led to a superior growth rate phenotype with a much larger number of mutations as determined with whole-genome sequencing. These results would be useful for the fundamental kinetics of the ALE process in designing ALE experiments and provide a basis for its quantitative description.

  1. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Dae-Hee Lee

    Full Text Available Adaptive laboratory evolution (ALE under controlled conditions has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a given selection pressure. Conventionally, the timescale in ALE experiments has been set in terms of number of generations. As mutations are believed to occur primarily during cell division in growing cultures, the cumulative number of cell divisions (CCD would be an alternative way to set the timescale for ALE. Here we show that in short-term ALE (up to 40-50 days, Escherichia coli, under growth rate selection pressure, was found to undergo approximately 10(11.2 total cumulative cell divisions in the population to produce a new stable growth phenotype that results from 2 to 8 mutations. Continuous exposure to a low level of the mutagen N-methyl-N'-nitro-N-nitrosoguanidine was found to accelerate this timescale and led to a superior growth rate phenotype with a much larger number of mutations as determined with whole-genome sequencing. These results would be useful for the fundamental kinetics of the ALE process in designing ALE experiments and provide a basis for its quantitative description.

  2. Adaptive evolution of foraging-related traits in a predator-prey community.

    Science.gov (United States)

    Zu, Jian; Mimura, Masayasu; Takeuchi, Yasuhiro

    2011-01-07

    In this paper, with the method of adaptive dynamics and geometric technique, we investigate the adaptive evolution of foraging-related phenotypic traits in a predator-prey community with trade-off structure. Specialization on one prey type is assumed to go at the expense of specialization on another. First, we identify the ecological and evolutionary conditions that allow for evolutionary branching in predator phenotype. Generally, if there is a small switching cost near the singular strategy, then this singular strategy is an evolutionary branching point, in which predator population will change from monomorphism to dimorphism. Second, we find that if the trade-off curve is globally convex, predator population eventually branches into two extreme specialists, each completely specializing on a particular prey species. However, if the trade-off curve is concave-convex-concave, after branching in predator phenotype, the two predator species will evolve to an evolutionarily stable dimorphism at which they can continue to coexist. The analysis reveals that an attractive dimorphism will always be evolutionarily stable and that no further branching is possible under this model. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

  3. Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

    Science.gov (United States)

    Velotta, Jonathan P.; Wegrzyn, Jill L.; Ginzburg, Samuel; Kang, Lin; Czesny, Sergiusz J.; O'Neill, Rachel J.; McCormick, Stephen; Michalak, Pawel; Schultz, Eric T.

    2017-01-01

    Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations after acclimation to fresh (0 ppt) and saltwater (35 ppt). Our results suggest that the gill transcriptome has evolved in primarily discordant ways between independent landlocked populations and their anadromous ancestor. By contrast, evolved shifts in the transcription of a small suite of well-characterized osmoregulatory genes exhibited a strong degree of parallelism. In particular, transcription of genes that regulate gill ion exchange has diverged in accordance with functional predictions: freshwater ion-uptake genes (most notably, the ‘freshwater paralog’ of Na+/K+-ATPase α-subunit) were more highly expressed in landlocked forms, whereas genes that regulate saltwater ion secretion (e.g. the ‘saltwater paralog’ of NKAα) exhibited a blunted response to saltwater. Parallel divergence of ion transport gene expression is associated with shifts in salinity tolerance limits among landlocked forms, suggesting that changes to the gill's transcriptional response to salinity facilitate freshwater adaptation.

  4. Adaptive evolution of simian immunodeficiency viruses isolated from two conventional progressor macaques with neuroaids

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian T [Los Alamos National Laboratory; Korber, Bette T [Los Alamos National Laboratory

    2008-01-01

    Simian immunodeficiency virus infection of macaques may result in neuroAIDS, a feature more commonly observed in macaques with rapid progressive disease than in those with conventional disease. This is the first report of two conventional progressors (H631 and H636) with encephalitis in rhesus macaques inoculated with a derivative of SIVsmES43-3. Phylogenetic analyses of viruses isolated from the cerebral spinal fluid (CSF) and plasma from both animals demonstrated tissue compartmentalization. Additionally, virus from the central nervous system (CNS) was able to infect primary macaque monocyte-derived macrophages more efficiently than virus from plasma. Conversely, virus isolated from plasma was able to replicate better in peripheral blood mononuclear cells than virus from CNS. We speculate that these viruses were under different selective pressures in their separate compartments. Furthermore, these viruses appear to have undergone adaptive evolution to preferentially replicate in their respective cell targets. Analysis of the number of potential N-linked glycosylation sites (PNGS) in gp160 showed that there was a statistically significant loss of PNGS in viruses isolated from CNS in both macaques compared to SIVsmE543-3. Moreover, virus isolated from the brain in H631, had statistically significant loss of PNGS compared to virus isolated from CSF and plasma of the same animal. It is possible that the brain isolate may have adapted to decrease the number of PNGS given that humoral immune selection pressure is less likely to be encountered in the brain. These viruses provide a relevant model to study the adaptations required for SIV to induce encephalitis.

  5. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

    DEFF Research Database (Denmark)

    Utrilla, José; O'Brien, Edward J.; Chen, Ke

    2016-01-01

    Pleiotropic regulatory mutations affect diverse cellular processes, posing a challenge to our understanding of genotype-phenotype relationships across multiple biological scales. Adaptive laboratory evolution (ALE) allows for such mutations to be found and characterized in the context of clear se...

  6. Evolution and adaptation of the pandemic A/H1N1 2009 influenza virus

    Directory of Open Access Journals (Sweden)

    Ducatez MF

    2011-07-01

    Full Text Available Mariette F Ducatez, Thomas P Fabrizio, Richard J WebbyDepartment of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USAAbstract: The emergence of the 2009 H1N1 pandemic influenza virus [A(H1N1pdm09] has provided the public health community with many challenges, but also the scientific community with an opportunity to monitor closely its evolution through the processes of drift and shift. To date, and despite having circulated in humans for nearly two years, little antigenic variation has been observed in the A(H1N1pdm09 viruses. However, as the A(H1N1pdm09 virus continues to circulate and the immunologic pressure within the human population increases, future antigenic change is almost a certainty. Several coinfections of A(H1N1pdm09 and seasonal A(H1N1 or A(H3N2 viruses have been observed, but no reassortant viruses have been described in humans, suggesting a lack of fitness of reassortant viruses or a lack of opportunities for interaction of different viral lineages. In contrast, multiple reassortment events have been detected in swine populations between A(H1N1 pdm09 and other endemic swine viruses. Somewhat surprisingly, many of the well characterized influenza virus virulence markers appear to have limited impact on the phenotype of the A(H1N1pdm09 viruses when they have been introduced into mutant viruses in laboratory settings. As such, it is unclear what the evolutionary path of the pandemic virus will be, but the monitoring of any changes in the circulating viruses will remain a global public and animal health priority.Keywords: influenza, pandemic, evolution, adaptation

  7. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

    Science.gov (United States)

    Studer, Romain A; Christin, Pascal-Antoine; Williams, Mark A; Orengo, Christine A

    2014-02-11

    A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO2 during photosynthesis. Although the majority of plants use the ancestral C3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C4 photosynthesis. The latter concentrates CO2, and C4 RubisCOs consequently have lower specificity for, and faster turnover of, CO2. The C4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C3 and C4 species. We were able to precisely track their past evolutionary trajectories, identify mutations on each branch of the phylogeny, and evaluate their stability effect. We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces. The C3 to C4 transition is preceded by a sustained period in which stability of the enzyme is increased, creating the capacity to accept the functionally necessary destabilizing mutations, and is immediately followed by compensatory mutations that restore global stability.

  8. The purpose of adaptation.

    Science.gov (United States)

    Gardner, Andy

    2017-10-06

    A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's 'fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.

  9. Transient MutS-Based Hypermutation System for Adaptive Evolution of Lactobacillus casei to Low pH.

    Science.gov (United States)

    Overbeck, Tom J; Welker, Dennis L; Hughes, Joanne E; Steele, James L; Broadbent, Jeff R

    2017-10-15

    This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of Lactobacillus casei MutS deletion derivatives of L. casei 12A and ATCC 334 were constructed and subjected to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subjected to this treatment. At the end of the process, the ΔmutS lesion was repaired in representative L. casei 12A and ATCC 334 ΔmutS mutant isolates. Growth studies in broth at pH 4.0 (titrated with lactic acid) showed that all four adapted strains grew more rapidly, to higher cell densities, and produced significantly more lactic acid than untreated wild-type cells. However, the adapted ΔmutS derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the L. casei 12A-adapted ΔmutS derivative revealed that it had a significantly smaller cell volume, a rougher cell surface, and significantly better survival at pH 2.5 than parental L. casei 12A. Genome sequence analysis confirmed that transient mutS inactivation decreased DNA replication fidelity in both L. casei strains, and it identified genetic changes that might contribute to the lactic acid-resistant phenotypes of adapted cells. Targeted inactivation of three genes that had acquired nonsense mutations in the adapted L. casei 12A ΔmutS mutant derivative showed that NADH dehydrogenase (ndh), phosphate transport ATP-binding protein PstB (pstB), and two-component signal transduction system (TCS) quorum-sensing histidine protein kinase (hpk) genes act in combination to increase lactic acid resistance in L. casei 12A.IMPORTANCE Adaptive evolution has been applied to microorganisms to increase industrially desirable phenotypes, including acid resistance. We developed a method to increase the adaptability of Lactobacillus casei 12A and ATCC 334 through transient inactivation of the DNA mismatch

  10. Evolution of adaptive phenotypic variation patterns by direct selection for evolvability

    Science.gov (United States)

    Pavlicev, Mihaela; Cheverud, James M.; Wagner, Günter P.

    2011-01-01

    A basic assumption of the Darwinian theory of evolution is that heritable variation arises randomly. In this context, randomness means that mutations arise irrespective of the current adaptive needs imposed by the environment. It is broadly accepted, however, that phenotypic variation is not uniformly distributed among phenotypic traits, some traits tend to covary, while others vary independently, and again others barely vary at all. Furthermore, it is well established that patterns of trait variation differ among species. Specifically, traits that serve different functions tend to be less correlated, as for instance forelimbs and hind limbs in bats and humans, compared with the limbs of quadrupedal mammals. Recently, a novel class of genetic elements has been identified in mouse gene-mapping studies that modify correlations among quantitative traits. These loci are called relationship loci, or relationship Quantitative Trait Loci (rQTL), and affect trait correlations by changing the expression of the existing genetic variation through gene interaction. Here, we present a population genetic model of how natural selection acts on rQTL. Contrary to the usual neo-Darwinian theory, in this model, new heritable phenotypic variation is produced along the selected dimension in response to directional selection. The results predict that selection on rQTL leads to higher correlations among traits that are simultaneously under directional selection. On the other hand, traits that are not simultaneously under directional selection are predicted to evolve lower correlations. These results and the previously demonstrated existence of rQTL variation, show a mechanism by which natural selection can directly enhance the evolvability of complex organisms along lines of adaptive change. PMID:21106581

  11. Adaptive evolution of the Hox gene family for development in bats and dolphins.

    Directory of Open Access Journals (Sweden)

    Lu Liang

    Full Text Available Bats and cetaceans (i.e., whales, dolphins, porpoises are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii and cetaceans (represented by Tursiops truncatus for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

  12. Adaptive evolution of the Hox gene family for development in bats and dolphins.

    Science.gov (United States)

    Liang, Lu; Shen, Yong-Yi; Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M; Zhang, Ya-Ping

    2013-01-01

    Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

  13. Evolution in functional complexity of heart rate dynamics: a measure of cardiac allograft adaptability.

    Science.gov (United States)

    Kresh, J Y; Izrailtyan, I

    1998-09-01

    The capacity of self-organized systems to adapt is embodied in the functional organization of intrinsic control mechanisms. Evolution in functional complexity of heart rate variability (HRV) was used as measure of the capacity of the transplanted heart to express newly emergent regulatory order. In a cross-sectional study of 100 patients after (0-10 yr) heart transplantation (HTX), heart rate dynamics were assessed using pointwise correlation dimension (PD2) analysis. A new observation is that, commencing with the acute event of allograft transplantation, the dynamics of rhythm formation proceed through complex phase transitions. At implantation, the donor heart manifested metronome-like chronotropic behavior (PD2 approximately 1.0). At 11-100 days, dimensional complexity of HRV reached a peak (PD2 approximately 2.0) associated with resurgence in the high-frequency component (0.15-0.5 Hz) of the power spectral density. Subsequent dimensional loss to PD2 approximately 1.0 at 20-30 mo after HTX was followed by a progressive near-linear gain in system complexity, reaching PD2 approximately 3.0 7-10 yr after HTX. The "dynamic reorganization" in the allograft rhythm-generating system, seen in the first 100 days, is a manifestation of the adaptive capacity of intrinsic control mechanisms. The loss of HRV 2 yr after HTX implies a withdrawal of intrinsic autonomic control and/or development of an entrained dynamic pattern characteristic of extrinsic sympathetic input. The subsequent long-term progressive rise in dimensional complexity of HRV can be attributed to the restoration of a functional order patterning parasympathetic control. The recognition that the decentralized heart can restitute the multidimensional state space of HR generator dynamics independent of external autonomic signaling may provide a new perspective on principles that constitute homeodynamic regulation.

  14. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas

    Energy Technology Data Exchange (ETDEWEB)

    Worden, Alexandra Z.; Lee, Jae-Hyeok; Mock, Thomas; Rouze, Pierre; Simmons, Melinda P.; Aerts, Andrea L.; Allen, Andrew E.; Cuvelier, Marie L.; Derelle, Evelyne; Everett, Meredieht V.; Foulon, Elodie; Grimwood, Jane; Gundlach, Heidrun; Henrissat, Bernard; Napoli, Carolyn; McDonald, Sarah M.; Parker, Micaela S.; Rombauts, Stephane; Salamov, Asaf; von Dassow, Peter; Badger, Jonathan G,; Coutinho, Pedro M.; Demir, Elif; Dubchak, Inna; Gentemann, Chelle; Eikrem, Wenche; Gready, Jill E.; John, Uwe; Lanier, William; Lindquist, Erika A.; Lucas, Susan; Mayer, Kluas F. X.; Moreau, Herve; Not, Fabrice; Otillar, Robert; Panaud, Olivier; Pangilinan, Jasmyn; Paulsen, Ian; Piegu, Benoit; Poliakov, Aaron; Robbens, Steven; Schmutz, Jeremy; Roulza, Eve; Wyss, Tania; Zelensky, Alexander; Zhou, Kemin; Armbrust, E. Virginia; Bhattacharya, Debashish; Goodenough, Ursula W.; Van de Peer, Yves; Grigoriev, Igor V.

    2009-10-14

    Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90percent of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

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

    Science.gov (United States)

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

    2015-09-29

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

  16. The evolution of the human pelvis: changing adaptations to bipedalism, obstetrics and thermoregulation.

    Science.gov (United States)

    Gruss, Laura Tobias; Schmitt, Daniel

    2015-03-05

    The fossil record of the human pelvis reveals the selective priorities acting on hominin anatomy at different points in our evolutionary history, during which mechanical requirements for locomotion, childbirth and thermoregulation often conflicted. In our earliest upright ancestors, fundamental alterations of the pelvis compared with non-human primates facilitated bipedal walking. Further changes early in hominin evolution produced a platypelloid birth canal in a pelvis that was wide overall, with flaring ilia. This pelvic form was maintained over 3-4 Myr with only moderate changes in response to greater habitat diversity, changes in locomotor behaviour and increases in brain size. It was not until Homo sapiens evolved in Africa and the Middle East 200 000 years ago that the narrow anatomically modern pelvis with a more circular birth canal emerged. This major change appears to reflect selective pressures for further increases in neonatal brain size and for a narrow body shape associated with heat dissipation in warm environments. The advent of the modern birth canal, the shape and alignment of which require fetal rotation during birth, allowed the earliest members of our species to deal obstetrically with increases in encephalization while maintaining a narrow body to meet thermoregulatory demands and enhance locomotor performance. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  17. The evolution of the human pelvis: changing adaptations to bipedalism, obstetrics and thermoregulation

    Science.gov (United States)

    Gruss, Laura Tobias; Schmitt, Daniel

    2015-01-01

    The fossil record of the human pelvis reveals the selective priorities acting on hominin anatomy at different points in our evolutionary history, during which mechanical requirements for locomotion, childbirth and thermoregulation often conflicted. In our earliest upright ancestors, fundamental alterations of the pelvis compared with non-human primates facilitated bipedal walking. Further changes early in hominin evolution produced a platypelloid birth canal in a pelvis that was wide overall, with flaring ilia. This pelvic form was maintained over 3–4 Myr with only moderate changes in response to greater habitat diversity, changes in locomotor behaviour and increases in brain size. It was not until Homo sapiens evolved in Africa and the Middle East 200 000 years ago that the narrow anatomically modern pelvis with a more circular birth canal emerged. This major change appears to reflect selective pressures for further increases in neonatal brain size and for a narrow body shape associated with heat dissipation in warm environments. The advent of the modern birth canal, the shape and alignment of which require fetal rotation during birth, allowed the earliest members of our species to deal obstetrically with increases in encephalization while maintaining a narrow body to meet thermoregulatory demands and enhance locomotor performance. PMID:25602067

  18. Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

    Science.gov (United States)

    Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

    2017-12-22

    We recently established a mouse model (288-330+/+) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 106 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 103 and 105 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Rare ecomorphological convergence on a complex adaptive landscape: Body size and diet mediate evolution of jaw shape in squirrels (Sciuridae).

    Science.gov (United States)

    Zelditch, Miriam Leah; Ye, Ji; Mitchell, Jonathan S; Swiderski, Donald L

    2017-03-01

    Convergence is widely regarded as compelling evidence for adaptation, often being portrayed as evidence that phenotypic outcomes are predictable from ecology, overriding contingencies of history. However, repeated outcomes may be very rare unless adaptive landscapes are simple, structured by strong ecological and functional constraints. One such constraint may be a limitation on body size because performance often scales with size, allowing species to adapt to challenging functions by modifying only size. When size is constrained, species might adapt by changing shape; convergent shapes may therefore be common when size is limiting and functions are challenging. We examine the roles of size and diet as determinants of jaw shape in Sciuridae. As expected, size and diet have significant interdependent effects on jaw shape and ecomorphological convergence is rare, typically involving demanding diets and limiting sizes. More surprising is morphological without ecological convergence, which is equally common between and within dietary classes. Those cases, like rare ecomorphological convergence, may be consequences of evolving on an adaptive landscape shaped by many-to-many relationships between ecology and function, many-to-one relationships between form and performance, and one-to-many relationships between functionally versatile morphologies and ecology. On complex adaptive landscapes, ecological selection can yield different outcomes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  20. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster

    Directory of Open Access Journals (Sweden)

    Jakobek Judy L

    2007-07-01

    Full Text Available Abstract Background The biosynthesis of aflatoxin (AF involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST and O-methylsterigmatocystin (OMST, the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus. Results To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL. With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species. Conclusion Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE or the copies may partition the ancestral function (aflA/aflB. In some gene modules, the

  1. Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

    Directory of Open Access Journals (Sweden)

    Barton Robert A

    2010-01-01

    Full Text Available Abstract Background Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question. Results We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position. Conclusions Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain

  2. Adaptive evolution of threonine deaminase in plant defense against insect herbivores

    Energy Technology Data Exchange (ETDEWEB)

    Gonzales-Vigil, Eliana; Bianchetti, Christopher M.; Phillips, Jr., George N.; Howe, Gregg A. (MSU); (UW)

    2011-11-07

    Gene duplication is a major source of plant chemical diversity that mediates plant-herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to {alpha}-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related Solanum species contain a duplicated TD paralog (TD2) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gut of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.

  3. Adaptive evolution of tight junction protein claudin-14 in echolocating whales.

    Science.gov (United States)

    Xu, Huihui; Liu, Yang; He, Guimei; Rossiter, Stephen J; Zhang, Shuyi

    2013-11-10

    Toothed whales and bats have independently evolved specialized ultrasonic hearing for echolocation. Recent findings have suggested that several genes including Prestin, Tmc1, Pjvk and KCNQ4 appear to have undergone molecular adaptations associated with the evolution of this ultrasonic hearing in mammals. Here we studied the hearing gene Cldn14, which encodes the claudin-14 protein and is a member of tight junction proteins that functions in the organ of Corti in the inner ear to maintain a cationic gradient between endolymph and perilymph. Particular mutations in human claudin-14 give rise to non-syndromic deafness, suggesting an essential role in hearing. Our results uncovered two bursts of positive selection, one in the ancestral branch of all toothed whales and a second in the branch leading to the delphinid, phocoenid and ziphiid whales. These two branches are the same as those previously reported to show positive selection in the Prestin gene. Furthermore, as with Prestin, the estimated hearing frequencies of whales significantly correlate with numbers of branch-wise non-synonymous substitutions in Cldn14, but not with synonymous changes. However, in contrast to Prestin, we found no evidence of positive selection in bats. Our findings from Cldn14, and comparisons with Prestin, strongly implicate multiple loci in the acquisition of echolocation in cetaceans, but also highlight possible differences in the evolutionary route to echolocation taken by whales and bats. © 2013.

  4. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

    Science.gov (United States)

    McGowen, Michael R.; Grossman, Lawrence I.; Wildman, Derek E.

    2012-01-01

    Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains. PMID:22740643

  5. Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae.

    Science.gov (United States)

    Baek, Seung-Ho; Kwon, Eunice Y; Kim, Yong Hwan; Hahn, Ji-Sook

    2016-03-01

    There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h).

  6. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown.

    Science.gov (United States)

    McGowen, Michael R; Grossman, Lawrence I; Wildman, Derek E

    2012-09-22

    Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10,000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains.

  7. Adaptive simplification and the evolution of gecko locomotion: morphological and biomechanical consequences of losing adhesion.

    Science.gov (United States)

    Higham, Timothy E; Birn-Jeffery, Aleksandra V; Collins, Clint E; Hulsey, C Darrin; Russell, Anthony P

    2015-01-20

    Innovations permit the diversification of lineages, but they may also impose functional constraints on behaviors such as locomotion. Thus, it is not surprising that secondary simplification of novel locomotory traits has occurred several times among vertebrates and could potentially lead to exceptional divergence when constraints are relaxed. For example, the gecko adhesive system is a remarkable innovation that permits locomotion on surfaces unavailable to other animals, but has been lost or simplified in species that have reverted to a terrestrial lifestyle. We examined the functional and morphological consequences of this adaptive simplification in the Pachydactylus radiation of geckos, which exhibits multiple unambiguous losses or bouts of simplification of the adhesive system. We found that the rates of morphological and 3D locomotor kinematic evolution are elevated in those species that have simplified or lost adhesive capabilities. This finding suggests that the constraints associated with adhesion have been circumvented, permitting these species to either run faster or burrow. The association between a terrestrial lifestyle and the loss/reduction of adhesion suggests a direct link between morphology, biomechanics, and ecology.

  8. Recent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium

    Science.gov (United States)

    de Been, Mark; van Schaik, Willem; Cheng, Lu; Corander, Jukka; Willems, Rob J.

    2013-01-01

    Reasons for the rising clinical impact of the bacterium Enterococcus faecium include the species’ rapid acquisition of adaptive genetic elements. Here, we focused on the impact of recombination on the evolution of E. faecium. We used the recently developed BratNextGen algorithm to detect recombinant regions in the core genome of 34 E. faecium strains, including three newly sequenced clinical strains. Recombination was found to have a significant impact on the E. faecium genome: of the original 1.2 million positions in the core genome, 0.5 million were predicted to have been affected by recombination in at least one strain. Importantly, strains in one of the two major E. faecium clades (clade B), which contains most of the E. faecium human gut commensals, formed the most important reservoir for donating foreign DNA to the second major E. faecium clade (clade A), which contains most of the clinical isolates. Also, several genomic regions were found to mainly recombine in specific hospital-associated E. faecium strains. One of these regions (the epa-like locus) likely encodes the biosynthesis of cell wall polysaccharides. These findings suggest a crucial role for recombination in the emergence of E. faecium as a successful hospital-associated pathogen. PMID:23882129

  9. Evolution of age-dependent sex-reversal under adaptive dynamics.

    Science.gov (United States)

    Calsina, Angel; Ripoll, Jordi

    2010-02-01

    We investigate the evolution of the age (or size) at sex-reversal in a model of sequential hermaphroditism, by means of the function-valued adaptive dynamics. The trait is the probability law of the age at sex-reversal considered as a random variable. Our analysis starts with the ecological model which was first introduced and analyzed by Calsina and Ripoll (Math Biosci 208(2), 393-418, 2007). The structure of the population is extended to a genotype class and a new model for an invading/mutant population is introduced. The invasion fitness functional is derived from the ecological setting, and it turns out to be controlled by a formula of Shaw-Mohler type. The problem of finding evolutionarily stable strategies is solved by means of infinite-dimensional linear optimization. We have found that these strategies correspond to sex-reversal at a single particular age (or size) even if the set of feasible strategies is considerably broader and allows for a probabilistic sex-reversal. Several examples, including in addition the population-dynamical stability, are illustrated. For a special case, we can show that an unbeatable size at sex-reversal must be larger than 69.3% of the expected size at death.

  10. Molecular Characterization of a Chromosomal Rearrangement Involved in the Adaptive Evolution of Yeast Strains

    Science.gov (United States)

    Pérez-Ortín, José E.; Querol, Amparo; Puig, Sergi; Barrio, Eladio

    2002-01-01

    Wine yeast strains show a high level of chromosome length polymorphism. This polymorphism is mainly generated by illegitimate recombination mediated by Ty transposons or subtelomeric repeated sequences. We have found, however, that the SSU1-R allele, which confers sulfite resistance to yeast cells, is the product of a reciprocal translocation between chromosomes VIII and XVI due to unequal crossing-over mediated by microhomology between very short sequences on the 5′ upstream regions of the SSU1 and ECM34 genes. We also show that this translocation is only present in wine yeast strains, suggesting that the use for millennia of sulfite as a preservative in wine production could have favored its selection. This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae. [The sequence data from this study have been submitted to EMBL under accession nos. AF239757, AF239758, and AJ458340–AJ458367. The following individual kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Goto-Yamamoto.] PMID:12368245

  11. Evolution of cooperation in the spatial public goods game with adaptive reputation assortment

    Science.gov (United States)

    Chen, Mei-huan; Wang, Li; Sun, Shi-wen; Wang, Juan; Xia, Cheng-yi

    2016-01-01

    We present a new spatial public goods game model, which takes the individual reputation and behavior diversity into account at the same time, to investigate the evolution of cooperation. Initially, each player x will be endowed with an integer Rx between 1 and Rmax to characterize his reputation value, which will be adaptively varied according to the strategy action at each time step. Then, the agents play the game and the system proceeds in accordance with a Fermi-like rule, in which a multiplicative factor (wy) to denote the individual difference to perform the strategy transfer will be placed before the traditional Fermi probability. For influential participants, wy is set to be 1.0, but be a smaller value w (0 reputation threshold (RC), and the greater the threshold, the higher the fraction of cooperators. The origin of promotion of cooperation will be attributed to the fact that the larger reputation threshold renders the higher heterogeneity in the fraction of two types of players and strategy spreading capability. Our work is conducive to a better understanding of the emergence of cooperation within many real-world systems.

  12. The roles of life-history selection and sexual selection in the adaptive evolution of mating behavior in a beetle.

    Science.gov (United States)

    Maklakov, Alexei A; Cayetano, Luis; Brooks, Robert C; Bonduriansky, Russell

    2010-05-01

    Although there is continuing debate about whether sexual selection promotes or impedes adaptation to novel environments, the role of mating behavior in such adaptation remains largely unexplored. We investigated the evolution of mating behavior (latency to mating, mating probability and duration) in replicate populations of seed beetles Callosobruchus maculatus subjected to selection on life-history ("Young" vs. "Old" reproduction) under contrasting regimes of sexual selection ("Monogamy" vs. "Polygamy"). Life-history selection is predicted to favor delayed mating in "Old" females, but sexual conflict under polygamy can potentially retard adaptive life-history evolution. We found that life-history selection yielded the predicted changes in mating behavior, but sexual selection regime had no net effect. In within-line crosses, populations selected for late reproduction showed equally reduced early-life mating probability regardless of mating system. In between-line crosses, however, the effect of life-history selection on early-life mating probability was stronger in polygamous lines than in monogamous ones. Thus, although mating system influenced male-female coevolution, removal of sexual selection did not affect the adaptive evolution of mating behavior. Importantly, our study shows that the interaction between sexual selection and life-history selection can result in either increased or decreased reproductive divergence depending on the ecological context.

  13. Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations.

    Directory of Open Access Journals (Sweden)

    Naoki Morimoto

    Full Text Available BACKGROUND: Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual's lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion. METHODOLOGY/PRINCIPAL FINDINGS: Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state. CONCLUSIONS/SIGNIFICANCE: These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.

  14. Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities

    Science.gov (United States)

    Soliveres, Santiago; Smit, Christian; Maestre, Fernando T.

    2015-01-01

    Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant–plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant–plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant–plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant–plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore

  15. Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.

    Science.gov (United States)

    Berlin, Sofia; Smith, Nick G C

    2005-11-10

    Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

  16. Type I Interferon Receptor Deficiency in Dendritic Cells Facilitates Systemic Murine Norovirus Persistence Despite Enhanced Adaptive Immunity.

    Science.gov (United States)

    Nice, Timothy J; Osborne, Lisa C; Tomov, Vesselin T; Artis, David; Wherry, E John; Virgin, Herbert W

    2016-06-01

    In order for a virus to persist, there must be a balance between viral replication and immune clearance. It is commonly believed that adaptive immunity drives clearance of viral infections and, thus, dysfunction or viral evasion of adaptive immunity is required for a virus to persist. Type I interferons (IFNs) play pleiotropic roles in the antiviral response, including through innate control of viral replication. Murine norovirus (MNoV) replicates in dendritic cells (DCs) and type I IFN signaling in DCs is important for early control of MNoV replication. We show here that the non-persistent MNoV strain CW3 persists systemically when CD11c positive DCs are unable to respond to type I IFN. Persistence in this setting is associated with increased early viral titers, maintenance of DC numbers, increased expression of DC activation markers and an increase in CD8 T cell and antibody responses. Furthermore, CD8 T cell function is maintained during the persistent phase of infection and adaptive immune cells from persistently infected mice are functional when transferred to Rag1-/- recipients. Finally, increased early replication and persistence are also observed in mixed bone marrow chimeras where only half of the CD11c positive DCs are unable to respond to type I IFN. These findings demonstrate that increased early viral replication due to a cell-intrinsic innate immune deficiency is sufficient for persistence and a functional adaptive immune response is not sufficient for viral clearance.

  17. Type I Interferon Receptor Deficiency in Dendritic Cells Facilitates Systemic Murine Norovirus Persistence Despite Enhanced Adaptive Immunity.

    Directory of Open Access Journals (Sweden)

    Timothy J Nice

    2016-06-01

    Full Text Available In order for a virus to persist, there must be a balance between viral replication and immune clearance. It is commonly believed that adaptive immunity drives clearance of viral infections and, thus, dysfunction or viral evasion of adaptive immunity is required for a virus to persist. Type I interferons (IFNs play pleiotropic roles in the antiviral response, including through innate control of viral replication. Murine norovirus (MNoV replicates in dendritic cells (DCs and type I IFN signaling in DCs is important for early control of MNoV replication. We show here that the non-persistent MNoV strain CW3 persists systemically when CD11c positive DCs are unable to respond to type I IFN. Persistence in this setting is associated with increased early viral titers, maintenance of DC numbers, increased expression of DC activation markers and an increase in CD8 T cell and antibody responses. Furthermore, CD8 T cell function is maintained during the persistent phase of infection and adaptive immune cells from persistently infected mice are functional when transferred to Rag1-/- recipients. Finally, increased early replication and persistence are also observed in mixed bone marrow chimeras where only half of the CD11c positive DCs are unable to respond to type I IFN. These findings demonstrate that increased early viral replication due to a cell-intrinsic innate immune deficiency is sufficient for persistence and a functional adaptive immune response is not sufficient for viral clearance.

  18. Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat.

    Science.gov (United States)

    Wynns, Anja Amtoft

    2015-07-21

    cyst are both shown to have evolved convergently within the bee habitat. The convergent evolution of these unusual ascocarps is hypothesized to be adaptive for bee-mediated dispersal. Elucidating the dispersal strategies of these fungal symbionts contributes to our understanding of their interaction with bees and provides insight into the factors which potentially drive the evolution of reduced ascocarps in Pezizomycotina.

  19. Which Beak Fits the Bill? An Activity Examining Adaptation, Natural Selection and Evolution

    Science.gov (United States)

    Darling, Randi

    2014-01-01

    Evolution is a unifying concept within biology. In fact, Dobzhansky, a noted evolutionary biologist, argued, "Nothing in biology makes sense except in the light of evolution" (Dobzhansky, 1973). However, often students have misconceptions about evolution. There are a number of available activities where students use tools (representing…

  20. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production.

    Science.gov (United States)

    Peris, David; Moriarty, Ryan V; Alexander, William G; Baker, EmilyClare; Sylvester, Kayla; Sardi, Maria; Langdon, Quinn K; Libkind, Diego; Wang, Qi-Ming; Bai, Feng-Yan; Leducq, Jean-Baptiste; Charron, Guillaume; Landry, Christian R; Sampaio, José Paulo; Gonçalves, Paula; Hyma, Katie E; Fay, Justin C; Sato, Trey K; Hittinger, Chris Todd

    2017-01-01

    Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to

  1. Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh in vertebrates.

    Directory of Open Access Journals (Sweden)

    Joana Pereira

    Full Text Available The Hedgehog (Hh gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog--Shh; Indian hedgehog--Ihh; and Desert hedgehog--Dhh, each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.

  2. Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

    Science.gov (United States)

    Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

    2014-01-01

    The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

  3. Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

    DEFF Research Database (Denmark)

    Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben

    2013-01-01

    Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular ev...

  4. Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis.

    Science.gov (United States)

    Oliver, Keith R; Greene, Wayne K

    2012-11-01

    In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. "Adaptive potential" and "evolutionary potential" are proposed as the extremes of a continuum of "intra-genomic potential" due to TE-Thrust. Specific data is given, indicating "adaptive potential" being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of "evolutionary potential" is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.

  5. Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes.

    Science.gov (United States)

    Xu, Shixia; Sun, Xiaohui; Niu, Xu; Zhang, Zepeng; Tian, Ran; Ren, Wenhua; Zhou, Kaiya; Yang, Guang

    2017-08-29

    Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in size regulation during brain development were investigated in representative cetacean lineages. Sequences of MCPH2-7 genes were intact in cetaceans but frameshift mutations and stop codons was identified in MCPH1. Extensive positive selection was identified in four of six intact MCPH genes: WDR62, CDK5RAP2, CEP152, and ASPM. Specially, positive selection at CDK5RAP2 and ASPM were examined along lineages of odontocetes with increased encephalization quotients (EQ) and mysticetes with reduced EQ but at WDR62 only found along odontocete lineages. Interestingly, a positive association between evolutionary rate (ω) and EQ was identified for CDK5RAP2 and ASPM. Furthermore, we tested the binding affinities between Calmodulin (CaM) and ASPM IQ motif in cetaceans because only CaM combined with IQ, can ASPM perform the function in determining brain size. Preliminary function assay showed binding affinities between CaM and IQ motif of the odontocetes with increased EQ was stronger than for the mysticetes with decreased EQ. In addition, evolution rate of ASPM and CDK5RAP2 were significantly related to mean group size (as one measure of social complexity). Our study investigated the genetic basis of cetacean brain size evolution. Significant positive selection was examined along lineages with both increased and decreased EQ at CDK5RAP2 and ASPM, which is well matched with cetacean complex brain size evolution. Evolutionary rate of CDK5RAP2 and ASPM were significantly related to EQ, suggesting that these two genes may have contributed to EQ expansion in cetaceans. This suggestion was further indicated by our preliminary function test that ASPM might be mainly linked to evolutionary increases in EQ. Most strikingly, our results suggested that cetaceans evolved large brains

  6. Natural selection and adaptive evolution of leptin in the ochotona family driven by the cold environmental stress.

    Directory of Open Access Journals (Sweden)

    Jie Yang

    Full Text Available BACKGROUND: Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism's fitness to stressful environments. Pikas (order Lagomorpha, endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. METHODOLOGY/PRINCIPAL FINDINGS: To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China and the leptin sequences of plateau pikas (O. curzonia from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase alpha and beta subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka and amino acid substitution (Aa, whereas altitude does not significantly affect synonymous substitution (Ks, Ka and Aa. CONCLUSIONS/SIGNIFICANCE: Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas' ecological adaptation to

  7. Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

    Science.gov (United States)

    Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

    2014-05-19

    The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

    Science.gov (United States)

    Flegr, Jaroslav

    2010-01-13

    Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

  9. Elastic, not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms

    Directory of Open Access Journals (Sweden)

    Flegr Jaroslav

    2010-01-01

    Full Text Available Abstract Background Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. Results The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Conclusion Frozen plasticity theory, which includes the Darwinian model of evolution as a special case - the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. Reviewers This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell.

  10. sigE facilitates the adaptation of Bordetella bronchiseptica to stress conditions and lethal infection in immunocompromised mice

    Directory of Open Access Journals (Sweden)

    Barchinger Sarah E

    2012-08-01

    Full Text Available Abstract Background The cell envelope of a bacterial pathogen can be damaged by harsh conditions in the environment outside a host and by immune factors during infection. Cell envelope stress responses preserve the integrity of this essential compartment and are often required for virulence. Bordetella species are important respiratory pathogens that possess a large number of putative transcription factors. However, no cell envelope stress responses have been described in these species. Among the putative Bordetella transcription factors are a number of genes belonging to the extracytoplasmic function (ECF group of alternative sigma factors, some of which are known to mediate cell envelope stress responses in other bacteria. Here we investigate the role of one such gene, sigE, in stress survival and pathogenesis of Bordetella bronchiseptica. Results We demonstrate that sigE encodes a functional sigma factor that mediates a cell envelope stress response. Mutants of B. bronchiseptica strain RB50 lacking sigE are more sensitive to high temperature, ethanol, and perturbation of the envelope by SDS-EDTA and certain β-lactam antibiotics. Using a series of immunocompromised mice deficient in different components of the innate and adaptive immune responses, we show that SigE plays an important role in evading the innate immune response during lethal infections of mice lacking B cells and T cells. SigE is not required, however, for colonization of the respiratory tract of immunocompetent mice. The sigE mutant is more efficiently phagocytosed and killed by peripheral blood polymorphonuclear leukocytes (PMNs than RB50, and exhibits decreased cytotoxicity toward macrophages. These altered interactions with phagocytes could contribute to the defects observed during lethal infection. Conclusions Much of the work on transcriptional regulation during infection in B. bronchiseptica has focused on the BvgAS two-component system. This study reveals that the Sig

  11. Starvation stress during larval development facilitates an adaptive response in adult worker honey bees (Apis mellifera L.).

    Science.gov (United States)

    Wang, Ying; Kaftanoglu, Osman; Brent, Colin S; Page, Robert E; Amdam, Gro V

    2016-04-01

    Most organisms are constantly faced with environmental changes and stressors. In diverse organisms, there is an anticipatory mechanism during development that can program adult phenotypes. The adult phenotype would be adapted to the predicted environment that occurred during organism maturation. However, whether this anticipatory mechanism is present in eusocial species is questionable because eusocial organisms are largely shielded from exogenous conditions by their stable nest environment. In this study, we tested whether food deprivation during development of the honey bee (Apis mellifera), a eusocial insect model, can shift adult phenotypes to better cope with nutritional stress. After subjecting fifth instar worker larvae to short-term starvation, we measured nutrition-related morphology, starvation resistance, physiology, endocrinology and behavior in the adults. We found that the larval starvation caused adult honey bees to become more resilient toward starvation. Moreover, the adult bees were characterized by reduced ovary size, elevated glycogen stores and juvenile hormone (JH) titers, and decreased sugar sensitivity. These changes, in general, can help adult insects survive and reproduce in food-poor environments. Overall, we found for the first time support for an anticipatory mechanism in a eusocial species, the honey bee. Our results suggest that this mechanism may play a role in honey bee queen-worker differentiation and worker division of labor, both of which are related to the responses to nutritional stress. © 2016. Published by The Company of Biologists Ltd.

  12. Climate adaptation is not enough: warming does not facilitate success of southern tundra plant populations in the high Arctic.

    Science.gov (United States)

    Bjorkman, Anne D; Vellend, Mark; Frei, Esther R; Henry, Gregory H R

    2017-04-01

    Rapidly rising temperatures are expected to cause latitudinal and elevational range shifts as species track their optimal climate north and upward. However, a lack of adaptation to environmental conditions other than climate - for example photoperiod, biotic interactions, or edaphic conditions - might limit the success of immigrants in a new location despite hospitable climatic conditions. Here, we present one of the first direct experimental tests of the hypothesis that warmer temperatures at northern latitudes will confer a fitness advantage to southern immigrants relative to native populations. As rates of warming in the Arctic are more than double the global average, understanding the impacts of warming in Arctic ecosystems is especially urgent. We established experimentally warmed and nonwarmed common garden plots at Alexandra Fiord, Ellesmere Island in the Canadian High Arctic with seeds of two forb species (Oxyria digyna and Papaver radicatum) originating from three to five populations at different latitudes across the Arctic. We found that plants from the local populations generally had higher survival and obtained a greater maximum size than foreign individuals, regardless of warming treatment. Phenological traits varied with latitude of the source population, such that southern populations demonstrated substantially delayed leaf-out and senescence relative to northern populations. Our results suggest that environmental conditions other than temperature may influence the ability of foreign populations and species to establish at more northerly latitudes as the climate warms, potentially leading to lags in northward range shifts for some species. © 2016 John Wiley & Sons Ltd.

  13. How rural land use management facilitates drought risk adaptation in a changing climate - A case study in arid northern China.

    Science.gov (United States)

    Lei, Yongdeng; Zhang, Hailin; Chen, Fu; Zhang, Linbo

    2016-04-15

    Under a warming climate, frequent drought and water scarcity in northern China have severely disrupted agricultural production and posed a substantial threat to farmers' livelihoods. Based on first-hand data collected through in-depth interviews with local managers and farmer households, this study evaluated the effectiveness of rural land use management in mitigating drought risk, ensuring food security and improving farmers' livelihoods. Our findings indicate that a) reforestation on low-yield cropland not only can improve the eco-environment but can also prominently mitigate the production risk to local farmers; b) replacing the traditional border irrigation with sprinkler irrigation has substantially curbed agricultural water usage and increased the per unit of output; and c) in recent years, instead of planting water-intensive grain crops, local farmers cultivated more forage crops to raise animals, which greatly diversified their income sources and reduced the drought risk of agricultural production. By performing an empirical case study in drought-prone Inner Mongolia, this study provides decision-makers with insights into how to strategically adapt to drought risk and reduce rural poverty within the broader context of climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Deriving urban dynamic evolution rules from self-adaptive cellular automata with multi-temporal remote sensing images

    Science.gov (United States)

    He, Yingqing; Ai, Bin; Yao, Yao; Zhong, Fajun

    2015-06-01

    Cellular automata (CA) have proven to be very effective for simulating and predicting the spatio-temporal evolution of complex geographical phenomena. Traditional methods generally pose problems in determining the structure and parameters of CA for a large, complex region or a long-term simulation. This study presents a self-adaptive CA model integrated with an artificial immune system to discover dynamic transition rules automatically. The model's parameters are allowed to be self-modified with the application of multi-temporal remote sensing images: that is, the CA can adapt itself to the changed and complex environment. Therefore, urban dynamic evolution rules over time can be efficiently retrieved by using this integrated model. The proposed AIS-based CA model was then used to simulate the rural-urban land conversion of Guangzhou city, located in the core of China's Pearl River Delta. The initial urban land was directly classified from TM satellite image in the year 1990. Urban land in the years 1995, 2000, 2005, 2009 and 2012 was correspondingly used as the observed data to calibrate the model's parameters. With the quantitative index figure of merit (FoM) and pattern similarity, the comparison was further performed between the AIS-based model and a Logistic CA model. The results indicate that the AIS-based CA model can perform better and with higher precision in simulating urban evolution, and the simulated spatial pattern is closer to the actual development situation.

  15. Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment.

    Science.gov (United States)

    Xu, Jian; Li, Jiong-Tang; Jiang, Yanliang; Peng, Wenzhu; Yao, Zongli; Chen, Baohua; Jiang, Likun; Feng, Jingyan; Ji, Peifeng; Liu, Guiming; Liu, Zhanjiang; Tai, Ruyu; Dong, Chuanju; Sun, Xiaoqing; Zhao, Zi-Xia; Zhang, Yan; Wang, Jian; Li, Shangqi; Zhao, Yunfeng; Yang, Jiuhui; Sun, Xiaowen; Xu, Peng

    2017-01-01

    The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbor genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization

    Science.gov (United States)

    Romão, Célia V.; Ladakis, Dimitrios; Lobo, Susana A. L.; Carrondo, Maria A.; Brindley, Amanda A.; Deery, Evelyne; Matias, Pedro M.; Pickersgill, Richard W.; Saraiva, Lígia M.; Warren, Martin J.

    2011-01-01

    The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe2+ or Co2+) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiXS from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit. PMID:21173279

  17. Revealing the brain's adaptability and the transcranial direct current stimulation facilitating effect in inhibitory control by multiscale entropy.

    Science.gov (United States)

    Liang, Wei-Kuang; Lo, Men-Tzung; Yang, Albert C; Peng, Chung-Kang; Cheng, Shih-Kuen; Tseng, Philip; Juan, Chi-Hung

    2014-04-15

    The abilities to inhibit impulses and withdraw certain responses are critical for human's survival in a fast-changing environment. These processes happen fast, in a complex manner, and sometimes are difficult to capture with fMRI or mean electrophysiological brain signal alone. Therefore, an alternative measure that can reveal the efficiency of the neural mechanism across multiple timescales is needed for the investigation of these brain functions. The present study employs a new approach to analyzing electroencephalography (EEG) signal: the multiscale entropy (MSE), which groups data points with different timescales to reveal any occurrence of repeated patterns, in order to theoretically quantify the complexity (indicating adaptability and efficiency) of neural systems during the process of inhibitory control. From this MSE perspective, EEG signals of successful stop trials are more complex and information rich than that of unsuccessful stop trials. We further applied transcranial direct current stimulation (tDCS), with anodal electrode over presupplementary motor area (preSMA), to test the relationship between behavioral modification with the complexity of EEG signals. We found that tDCS can further increase the EEG complexity of the frontal lobe. Furthermore, the MSE pattern was found to be different between high and low performers (divided by their stop-signal reaction time), where the high-performing group had higher complexity in smaller scales and less complexity in larger scales in comparison to the low-performing group. In addition, this between-group MSE difference was found to interact with the anodal tDCS, where the increase of MSE in low performers benefitted more from the anodal tDCS. Together, the current study demonstrates that participants who suffer from poor inhibitory control can efficiently improve their performance with 10min of electrical stimulation, and such cognitive improvement can be effectively traced back to the complexity within the

  18. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.

    Science.gov (United States)

    Fong, Stephen S; Marciniak, Jennifer Y; Palsson, Bernhard Ø

    2003-11-01

    Genome-scale in silico metabolic networks of Escherichia coli have been reconstructed. By using a constraint-based in silico model of a reconstructed network, the range of phenotypes exhibited by E. coli under different growth conditions can be computed, and optimal growth phenotypes can be predicted. We hypothesized that the end point of adaptive evolution of E. coli could be accurately described a priori by our in silico model since adaptive evolution should lead to an optimal phenotype. Adaptive evolution of E. coli during prolonged exponential growth was performed with M9 minimal medium supplemented with 2 g of alpha-ketoglutarate per liter, 2 g of lactate per liter, or 2 g of pyruvate per liter at both 30 and 37 degrees C, which produced seven distinct strains. The growth rates, substrate uptake rates, oxygen uptake rates, by-product secretion patterns, and growth rates on alternative substrates were measured for each strain as a function of evolutionary time. Three major conclusions were drawn from the experimental results. First, adaptive evolution leads to a phenotype characterized by maximized growth rates that may not correspond to the highest biomass yield. Second, metabolic phenotypes resulting from adaptive evolution can be described and predicted computationally. Third, adaptive evolution on a single substrate leads to changes in growth characteristics on other substrates that could signify parallel or opposing growth objectives. Together, the results show that genome-scale in silico metabolic models can describe the end point of adaptive evolution a priori and can be used to gain insight into the adaptive evolutionary process for E. coli.

  19. Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks.

    Science.gov (United States)

    Wilson, Laura A B; Colombo, Marco; Sánchez-Villagra, Marcelo R; Salzburger, Walter

    2015-11-20

    Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

  20. Toxin-Resistant Sodium Channels: Parallel Adaptive Evolution across a Complete Gene Family

    National Research Council Canada - National Science Library

    Jost, Manda Clair; Hillis, David M; Lu, Ying; Kyle, John W; Fozzard, Harry A; Zakon, Harold H

    2008-01-01

    Approximately 75% of vertebrate proteins belong to protein families encoded by multiple evolutionarily related genes, a pattern that emerged as a result of gene and genome duplications over the course of vertebrate evolution...

  1. Self-adaptive Differential Evolution Based Optimal Power Flow for Units with Non-smooth Fuel Cost Functions

    Directory of Open Access Journals (Sweden)

    C. Thitithamrongchai

    2007-06-01

    Full Text Available This paper presents a self-adaptive differential evolution with augmented Lagrange multiplier method (SADE_ALM for solving optimal power flow (OPF problems with non-smooth generator fuel cost curves. The SADE_ALM is a modified version of conventional differential evolution (DE by integrating mutation factor (F and crossover constant (CR as additional control variables.An augmented Lagrange multiplier method (ALM is applied to handle inequality constraints instead of traditional penalty function method, whereas the sum of the violated constraint (SVC index is employed to ensure that the final result is the feasible global or quasi-global optimum.The proposed algorithm has been tested with the IEEE 30-bus system with different fuel cost characteristics, i.e. 1 quadratic cost curve model, and 2 quadratic cost curve with rectified sine component model (valve-point effects. Numerical results show that the SADE_ALM provides very impressive results compared with the previous reports.

  2. Robot manipulator identification based on adaptive multiple-input and multiple-output neural model optimized by advanced differential evolution algorithm

    Directory of Open Access Journals (Sweden)

    Nguyen Ngoc Son

    2016-12-01

    Full Text Available This article proposes a novel advanced differential evolution method which combines the differential evolution with the modified back-propagation algorithm. This new proposed approach is applied to train an adaptive enhanced neural model for approximating the inverse model of the industrial robot arm. Experimental results demonstrate that the proposed modeling procedure using the new identification approach obtains better convergence and more precision than the traditional back-propagation method or the lonely differential evolution approach. Furthermore, the inverse model of the industrial robot arm using the adaptive enhanced neural model performs outstanding results.

  3. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae).

    Science.gov (United States)

    Zhou, Dangwei; Zhou, Jie; Meng, Lihua; Wang, Qingbiao; Xie, He; Guan, Yucheng; Ma, Zeyang; Zhong, Yang; Chen, Fan; Liu, Jianquan

    2009-07-15

    Plants have evolved diverse adaptive mechanisms that enable them to tolerate abiotic stresses, to varying degrees, and such stresses may have strongly influenced evolutionary changes at levels ranging from molecular to morphological. Previous studies on these phenomena have focused on the adaptive evolution of stress-related orthologous genes in specific lineages. However, heterogenetic evolution of the paralogous genes following duplication has only been examined in a very limited number of stress-response gene families. The COR15 gene encodes a low molecular weight protein that plays an important role in protecting plants from cold stresses. Although two different copies of this gene have been found in the model species, Arabidopsis thaliana, evolutionary patterns of this small gene family in plants have not been previously explored. In this study, we cloned COR15-like sequences and performed evolutionary analyses of these sequences (including those previously reported) in the highly cold-tolerant Draba lineage and related lineages of Brassicaceae. Our phylogenetic analyses indicate that all COR15-like sequences clustered into four clades that corresponded well to the morphological lineages. Gene conversions were found to have probably occurred before/during the divergence of Brassica and Draba lineage. However, repeated, independent duplications of this gene have occurred in different lineages of Brassicaceae. Further comparisons of all sequences suggest that there have been significant inter-lineage differences in evolutionary rates between the duplicated and original genes. We assessed the likelihood that the differences between two well-supported gene subfamilies that appear to have originated from a single duplication, COR15a and COR15b, within the Draba lineage have been driven by adaptive evolution. Comparisons of their non-synonymous/synonymous substitution ratios and rates of predicted amino acid changes indicate that these two gene groups are evolving

  4. Lineage-specific evolution of bitter taste receptor genes in the giant and red pandas implies dietary adaptation.

    Science.gov (United States)

    Shan, Lei; Wu, Qi; Wang, Le; Zhang, Lei; Wei, Fuwen

    2017-11-23

    Bitter taste receptor genes (TAS2Rs) mediate bitterness perception in mammals. It is believed that these genes evolved in response to species-specific diets. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens styani) in the order Carnivora are specialized herbivores with an almost exclusive bamboo diet (>90% bamboo). Because bamboo is full of bitter tasting compounds, we hypothesized that adaptive evolution have occurred at TAS2R genes in giant and red pandas throughout the course of their dietary shift. Here, we characterized 195 TAS2Rs in nine Carnivora species and examined selective pressures on these genes. We found that both pandas harbour more putative functional TAS2Rs than other carnivores, and pseudogenized TAS2Rs in the giant panda are different from the red panda. The purifying selection on TAS2R1, TAS2R9 and TAS2R38 in the giant panda, and TAS2R62 in the red panda, has been strengthened throughout the course of adaptation to bamboo diet, while selective constraint on TAS2R4 and TAS2R38 in the red panda is relaxed. Remarkably, a few positively selected sites has been lineage-specifically detected on TAS2R42 in the giant panda. These results suggest an adaptive response in both pandas to a dietary shift from carnivory to herbivory, and TAS2Rs evolved independently in the two pandas. Our findings provide new insights into the molecular basis of mammalian sensory evolution and the process of adaptation to new ecological niches. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  5. Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature.

    Science.gov (United States)

    Bradbury, Ian R; Hubert, Sophie; Higgins, Brent; Borza, Tudor; Bowman, Sharen; Paterson, Ian G; Snelgrove, Paul V R; Morris, Corey J; Gregory, Robert S; Hardie, David C; Hutchings, Jeffrey A; Ruzzante, Daniel E; Taggart, Chris T; Bentzen, Paul

    2010-12-22

    Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n=40) for which allele frequencies show parallel temperature-associated clines (pAtlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.

  6. Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes

    OpenAIRE

    Castoe, Todd A.; Jiang, Zhi J.; Wanjun Gu; Wang, Zhengyuan O.; Pollock, David D.

    2008-01-01

    BACKGROUND: Adaptive evolutionary episodes in core metabolic proteins are uncommon, and are even more rarely linked to major macroevolutionary shifts. METHODOLOGY/PRINCIPAL FINDINGS: We conducted extensive molecular evolutionary analyses on snake mitochondrial proteins and discovered multiple lines of evidence suggesting that the proteins at the core of aerobic metabolism in snakes have undergone remarkably large episodic bursts of adaptive change. We show that snake mitochondrial proteins ex...

  7. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain.

    Science.gov (United States)

    Ji, Boyang; Zhang, Sheng-Da; Arnoux, Pascal; Rouy, Zoe; Alberto, François; Philippe, Nadège; Murat, Dorothée; Zhang, Wei-Jia; Rioux, Jean-Baptiste; Ginet, Nicolas; Sabaty, Monique; Mangenot, Sophie; Pradel, Nathalie; Tian, Jiesheng; Yang, Jing; Zhang, Lichen; Zhang, Wenyan; Pan, Hongmiao; Henrissat, Bernard; Coutinho, Pedro M; Li, Ying; Xiao, Tian; Médigue, Claudine; Barbe, Valérie; Pignol, David; Talla, Emmanuel; Wu, Long-Fei

    2014-02-01

    Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose.

    Science.gov (United States)

    Wang, Yongze; Manow, Ryan; Finan, Christopher; Wang, Jinhua; Garza, Erin; Zhou, Shengde

    2011-09-01

    Due to its excellent capability to ferment five-carbon sugars, Escherichia coli has been considered one of the platform organisms to be engineered for production of cellulosic ethanol. Nevertheless, genetically engineered ethanologenic E. coli lacks the essential trait of alcohol tolerance. Development of ethanol tolerance is required for cost-effective ethanol fermentation. In this study, we improved alcohol tolerance of a nontransgenic E. coli KC01 (ldhA pflB ackA frdBC pdhR::pflBp6-aceEF-lpd) through adaptive evolution. During ~350 generations of adaptive evolution, a gradually increased concentration of ethanol was used as a selection pressure to enrich ethanol-tolerant mutants. The evolved mutant, E. coli SZ470, was able to grow anaerobically at 40 g l(-1) ethanol, a twofold improvement over parent KC01. When compared with KC01 for small-scale (500 ml) xylose (50 g l(-1)) fermentation, SZ470 achieved 67% higher cell mass, 48% faster volumetric ethanol productivity, and 50% shorter time to complete fermentation with ethanol titer of 23.5 g l(-1) and yield of 94%. These results demonstrate that an industry-oriented nontransgenic E. coli strain could be developed through incremental improvements of desired traits by a combination of molecular biology and traditional microbiology techniques.

  9. Tackling the Difficulties in Learning Evolution: Effects of Adaptive Self-Explanation Prompts

    Science.gov (United States)

    Neubrand, Charlotte; Harms, Ute

    2017-01-01

    Teaching and learning evolution is challenging. Biology education research shows that the underlying evolutionary concepts are poorly understood among students. This prevents a meaningful understanding of the central biological concepts. The instructional format of self-explanation prompts seems to be promising to respond to these difficulties.…

  10. Evolution of fitness trade-offs in locally adapted populations of Pseudomonas fluorescens

    DEFF Research Database (Denmark)

    Schick, Alana; Bailey, Susan; Kassen, Rees

    2015-01-01

    characterize the genetic causes of trade-offs generating local adaptation in populations of Pseudomonas fluorescens that had previously been evolved for specialization on three different carbon resources. We measured the fitness effects of mutations that arose during selection in that environment...... and in alternative environments to quantify the degree of specialization. We find that all mutations are beneficial in the environment of selection and that those arising later during adaptation are associated with increasingly antagonistic effects in alternative environments compared with those arising earlier......, consistent with a multioptima version of Fisher’s geometric model of adaptation. We also find that fitness of pairs of beneficial mutations are consistently less than additive in selection environments, producing a pattern of diminishing returns, but are more variable in alternative environments, being...

  11. The evolution of an annual life cycle in killifish: adaptation to ephemeral aquatic environments through embryonic diapause.

    Science.gov (United States)

    Furness, Andrew I

    2016-08-01

    An annual life cycle is characterized by growth, maturity, and reproduction condensed into a single, short season favourable to development, with production of embryos (seeds, cysts, or eggs) capable of surviving harsh conditions which juveniles or adults cannot tolerate. More typically associated with plants in desert environments, or temperate-zone insects exposed to freezing winters, the evolution of an annual life cycle in vertebrates is fairly novel. Killifish, small sexually dimorphic fishes in the Order Cyprinodontiformes, have adapted to seasonally ephemeral water bodies across much of Africa and South America through the independent evolution of an annual life history. These annual killifish produce hardy desiccation-resistant eggs that undergo diapause (developmental arrest) and remain buried in the soil for long periods when fish have perished due to the drying of their habitat. Killifish are found in aquatic habitats that span a continuum from permanent and stable to seasonal and variable, thus providing a useful system in which to piece together the evolutionary history of this life cycle using natural comparative variation. I first review adaptations for life in ephemeral aquatic environments in killifish, with particular emphasis on the evolution of embryonic diapause. I then bring together available evidence from a variety of approaches and provide a scenario for how this annual life cycle evolved. There are a number of features within Aplocheiloidei killifish including their inhabitation of marginal or edge aquatic habitat, their small size and rapid attainment of maturity, and egg properties that make them particularly well suited to the colonization of ephemeral waters. © 2015 Cambridge Philosophical Society.

  12. Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago

    Science.gov (United States)

    De Mita, Stéphane; Santoni, Sylvain; Ronfort, Joëlle; Bataillon, Thomas

    2007-01-01

    Background The NODULATION RECEPTOR KINASE (NORK) gene encodes a Leucine-Rich Repeat (LRR)-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrence of numerous amino acid changes driven by directional selection has been reported in this gene, using a limited number of messenger RNA sequences, but the functional reason of these changes remains obscure. The Medicago genus, where changes in rhizobial associations have been previously examined, is a good model to test whether the evolution of NORK is influenced by rhizobial interactions. Results We sequenced a region of 3610 nucleotides (encoding a 392 amino acid-long region of the NORK protein) in 32 Medicago species. We confirm that positive selection in NORK has occurred within the Medicago genus and find that the amino acid positions targeted by selection occur in sites outside of solvent-exposed regions in LRRs, and other sites in the N-terminal region of the protein. We tested if branches of the Medicago phylogeny where changes of rhizobial symbionts occurred displayed accelerated rates of amino acid substitutions. Only one branch out of five tested, leading to M. noeana, displays such a pattern. Among other branches, the most likely for having undergone positive selection is not associated with documented shift of rhizobial specificity. Conclusion Adaptive changes in the sequence of the NORK receptor have involved the LRRs, but targeted different sites than in most previous studies of LRR proteins evolution. The fact that positive selection in NORK tends not to be associated to changes in rhizobial specificity indicates that this gene was probably not involved in evolving rhizobial preferences. Other explanations (e.g. coevolutionary arms race) must be tested to explain the adaptive evolution of NORK. PMID:17986323

  13. Adaptive grid based multi-objective Cauchy differential evolution for stochastic dynamic economic emission dispatch with wind power uncertainty

    Science.gov (United States)

    Lei, Xiaohui; Wang, Chao; Yue, Dong; Xie, Xiangpeng

    2017-01-01

    Since wind power is integrated into the thermal power operation system, dynamic economic emission dispatch (DEED) has become a new challenge due to its uncertain characteristics. This paper proposes an adaptive grid based multi-objective Cauchy differential evolution (AGB-MOCDE) for solving stochastic DEED with wind power uncertainty. To properly deal with wind power uncertainty, some scenarios are generated to simulate those possible situations by dividing the uncertainty domain into different intervals, the probability of each interval can be calculated using the cumulative distribution function, and a stochastic DEED model can be formulated under different scenarios. For enhancing the optimization efficiency, Cauchy mutation operation is utilized to improve differential evolution by adjusting the population diversity during the population evolution process, and an adaptive grid is constructed for retaining diversity distribution of Pareto front. With consideration of large number of generated scenarios, the reduction mechanism is carried out to decrease the scenarios number with covariance relationships, which can greatly decrease the computational complexity. Moreover, the constraint-handling technique is also utilized to deal with the system load balance while considering transmission loss among thermal units and wind farms, all the constraint limits can be satisfied under the permitted accuracy. After the proposed method is simulated on three test systems, the obtained results reveal that in comparison with other alternatives, the proposed AGB-MOCDE can optimize the DEED problem while handling all constraint limits, and the optimal scheme of stochastic DEED can decrease the conservation of interval optimization, which can provide a more valuable optimal scheme for real-world applications. PMID:28961262

  14. Adaptive grid based multi-objective Cauchy differential evolution for stochastic dynamic economic emission dispatch with wind power uncertainty.

    Science.gov (United States)

    Zhang, Huifeng; Lei, Xiaohui; Wang, Chao; Yue, Dong; Xie, Xiangpeng

    2017-01-01

    Since wind power is integrated into the thermal power operation system, dynamic economic emission dispatch (DEED) has become a new challenge due to its uncertain characteristics. This paper proposes an adaptive grid based multi-objective Cauchy differential evolution (AGB-MOCDE) for solving stochastic DEED with wind power uncertainty. To properly deal with wind power uncertainty, some scenarios are generated to simulate those possible situations by dividing the uncertainty domain into different intervals, the probability of each interval can be calculated using the cumulative distribution function, and a stochastic DEED model can be formulated under different scenarios. For enhancing the optimization efficiency, Cauchy mutation operation is utilized to improve differential evolution by adjusting the population diversity during the population evolution process, and an adaptive grid is constructed for retaining diversity distribution of Pareto front. With consideration of large number of generated scenarios, the reduction mechanism is carried out to decrease the scenarios number with covariance relationships, which can greatly decrease the computational complexity. Moreover, the constraint-handling technique is also utilized to deal with the system load balance while considering transmission loss among thermal units and wind farms, all the constraint limits can be satisfied under the permitted accuracy. After the proposed method is simulated on three test systems, the obtained results reveal that in comparison with other alternatives, the proposed AGB-MOCDE can optimize the DEED problem while handling all constraint limits, and the optimal scheme of stochastic DEED can decrease the conservation of interval optimization, which can provide a more valuable optimal scheme for real-world applications.

  15. Environmental disruption of Host-Microbe co-adaptation as a potential driving force in evolution

    Directory of Open Access Journals (Sweden)

    Yoav eSoen

    2014-06-01

    Full Text Available The microbiome is known to have a profound effect on the development, physiology and health of its host. Whether and how it also contributes to evolutionary diversification of the host is, however, unclear. Here we hypothesize that disruption of the microbiome by new stressful environments interferes with host-microbe co-adaption, contributes to host destabilization, and can drive irreversible changes in the host prior to its genetic adaptation. This hypothesis is based on 3 presumptions: (1 The microbiome consists of heritable partners which contribute to the stability (canalization of host development and physiology in frequently encountered environments, (2 Upon encountering a stressful new environment, the microbiome adapts much faster than the host, and (3 This differential response disrupts cooperation, contributes to host destabilization and promotes reciprocal changes in the host and its microbiome. This dynamic imbalance relaxes as the host and its microbiome establish a new equilibrium state in which they are adapted to one another and to the altered environment. Over long time in this new environment, the changes in the microbiome contribute to the canalization of the altered state. This scenario supports stability of the adapted patterns, while promoting variability which may be beneficial in new stressful conditions, thus allowing the organism to balance stability and flexibility based on contextual demand. Additionally, interaction between heritable microbial (and/or epigenetic changes can promote new outcomes which persist over a wide range of timescales. A sufficiently persistent stress can further induce irreversible changes in the microbiome which may permanently alter the organism prior to genetic changes in the host. Epigenetic and microbial changes therefore provide a potential infrastructure for causal links between immediate responses to new environments and longer-term establishment of evolutionary adaptations.

  16. Natural selection causes adaptive genetic resistance in wild emmer wheat against powdery mildew at "Evolution Canyon" microsite, Mt. Carmel, Israel.

    Directory of Open Access Journals (Sweden)

    Huayan Yin

    Full Text Available "Evolution Canyon" (ECI at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric "African" slope (AS and the temperate-mesic "European" slope (ES, separated on average by 250 m.We examined 278 single sequence repeats (SSRs and the phenotype diversity of the resistance to powdery mildew between the opposite slopes. Furthermore, 18 phenotypes on the AS and 20 phenotypes on the ES, were inoculated by both Bgt E09 and a mixture of powdery mildew races.In the experiment of genetic diversity, very little polymorphism was identified intra-slope in the accessions from both the AS or ES. By contrast, 148 pairs of SSR primers (53.23% amplified polymorphic products between the phenotypes of AS and ES. There are some differences between the two wild emmer wheat genomes and the inter-slope SSR polymorphic products between genome A and B. Interestingly, all wild emmer types growing on the south-facing slope (SFS=AS were susceptible to a composite of Blumeria graminis, while the ones growing on the north-facing slope (NFS=ES were highly resistant to Blumeria graminis at both seedling and adult stages.Remarkable inter-slope evolutionary divergent processes occur in wild emmer wheat, T. dicoccoides at EC I, despite the shot average distance of 250 meters. The AS, a dry and hot slope, did not develop resistance to powdery mildew, whereas the ES, a cool and humid slope, did develop resistance since the disease stress was strong there. This is a remarkable demonstration in host-pathogen interaction on how resistance develops when stress causes an adaptive result at a micro-scale distance.

  17. Active disturbance rejection controller design for dynamically positioned vessels based on adaptive hybrid biogeography-based optimization and differential evolution.

    Science.gov (United States)

    Wu, Defeng; Ren, Fengkun; Qiao, Lei; Zhang, Weidong

    2017-11-01

    Vessels with a dynamic positioning system (DPS) are widely applied in ocean resource exploration. Because of the inaccuracy and coupling of the vessel dynamic model, it is important to design a controller that performs well in an oceanic environment. The active disturbance rejection controller (ADRC) is introduced in this study to control the vessel movement and positioning in the DPS. The merit of the ADRC is that it does not need an accurate plant and disturbance model. In the proposed method, an adaptive hybrid biogeography-based optimization (BBO) and differential evolution (DE) are developed. The orthogonal learning (OL) mechanism is employed to achieve adaptive switching to different searching mechanisms between BBO and DE. The proposed adaptive hybrid BBO-DE (AHBBODE) algorithm is then used to optimize the parameters of ADRC; these parameters are not easy to determine by using the trial and error method. Finally, the proposed method is compared with the BBO- and DE-based methods. The results show that better performance is obtained by the proposed method. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  18. Growth Description for Vessel Wall Adaptation: A Thick-Walled Mixture Model of Abdominal Aortic Aneurysm Evolution.

    Science.gov (United States)

    Grytsan, Andrii; Eriksson, Thomas S E; Watton, Paul N; Gasser, T Christian

    2017-08-25

    (1) Background: Vascular tissue seems to adapt towards stable homeostatic mechanical conditions, however, failure of reaching homeostasis may result in pathologies. Current vascular tissue adaptation models use many ad hoc assumptions, the implications of which are far from being fully understood; (2) Methods: The present study investigates the plausibility of different growth kinematics in modeling Abdominal Aortic Aneurysm (AAA) evolution in time. A structurally motivated constitutive description for the vessel wall is coupled to multi-constituent tissue growth descriptions; Constituent deposition preserved either the constituent's density or its volume, and Isotropic Volume Growth (IVG), in-Plane Volume Growth (PVG), in-Thickness Volume Growth (TVG) and No Volume Growth (NVG) describe the kinematics of the growing vessel wall. The sensitivity of key modeling parameters is explored, and predictions are assessed for their plausibility; (3) Results: AAA development based on TVG and NVG kinematics provided not only quantitatively, but also qualitatively different results compared to IVG and PVG kinematics. Specifically, for IVG and PVG kinematics, increasing collagen mass production accelerated AAA expansion which seems counterintuitive. In addition, TVG and NVG kinematics showed less sensitivity to the initial constituent volume fractions, than predictions based on IVG and PVG; (4) Conclusions: The choice of tissue growth kinematics is of crucial importance when modeling AAA growth. Much more interdisciplinary experimental work is required to develop and validate vascular tissue adaption models, before such models can be of any practical use.

  19. Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection.

    Directory of Open Access Journals (Sweden)

    Jayna Raghwani

    2016-01-01

    Full Text Available Analysis of HIV-1 gene sequences sampled longitudinally from infected individuals can reveal the evolutionary dynamics that underlie associations between disease outcome and viral genetic diversity and divergence. Here we extend a statistical framework to estimate rates of viral molecular adaptation by considering sampling error when computing nucleotide site-frequencies. This is particularly beneficial when analyzing viral sequences from within-host viral infections if the number of sequences per time point is limited. To demonstrate the utility of this approach, we apply our method to a cohort of 24 patients infected with HIV-1 at birth. Our approach finds that viral adaptation arising from recurrent positive natural selection is associated with the rate of HIV-1 disease progression, in contrast to previous analyses of these data that found no significant association. Most surprisingly, we discover a strong negative correlation between viral population size and the rate of viral adaptation, the opposite of that predicted by standard molecular evolutionary theory. We argue that this observation is most likely due to the existence of a confounding third variable, namely variation in selective pressure among hosts. A conceptual non-linear model of virus adaptation that incorporates the two opposing effects of host immunity on the virus population can explain this counterintuitive result.

  20. Setal morphology and cirral setation of thoracican barnacle cirri: adaptations and implications for thoracican evolution

    DEFF Research Database (Denmark)

    Chan, B.K.K.; Garm, A.; Høeg, Jens Thorvald

    2008-01-01

    in the mantle cavity using the setae on their three pairs of maxillipeds. Our results indicate that in thoracican barnacles, adaptations in feeding behaviour are associated with changes in the setation pattern of the cirri. In addition, the setal types and their distribution on the cirri are potential new...

  1. Insect oviposition behavior affects the evolution of adaptation to Bt crops: consequences for refuge policies

    NARCIS (Netherlands)

    Jongsma, M.A.; Gould, F.; Legros, M.; Yang, L.; Loon, van J.J.A.; Dicke, M.

    2010-01-01

    The major lepidopteran insect pests of cotton and maize harbor intra-specific variation for behavior determining the selection of host plants for oviposition. Yet, the consequences of behavioral adaptation for fitness have neither been modeled nor monitored for Bt cotton and maize crops, the most

  2. The Predictive Adaptive Response: Modeling the Life-History Evolution of the Butterfly

    NARCIS (Netherlands)

    Heuvel, van den J.; Saastamoinen, M.; Brakefield, P.M.; Kirkwood, T.B.; Zwaan, B.J.; Shanley, D.P.

    2013-01-01

    A predictive adaptive response (PAR) is a type of developmental plasticity where the response to an environmental cue is not immediately advantageous but instead is later in life. The PAR is a way for organisms to maximize fitness in varying environments. Insects living in seasonal environments are

  3. Environmental needs and facilitators available for children and adolescents with cerebral palsy: adaptation and validation of the European Child Environment Questionnaire (ECEQ) Spanish version.

    Science.gov (United States)

    Badia, Marta; Orgaz, Begoña; Gómez-Vela, María; Longo, Egmar

    2014-01-01

    The objective of this study is to present the process of translating, adapting and validating the European Child Environment Questionnaire (ECEQ) in the Spanish context. The participants were 200 parents of children and adolescents with cerebral palsy (CP) aged 8-18 years, from seven regions in Spain. The adaptation of the ECEQ original version was carried out through the translation and back translation into Spanish. Construct validity was assessed by Factor analysis, Rasch model, and analysing group differences in need and availability of environmental features (EFs) according to level GMFCS. We obtained a high rate of parental response. The ECEQ Spanish version contains 59 items and we identified four domains: Products and technology - home, school and community - services, systems and policies, support and relations, and Attitudes. Seventeen items were dropped as they did not fit well into plausible domains. Construct validity in terms of distinguishing between groups with expected for both need and availability. The ECEQ Spanish version was more appropriate to assess the needs of and access to EFs in the following domains: Products and technology and services, systems and policies, and it proved less appropriate for the support and relations, and attitudes domains. Implications for Rehabilitation Identification of barriers and environmental facilitators are key aspects to ensure the participation of children and adolescents with CP. The ECEQ is a useful tool for identifying needs and availability of the environmental features for children and adolescents with CP in Spain. This tool contains 59 items that are consistent with ICF framework. The Spanish version of ECEQ provides valuable information, which could be helpful to guide public services and organization services in order to optimize participation of children and adolescents with CP.

  4. Evolution and adaptation of marine annelids in interstitial and cave habitats

    DEFF Research Database (Denmark)

    Martinez Garcia, Alejandro

    The origin of anchialine and marine cave fauna is still a highly debated topic in Evolutionary Biology. Restricted and disjunct distribution and uncertain affinities of some marine cave endemic lineages have favored their interpretation as living fossils, surviving the extinction of their coastal....... The results yielded new data on poorly understood groups of annelids, but also on some more general aspects of regarding colonization and speciation processes to submarine caves. From an annelid evolution perspective, we produced new phylogenetic studies for Protodrilidae (with the description of four new...... genera), Saccocirridae and Nerillidae, as well as novel results on the character evolution and diversity of these groups. From the more general prospective of the cave colonization, our results highlight the importance of shift of habitats is a crucial process to understand the morphological change...

  5. Evolution of Lower Brachyceran Flies (Diptera and Their Adaptive Radiation with Angiosperms

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2017-04-01

    Full Text Available The Diptera (true flies is one of the most species-abundant orders of Insecta, and it is also among the most important flower-visiting insects. Dipteran fossils are abundant in the Mesozoic, especially in the Late Jurassic and Early Cretaceous. Here, we review the fossil record and early evolution of some Mesozoic lower brachyceran flies together with new records in Burmese amber, including Tabanidae, Nemestrinidae, Bombyliidae, Eremochaetidae, and Zhangsolvidae. The fossil records reveal that some flower-visiting groups had diversified during the mid-Cretaceous, consistent with the rise of angiosperms to widespread floristic dominance. These brachyceran groups played an important role in the origin of co-evolutionary relationships with basal angiosperms. Moreover, the rise of angiosperms not only improved the diversity of flower-visiting flies, but also advanced the turnover and evolution of other specialized flies.

  6. Evolution

    Science.gov (United States)

    Peter, Ulmschneider

    When we are looking for intelligent life outside the Earth, there is a fundamental question: Assuming that life has formed on an extraterrestrial planet, will it also develop toward intelligence? As this is hotly debated, we will now describe the development of life on Earth in more detail in order to show that there are good reasons why evolution should culminate in intelligent beings.

  7. Adaptive Evolution of Social Traits: Origin, Trajectories, and Correlations of Altruism and Mobility

    OpenAIRE

    Le Galliard, J.-F.; Ferriere, R.; Dieckmann, U

    2005-01-01

    Social behavior involves "staying and helping", two individual attributes that vary considerably among organisms. Investigating the ultimate causes of such variation, this study integrtes previously separate lines of research by analyzing the joint evolution of altruism and mobility. We unfold the network of selective pressures and derive how these depend on physiological costs, eco-evolutionary feedbacks, and a complex interaction between the evolving traits. Our analysis highlights habitat ...

  8. [Method of Entirely Parallel Differential Evolution for Model Adaptation in Systems Biology].

    Science.gov (United States)

    Kozlov, K N; Samsonov, A M; Samsonova, M G

    2015-01-01

    We developed a method of entirely parallel differential evolution for identification of unknown parameters of mathematical models by minimization of the objective function that describes the discrepancy of the model solution and the experimental data. The method is implemented in the free and open source software available on the Internet. The method demonstrated a good performance comparable to the top three methods from CEC-2014 and was successfully applied to several biological problems.

  9. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

    OpenAIRE

    Vonk, F.J.; Casewell, N. R.; Henkel, C.V.; Heimberg, A. M.; Jansen, H.J.; McCleary, R.J.R.; Kerkkamp, H. M. E.; Vos, R. A.; Guerreiro, I.; Calvete, J. J.; Wüster, W; Woods, A E; Logan, J. M.; Harrison, R. A.; Castoe, T. A.

    2013-01-01

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from ...

  10. Cross-sector surveys assessing perceptions of key stakeholders towards barriers, concerns and facilitators to the appropriate use of adaptive designs in confirmatory trials.

    Science.gov (United States)

    Dimairo, Munyaradzi; Julious, Steven A; Todd, Susan; Nicholl, Jonathan P; Boote, Jonathan

    2015-12-23

    Appropriately conducted adaptive designs (ADs) offer many potential advantages over conventional trials. They make better use of accruing data, potentially saving time, trial participants, and limited resources compared to conventional, fixed sample size designs. However, one can argue that ADs are not implemented as often as they should be, particularly in publicly funded confirmatory trials. This study explored barriers, concerns, and potential facilitators to the appropriate use of ADs in confirmatory trials among key stakeholders. We conducted three cross-sectional, online parallel surveys between November 2014 and January 2015. The surveys were based upon findings drawn from in-depth interviews of key research stakeholders, predominantly in the UK, and targeted Clinical Trials Units (CTUs), public funders, and private sector organisations. Response rates were as follows: 30(55 %) UK CTUs, 17(68 %) private sector, and 86(41 %) public funders. A Rating Scale Model was used to rank barriers and concerns in order of perceived importance for prioritisation. Top-ranked barriers included the lack of bridge funding accessible to UK CTUs to support the design of ADs, limited practical implementation knowledge, preference for traditional mainstream designs, difficulties in marketing ADs to key stakeholders, time constraints to support ADs relative to competing priorities, lack of applied training, and insufficient access to case studies of undertaken ADs to facilitate practical learning and successful implementation. Associated practical complexities and inadequate data management infrastructure to support ADs were reported as more pronounced in the private sector. For funders of public research, the inadequate description of the rationale, scope, and decision-making criteria to guide the planned AD in grant proposals by researchers were all viewed as major obstacles. There are still persistent and important perceptions of individual and organisational obstacles

  11. Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups

    Directory of Open Access Journals (Sweden)

    He Shao-Heng

    2006-10-01

    Full Text Available Abstract Background It is believed that animal-to-human transmission of severe acute respiratory syndrome (SARS coronavirus (CoV is the cause of the SARS outbreak worldwide. The spike (S protein is one of the best characterized proteins of SARS-CoV, which plays a key role in SARS-CoV overcoming species barrier and accomplishing interspecies transmission from animals to humans, suggesting that it may be the major target of selective pressure. However, the process of adaptive evolution of S protein and the exact positively selected sites associated with this process remain unknown. Results By investigating the adaptive evolution of S protein, we identified twelve amino acid sites (75, 239, 244, 311, 479, 609, 613, 743, 765, 778, 1148, and 1163 in the S protein under positive selective pressure. Based on phylogenetic tree and epidemiological investigation, SARS outbreak was divided into three epidemic groups: 02–04 interspecies, 03-early-mid, and 03-late epidemic groups in the present study. Positive selection was detected in the first two groups, which represent the course of SARS-CoV interspecies transmission and of viral adaptation to human host, respectively. In contrast, purifying selection was detected in 03-late group. These indicate that S protein experiences variable positive selective pressures before reaching stabilization. A total of 25 sites in 02–04 interspecies epidemic group and 16 sites in 03-early-mid epidemic group were identified under positive selection. The identified sites were different between these two groups except for site 239, which suggests that positively selected sites are changeable between groups. Moreover, it was showed that a larger proportion (24% of positively selected sites was located in receptor-binding domain (RBD than in heptad repeat (HR1-HR2 region in 02–04 interspecies epidemic group (p = 0.0208, and a greater percentage (25% of these sites occurred in HR1–HR2 region than in RBD in 03-early

  12. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation

    Science.gov (United States)

    Pagel, Mark; Lutzoni, Francois

    We describe the application of Markov Chain Monte Carlo (MCMC) methods to two fundamental problems in evolutionary biology. Evolutionary biologists frequently wish to investigate the evolution of traits across a range of species. This is known as a comparative study. Comparative studies require constructing a phylogeny of the species and then investigating the evolutionary transitions in the trait on that phylogeny. A difficulty with this approach is that phylogenies themselves are sel dom known with certainty and different phylogenies can give different answers to the comparative hypotheses. MCMC methods make it possible to avoid both of these problems by constructing a random sample of phylogenies from the universe of possible phylogenetic trees for a given data set. Once this sample is obtained the comparative hypotheses can be investigated separately in each tree in the MCMC sample. Given the statistical properties of the sample of trees - trees are sampled in proportion to the probab ility under a model of evolution - the combined results across trees can be interpreted as being independent of the underlying phylogeny. Thus, investigators can test comparative hypotheses without the real concern that results are valid only for the particular tree used in the investigation. We illustrate these ideas with an example from the evolution of lichen formation in fungi.

  13. Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

    Science.gov (United States)

    Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

    2016-01-07

    Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

  14. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

    Directory of Open Access Journals (Sweden)

    Monjane Adérito L

    2011-12-01

    Full Text Available Abstract Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae, the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots

  15. Experiences with HPTN 067/ADAPT Study-Provided Open-Label PrEP Among Women in Cape Town: Facilitators and Barriers Within a Mutuality Framework.

    Science.gov (United States)

    Amico, K Rivet; Wallace, Melissa; Bekker, Linda-Gail; Roux, Surita; Atujuna, Millicent; Sebastian, Elaine; Dye, Bonnie J; Elharrar, Vanessa; Grant, Robert M

    2017-05-01

    Placebo-controlled trials of pre-exposure prophylaxis (PrEP) have reported challenges with study-product uptake and use, with the greatest challenges reported in studies with young women in sub-Saharan Africa. We conducted a qualitative sub-study to explore experiences with open-label PrEP among young women in Cape Town, South Africa participating in HTPN 067/Alternative Dosing to Augment Pre-Exposure Prophylaxis Pill Taking (ADAPT). HPTN 067/ADAPT provided open label oral FTC/TDF PrEP to young women in Cape Town, South Africa who were randomized to daily and non-daily PrEP regimens. Following completion of study participation, women were invited into a qualitative sub-study including focus groups and in-depth interviews. Interviews and groups followed a semi-structured guide, were recorded, transcribed, and translated to English from isiXhosa, and coded using framework analysis. Sixty of the 179 women enrolled in HPTN 067/ADAPT participated in either a focus group (six groups for a total of 42 participants) or an in-depth interview (n = 18). This sample of mostly young, unmarried women identified facilitators of and barriers to PrEP use, as well as factors influencing study participation. Cross-cutting themes characterizing discourse suggested that women placed high value on contributing to the well-being of one's community (Ubuntu), experienced a degree of skepticism towards PrEP and the study more generally, and reported a wide range of approaches towards PrEP (ranging from active avoidance to high levels of persistence and adherence). A Mutuality Framework is proposed that identifies four dynamics (distrust, uncertainty, alignment, and mutuality) that represent distinct interactions between self, community and study and serve to contextualize women's experiences. Implications for better understanding PrEP use, and non-use, and intervention opportunities are discussed. In this sample of women, PrEP use in the context of an open-label research trial was heavily

  16. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Directory of Open Access Journals (Sweden)

    Matteo Fumagalli

    2011-11-01

    Full Text Available Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the

  17. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.

    Science.gov (United States)

    Fumagalli, Matteo; Sironi, Manuela; Pozzoli, Uberto; Ferrer-Admetlla, Anna; Ferrer-Admettla, Anna; Pattini, Linda; Nielsen, Rasmus

    2011-11-01

    Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some

  18. Digestive adaptation: A new surgical proposal to treat obesity based on physiology and evolution

    OpenAIRE

    Sérgio Santoro; Manoel Carlos Prieto Velhote; Carlos Eduardo Malzoni; Alexandre Sérgio Gracia Mechenas; Victor Strassmann; Morton Scheinberg

    2003-01-01

    Objective: To report on a new surgical technique to treat obesity -Digestive Adaptation - and to present its preliminary results.Method: The technique includes a vertical (sleeve) gastrectomy,omentectomy and enterectomy maintaining the initial 150-cmportionof the jejunum and the final 150-cm-portion of the ileum.The three first obese patients operated on are described. Results:With a minimum follow-up of 6 months, all patients refer earlysatiety, are free of symptoms and have a BMI

  19. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.

    Science.gov (United States)

    Zhang, Guo-Qiang; Xu, Qing; Bian, Chao; Tsai, Wen-Chieh; Yeh, Chuan-Ming; Liu, Ke-Wei; Yoshida, Kouki; Zhang, Liang-Sheng; Chang, Song-Bin; Chen, Fei; Shi, Yu; Su, Yong-Yu; Zhang, Yong-Qiang; Chen, Li-Jun; Yin, Yayi; Lin, Min; Huang, Huixia; Deng, Hua; Wang, Zhi-Wen; Zhu, Shi-Lin; Zhao, Xiang; Deng, Cao; Niu, Shan-Ce; Huang, Jie; Wang, Meina; Liu, Guo-Hui; Yang, Hai-Jun; Xiao, Xin-Ju; Hsiao, Yu-Yun; Wu, Wan-Lin; Chen, You-Yi; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Luo, Yi-Bo; Van de Peer, Yves; Liu, Zhong-Jian

    2016-01-12

    Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.

  20. Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents.

    Science.gov (United States)

    Vicens, Alberto; Gómez Montoto, Laura; Couso-Ferrer, Francisco; Sutton, Keith A; Roldan, Eduardo R S

    2015-02-01

    PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at "Evolution Canyon", Mount Carmel, Israel.

    Science.gov (United States)

    Beiles, Avigdor; Raz, Shmuel; Ben-Abu, Yuval; Nevo, Eviatar

    2015-10-14

    The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (D. melanogaster) from the ecologically tropic, hot, and dry south-facing slope (SFS) or "African" slope (AS) of EC and compared it with the TE frequencies on the temperate-cool and humid north-facing slope (NFS) or "European" slope (ES), separated, on average, by 250 m. The flies were sampled from two stations on each slope. We received their results, including the frequencies of each TE on each slope, and the probabilities of the statistical analyses (G-tests) of each TE separately. We continued the analysis of the inter-slope differences of the frequencies of the TEs, and based our different conclusions on that analysis and on the difference between micro (=EC) and macro (2000 km.) comparisons [Gonzalez et al. 2015 doi: 10.1186/s13062-015-0075-4 ]. Our collaborators based all their conclusions on the non-significant results of each of the individual tests of the 28 TEs. We analysed also the distribution of the TE differences between the slopes, based on their results. Thirteen TEs were more frequent on the SFS, 11 were more frequent on the NFS, and four had equal frequencies. Because of the equalizing effect of the ongoing migration, only small and temporary differences between the slopes (0 - 0.06) were regarded by us as random fluctuations (drift). Three TEs were intermediate (0.08-0.09) and await additional research. The 11 TEs with large frequency differences (0.12 - 0.22) were regarded by us as putative adaptive TEs, because the equalizing power of ongoing migration will eliminate random large differences. Five of them were higher on the SFS and six were higher on the NFS. Gaps in the distribution of the differences distinguished between the large and

  2. Using the Technology Acceptance Model to explore community dwelling older adults' perceptions of a 3D interior design application to facilitate pre-discharge home adaptations.

    Science.gov (United States)

    Money, Arthur G; Atwal, Anita; Young, Katherine L; Day, Yasmin; Wilson, Lesley; Money, Kevin G

    2015-08-26

    In the UK occupational therapy pre-discharge home visits are routinely carried out as a means of facilitating safe transfer from the hospital to home. Whilst they are an integral part of practice, there is little evidence to demonstrate they have a positive outcome on the discharge process. Current issues for patients are around the speed of home visits and the lack of shared decision making in the process, resulting in less than 50 % of the specialist equipment installed actually being used by patients on follow-up. To improve practice there is an urgent need to examine other ways of conducting home visits to facilitate safe discharge. We believe that Computerised 3D Interior Design Applications (CIDAs) could be a means to support more efficient, effective and collaborative practice. A previous study explored practitioners perceptions of using CIDAs; however it is important to ascertain older adult's views about the usability of technology and to compare findings. This study explores the perceptions of community dwelling older adults with regards to adopting and using CIDAs as an assistive tool for the home adaptations process. Ten community dwelling older adults participated in individual interactive task-focused usability sessions with a customised CIDA, utilising the think-aloud protocol and individual semi-structured interviews. Template analysis was used to carry out both deductive and inductive analysis of the think-aloud and interview data. Initially, a deductive stance was adopted, using the three pre-determined high-level themes of the technology acceptance model (TAM): Perceived Usefulness (PU), Perceived Ease of Use (PEOU), Actual Use (AU). Inductive template analysis was then carried out on the data within these themes, from which a number of sub-thmes emerged. Regarding PU, participants believed CIDAs served as a useful visual tool and saw clear potential to facilitate shared understanding and partnership in care delivery. For PEOU, participants were

  3. Flood susceptibility assessment in Hengfeng area coupling adaptive neuro-fuzzy inference system with genetic algorithm and differential evolution.

    Science.gov (United States)

    Hong, Haoyuan; Panahi, Mahdi; Shirzadi, Ataollah; Ma, Tianwu; Liu, Junzhi; Zhu, A-Xing; Chen, Wei; Kougias, Ioannis; Kazakis, Nerantzis

    2017-10-23

    Floods are among Earth's most common natural hazards, and they cause major economic losses and seriously affect peoples' lives and health. This paper addresses the development of a flood susceptibility assessment that uses intelligent techniques and GIS. An adaptive neuro-fuzzy inference system (ANFIS) was coupled with a genetic algorithm and differential evolution for flood spatial modelling. The model considers thirteen hydrologic, morphologic and lithologic parameters for the flood susceptibility assessment, and Hengfeng County in China was chosen for the application of the model due to data availability and the 195 total flood events. The flood locations were randomly divided into two subsets, namely, training (70% of the total) and testing (30%). The Step-wise Weight Assessment Ratio Analysis (SWARA) approach was used to assess the relation between the floods and influencing parameters. Subsequently, two data mining techniques were combined with the ANFIS model, including the ANFIS-Genetic Algorithm and the ANFIS-Differential Evolution, to be used for flood spatial modelling and zonation. The flood susceptibility maps were produced, and their robustness was checked using the Receiver Operating Characteristic (ROC) curve. The results showed that the area under the curve (AUC) for all models was >0.80. The highest AUC value was for the ANFIS-DE model (0.852), followed by ANFIS-GA (0.849). According to the RMSE and MSE methods, the ANFIS-DE hybrid model is more suitable for flood susceptibility mapping in the study area. The proposed method is adaptable and can easily be applied in other sites for flood management and prevention. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. The evolution of the Indian Ocean parrots (Psittaciformes): extinction, adaptive radiation and eustacy.

    Science.gov (United States)

    Kundu, S; Jones, C G; Prys-Jones, R P; Groombridge, J J

    2012-01-01

    Parrots are among the most recognisable and widely distributed of all bird groups occupying major parts of the tropics. The evolution of the genera that are found in and around the Indian Ocean region is particularly interesting as they show a high degree of heterogeneity in distribution and levels of speciation. Here we present a molecular phylogenetic analysis of Indian Ocean parrots, identifying the possible geological and geographical factors that influenced their evolution. We hypothesise that the Indian Ocean islands acted as stepping stones in the radiation of the Old-World parrots, and that sea-level changes may have been an important determinant of current distributions and differences in speciation. A multi-locus phylogeny showing the evolutionary relationships among genera highlights the interesting position of the monotypic Psittrichas, which shares a common ancestor with the geographically distant Coracopsis. An extensive species-level molecular phylogeny indicates a complex pattern of radiation including evidence for colonisation of Africa, Asia and the Indian Ocean islands from Australasia via multiple routes, and of island populations 'seeding' continents. Moreover, comparison of estimated divergence dates and sea-level changes points to the latter as a factor in parrot speciation. This is the first study to include the extinct parrot taxa, Mascarinus mascarinus and Psittacula wardi which, respectively, appear closely related to Coracopsis nigra and Psittacula eupatria. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread.

    Science.gov (United States)

    Kerr, Peter J; Rogers, Matthew B; Fitch, Adam; Depasse, Jay V; Cattadori, Isabella M; Twaddle, Alan C; Hudson, Peter J; Tscharke, David C; Read, Andrew F; Holmes, Edward C; Ghedin, Elodie

    2013-12-01

    The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.

  6. Predictability in evolution: Adaptation of the Bonaire anole (Anolis bonairensis) to an extreme environment

    Science.gov (United States)

    Thorpe, Roger S.

    2017-01-01

    The extent to which evolution is deterministic (predictable), or random, is a fundamental question in evolution. This case study attempts to determine the extent to which interspecific divergence can be predicted from intraspecific trends related species. The mountainous Lesser Antilles are occupied by one or two anole species with very substantial intraspecific differences in the quantitative traits between xeric and rainforest habitats. These ecologically determined differences tend to be in parallel in each island species. A related species (Anolis bonairensis) lives on the far more xeric island of Bonaire, and this study tests the extent to which its interspecific divergence in hue and pattern traits can be predicted from the parallel intraspecific variation exhibited in Lesser Antillean anoles. Regression against a multivariate climate variable suggests that the hue and pattern of the Bonaire anole are consistently predicted from the ecologically determined intraspecific variation of its Lesser Antillean relatives. However, this predictability may be less consistent with other character systems, for example, scalation. PMID:28459829

  7. Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

    Science.gov (United States)

    Sattath, Shmuel; Elyashiv, Eyal; Kolodny, Oren; Rinott, Yosef; Sella, Guy

    2011-01-01

    In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence—in particular, conclusions about the rate and strength of beneficial substitutions—remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation

  8. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Directory of Open Access Journals (Sweden)

    Shmuel Sattath

    2011-02-01

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  9. Life in the Fast Lane: The Evolution of an Adaptive Vehicle Control System

    OpenAIRE

    Jochem, Todd; Pomerleau, Dean

    1996-01-01

    Giving robots the ability to operate in the real world has been, and continues to be, one of the most difficult tasks in AI research. Since 1987, researchers at Carnegie Mellon University have been investigating one such task. Their research has been focused on using adaptive, vision-based systems to increase the driving performance of the Navlab line of on-road mobile robots. This research has led to the development of a neural network system that can learn to drive on many road types simply...

  10. Adaptive evolution of M3 lysin--a candidate gamete recognition protein in the Mytilus edulis species complex.

    Science.gov (United States)

    Lima, Thiago G; McCartney, Michael A

    2013-12-01

    Marine invertebrate gamete recognition proteins (GRPs) are classic examples of rapid adaptive evolution of reproductive proteins, and hybridizing Mytilus blue mussels allow us to study the evolution of GRPs during speciation following secondary contact. Even with frequent hybridization, positive selection drives divergence of M7 lysin, one of the three Mytilus egg vitelline envelope (VE) lysins. Mytilus trossulus and M. edulis form a broad hybrid zone in the Canadian Maritimes and eastern Maine, isolated by strong (but partial) gamete incompatibility. M7 lysin, however, is an unlikely GRP controlling this gametic incompativility, as earlier studies showed either weak or no positive selection and extensive introgression between the two species. We used reverse transcriptase-polymerase chain reaction and cloned several alleles of M3 lysin, a potent VE lysin encoded by a nonhomologous gene whose evolution has not been studied. McDonald-Kreitman and HKA tests reveal strong positive selection, which PAML branch-site models detect in 19.7% of the codons. Protein structure predictions show that replacements map exclusively to one face of the carbohydrate recognition domain (CRD) of this C-type lectin, with codons under positive selection localizing to CRD regions known to control ligand specificity. Polymorphism/divergence analyses show that selective sweep has purged M. edulis but not M. trossulus of polymorphism, and unique to M3 is an absence of fixed substitutions and broad haplotype sharing between M. edulis and Mediterranean M. galloprovincialis. Taken together, these results suggest that different lysins serve as GRPs in different Mytilus hybrid zones, with M3 likely co-opted to play this role in the western Atlantic.

  11. The Evolution of Two-Component Systems in Bacteria RevealsDifferent Strategies for Niche Adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Alm, Eric; Huang, Katherine; Arkin, Adam

    2006-09-13

    Two-component systems including histidine protein kinasesrepresent the primary signal transduction paradigm in prokaryoticorganisms. To understand how these systems adapt to allow organisms todetect niche-specific signals, we analyzed the phylogenetic distributionof nearly 5000 histidine protein kinases from 207 sequenced prokaryoticgenomes. We found that many genomes carry a large repertoire of recentlyevolved signaling genes, which may reflect selective pressure to adapt tonew environmental conditions. Both lineage-specific gene family expansionand horizontal gene transfer play major roles in the introduction of newhistidine kinases into genomes; however, there are differences in howthese two evolutionary forces act. Genes imported via horizontal transferare more likely to retain their original functionality as inferred from asimilar complement of signaling domains, while gene family expansionaccompanied by domain shuffling appears to be a major source of novelgenetic diversity. Family expansion is the dominantsource of newhistidine kinase genes in the genomes most enriched in signalingproteins, and detailed analysis reveals that divergence in domainstructure and changes in expression patterns are hallmarks of recentexpansions. Finally, while these two modes of gene acquisition arewidespread across bacterial taxa, there are clear species-specificpreferences for which mode is used.

  12. Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations.

    Science.gov (United States)

    Savage, Anna E; Zamudio, Kelly R

    2016-03-30

    Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis. © 2016 The Authors.

  13. Colloquium paper: adaptive specializations, social exchange, and the evolution of human intelligence.

    Science.gov (United States)

    Cosmides, Leda; Barrett, H Clark; Tooby, John

    2010-05-11

    Blank-slate theories of human intelligence propose that reasoning is carried out by general-purpose operations applied uniformly across contents. An evolutionary approach implies a radically different model of human intelligence. The task demands of different adaptive problems select for functionally specialized problem-solving strategies, unleashing massive increases in problem-solving power for ancestrally recurrent adaptive problems. Because exchange can evolve only if cooperators can detect cheaters, we hypothesized that the human mind would be equipped with a neurocognitive system specialized for reasoning about social exchange. Whereas humans perform poorly when asked to detect violations of most conditional rules, we predicted and found a dramatic spike in performance when the rule specifies an exchange and violations correspond to cheating. According to critics, people's uncanny accuracy at detecting violations of social exchange rules does not reflect a cheater detection mechanism, but extends instead to all rules regulating when actions are permitted (deontic conditionals). Here we report experimental tests that falsify these theories by demonstrating that deontic rules as a class do not elicit the search for violations. We show that the cheater detection system functions with pinpoint accuracy, searching for violations of social exchange rules only when these are likely to reveal the presence of someone who intends to cheat. It does not search for violations of social exchange rules when these are accidental, when they do not benefit the violator, or when the situation would make cheating difficult.

  14. Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis.

    Science.gov (United States)

    Chaudhry, Vasvi; Patil, Prabhu B

    2016-01-13

    Staphylococcus epidermidis is a major human associated bacterium and also an emerging nosocomial pathogen. There are reports of its association to rodents, sheep and plants. However, comparative and evolutionary studies of ecologically diverse strains of S. epidermidis are lacking. Here, we report the whole genome sequences of four S. epidermidis strains isolated from surface sterilized rice seeds along with genome sequence of type strain. Phylogenomic analysis of rice endophytic S. epidermidis (RESE) with "type strain" unequivocally established their species identity. Whole genome based tree of 93 strains of S. epidermidis revealed RESE as distinct sub-lineage which is more related to rodent sub-lineage than to majority of human lineage strains. Furthermore, comparative genomics revealed 20% variable gene-pool in S. epidermidis, suggesting that genomes of ecologically diverse strains are under flux. Interestingly, we were also able to map several genomic regions that are under flux and gave rise to RESE strains. The largest of these genomic regions encodes a cluster of genes unique to RESE that are known to be required for survival and stress tolerance, apart from those required for adaptation to plant habitat. The genomes and genes of RESE represent distinct ecological resource/sequences and provided first evolutionary insights into adaptation of S. epidermidis to plants.

  15. Ecological adaptations and commensal evolution of the Polynoidae (Polychaeta) in the Southwest Indian Ocean Ridge: A phylogenetic approach

    Science.gov (United States)

    Serpetti, Natalia; Taylor, M. L.; Brennan, D.; Green, D. H.; Rogers, A. D.; Paterson, G. L. J.; Narayanaswamy, B. E.

    2017-03-01

    The polychaete family polynoid is very large and includes a high diversity of behaviours, including numerous examples of commensal species. The comparison between free-living and commensal behaviours and the evolution of the relationships between commensal species and their hosts are valuable case studies of ecological adaptations. Deep-sea species of Polynoidae were sampled at four seamounts in the Southwest Indian Ridge and twenty specimens from seven species were selected to be analysed. Among them, there were free-living species, living within the three-dimensional framework of cold-water coral reefs, on coral rubble and on mobile sediments, and commensal species, associated with octocorals, hydrocorals (stylasterids), antipatharians and echinoderms (holothurian and ophiuroids). We analysed two mitochondrial (COI, 16S) and two nuclear (18S, 28S) ribosomal genetic markers and their combined sequences were compared with other Genbank sequences to assess the taxonomic relationships within the species under study, and the potential role of hosts in speciation processes. Most basal species of the sub-family Polynoinae are obligate symbionts showing specific morphological adaptations. Obligate and facultative commensal species and free-living species have evolved a number of times, although, according to our results, the obligate coral commensal species appear to be monophyletic.

  16. Sequence and expression variations suggest an adaptive role for the DA1-like gene family in the evolution of soybeans.

    Science.gov (United States)

    Zhao, Man; Gu, Yongzhe; He, Lingli; Chen, Qingshan; He, Chaoying

    2015-05-15

    The DA1 gene family is plant-specific and Arabidopsis DA1 regulates seed and organ size, but the functions in soybeans are unknown. The cultivated soybean (Glycine max) is believed to be domesticated from the annual wild soybeans (Glycine soja). To evaluate whether DA1-like genes were involved in the evolution of soybeans, we compared variation at both sequence and expression levels of DA1-like genes from G. max (GmaDA1) and G. soja (GsoDA1). Sequence identities were extremely high between the orthologous pairs between soybeans, while the paralogous copies in a soybean species showed a relatively high divergence. Moreover, the expression variation of DA1-like paralogous genes in soybean was much greater than the orthologous gene pairs between the wild and cultivated soybeans during development and challenging abiotic stresses such as salinity. We further found that overexpressing GsoDA1 genes did not affect seed size. Nevertheless, overexpressing them reduced transgenic Arabidopsis seed germination sensitivity to salt stress. Moreover, most of these genes could improve salt tolerance of the transgenic Arabidopsis plants, corroborated by a detection of expression variation of several key genes in the salt-tolerance pathways. Our work suggested that expression diversification of DA1-like genes is functionally associated with adaptive radiation of soybeans, reinforcing that the plant-specific DA1 gene family might have contributed to the successful adaption to complex environments and radiation of the plants.

  17. Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments.

    Science.gov (United States)

    Guo, Wuxia; Wu, Haidan; Zhang, Zhang; Yang, Chao; Hu, Ling; Shi, Xianggang; Jian, Shuguang; Shi, Suhua; Huang, Yelin

    2017-01-01

    Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936-48,845 unigenes with N50 values of 982-1,185 bp and 61.42-69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya), suggesting that the transgression during the Paleocene-Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous-Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of Rhizophoraceae mangroves, which were

  18. Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

    Directory of Open Access Journals (Sweden)

    Wuxia Guo

    2017-05-01

    Full Text Available Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936–48,845 unigenes with N50 values of 982–1,185 bp and 61.42–69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya, suggesting that the transgression during the Paleocene–Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous–Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of

  19. Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates.

    Science.gov (United States)

    Seiffert, Erik R; Perry, Jonathan M G; Simons, Elwyn L; Boyer, Doug M

    2009-10-22

    Adapiform or 'adapoid' primates first appear in the fossil record in the earliest Eocene epoch ( approximately 55 million years (Myr) ago), and were common components of Palaeogene primate communities in Europe, Asia and North America. Adapiforms are commonly referred to as the 'lemur-like' primates of the Eocene epoch, and recent phylogenetic analyses have placed adapiforms as stem members of Strepsirrhini, a primate suborder whose crown clade includes lemurs, lorises and galagos. An alternative view is that adapiforms are stem anthropoids. This debate has recently been rekindled by the description of a largely complete skeleton of the adapiform Darwinius, from the middle Eocene of Europe, which has been widely publicised as an important 'link' in the early evolution of Anthropoidea. Here we describe the complete dentition and jaw of a large-bodied adapiform (Afradapis gen. nov.) from the earliest late Eocene of Egypt ( approximately 37 Myr ago) that exhibits a striking series of derived dental and gnathic features that also occur in younger anthropoid primates-notably the earliest catarrhine ancestors of Old World monkeys and apes. Phylogenetic analysis of 360 morphological features scored across 117 living and extinct primates (including all candidate stem anthropoids) does not place adapiforms as haplorhines (that is, members of a Tarsius-Anthropoidea clade) or as stem anthropoids, but rather as sister taxa of crown Strepsirrhini; Afradapis and Darwinius are placed in a geographically widespread clade of caenopithecine adapiforms that left no known descendants. The specialized morphological features that these adapiforms share with anthropoids are therefore most parsimoniously interpreted as evolutionary convergences. As the largest non-anthropoid primate ever documented in Afro-Arabia, Afradapis nevertheless provides surprising new evidence for prosimian diversity in the Eocene of Africa, and raises the possibility that ecological competition between

  20. Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

    Science.gov (United States)

    Chen, Sunlu; Zheng, Huizhen; Kishima, Yuji

    2017-06-01

    The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

  1. Adaptive response to DNA-damaging agents in natural Saccharomyces cerevisiae populations from "Evolution Canyon", Mt. Carmel, Israel.

    Directory of Open Access Journals (Sweden)

    Gabriel A Lidzbarsky

    Full Text Available BACKGROUND: Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the "Evolution Canyon" microsite (Nahal Oren, Mt. Carmel, Israel. The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%-800% more on the "African" slope caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid "African" environment while the north-facing slope is represented by temperate, "European" forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS in order to evaluate the interslope effect on the strains' ability to withstand DNA-damaging agents. METHODOLOGY/PRINCIPAL FINDINGS: We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the "African" slope were more resilient to both UVA and MMS than the strains from the "European" slope. In contrast, we found that there was almost no difference between strains (with similar ploidy from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the "African" strains are more adapted to higher solar radiation than the "European" strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation. CONCLUSIONS/SIGNIFICANCE: Our results and the results of parallel studies with several other

  2. Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

    Directory of Open Access Journals (Sweden)

    Sunlu Chen

    2017-06-01

    Full Text Available The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs, have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

  3. CHO-K1 host cells adapted to growth in glutamine-free medium by FACS-assisted evolution.

    Science.gov (United States)

    Bort, Juan A Hernández; Stern, Beate; Borth, Nicole

    2010-10-01

    During the process of recombinant cell line optimisation for production of biopharmaceuticals, multiple cellular properties like robustness against stress, the attainment of high cell concentrations and maintenance of high viability must be considered to maximize protein yield. To improve growth and viability, glutamine is supplemented as an alternative energy source for rapidly dividing cells that oxidize glucose inefficiently. However, the resulting by-product ammonia is toxic at high concentrations and has a negative impact on protein glycosylation, a major quality-determining parameter of biopharmaceuticals. In this work, the CHO-K1 cell line was adapted to a chemically defined medium and suspension growth within 3 weeks. Subsequently, the glutamine concentration was stepwise reduced from 8 to 4 and 2 mM. After each reduction, both the final cell concentration in the batch and the viability decreased. To force a rapid evolution of cells to achieve high final cell concentrations, cells were seeded at high densities (10(7) cells/mL) and surviving cells were sorted by FACS or MACS when viability declined to 10% (typically after 24 h). Sorted cells were grown in batch until viability declined to 10% and viable cells recovered again. The final sorted population was able to reach comparable or even better viable cell concentrations and showed a significantly improved viability compared to their ancestors. The 2 mM glutamine-adapted cell line was directly transferred into glutamine-free medium and was able to grow at comparable rates without requiring further adaptation. Cells compensated the lack of glutamine by increasing their consumption of glutamate and aspartate.

  4. Adaptative evolution of metallothionein 3 in the Cd/Zn hyperaccumulator Thlaspi caerulescens

    Energy Technology Data Exchange (ETDEWEB)

    Roosens, N.H.; Bernard, C.; Verbruggen, N. [Lab. de Physiologie et Genetique Moleculaire des Plantes, Univ. Libre de Bruxelles, Brussels (Belgium); Leplae, R. [Service de Conformation des Macromolecules Biologiques et Bioinformatique, Univ. Libre de Bruxelles, Brussels (Belgium)

    2005-04-01

    A functional screening in yeast allowed to identify various cDNAs from the Cd/Zn hyper-accumulator Thlaspi caerulescens. TcMT3 displayed high identity with its closest homologue in Arabidopsis thaliana but variation in its Cys residues. Functional analysis in yeast supported a higher binding capacity for Cu, but not for Cd or Zn, of TcMT3 compared to AtMT3. Expression analysis in plants indicated that metallothionein 3 (MT3) like all the other T. caerulescens genes from the screen studied is overexpressed in all studied populations of T. caerulescens compared to A. thaliana. TcMT3 was induced by Cu, but not by Cd. Moreover significant variation in expression within T. caerulescens populations that have contrasting tolerance and accumulation capacities indicated a possible local adaptation of MT3. (orig.)

  5. CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems

    DEFF Research Database (Denmark)

    Shah, Shiraz Ali; Garrett, Roger Antony

    2011-01-01

    CRISPR/Cas and CRISPR/Cmr immune machineries of archaea and bacteria provide an adaptive and effective defence mechanism directed specifically against viruses and plasmids. Present data suggest that both CRISPR/Cas and Cmr modules can behave like integral genetic elements. They tend to be located...... in the more variable regions of chromosomes and are displaced by genome shuffling mechanisms including transposition. CRISPR loci may be broken up and dispersed in chromosomes by transposons with the potential for creating genetic novelty. Both CRISPR/Cas and Cmr modules appear to exchange readily between...... the significant barriers imposed by their differing conjugative, transcriptional and translational mechanisms. There are parallels between the CRISPR crRNAs and eukaryal siRNAs, most notably to germ cell piRNAs which are directed, with the help of effector proteins, to silence or destroy transposons...

  6. Recovery of Phenotypes Obtained by Adaptive Evolution through Inverse Metabolic Engineering

    DEFF Research Database (Denmark)

    Hong, Kuk-Ki; Nielsen, Jens

    2012-01-01

    In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one...... of the mutations RAS2Lys77, RAS2Tyr112, and ERG5Pro370 were constructed and evaluated. The mutants were also combined with overexpression of PGM2, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites......, and the results were compared to those obtained from reference strains and the evolved strains. The RAS2Lys77 mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The RAS2Tyr112 mutation also improved the specific...

  7. Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments.

    Science.gov (United States)

    Porter, Megan L; Roberts, Nicholas W; Partridge, Julian C

    2016-12-01

    Understanding the link between how proteins function in animals that live in extreme environments and selection on specific properties of amino acids has proved extremely challenging. Here we present the discovery of how the compressibility of opsin proteins in two evolutionarily distinct animal groups, teleosts and cephalopods, appears to be adapted to the high-pressure environment of the deep-sea. We report how in both groups, opsins in deeper living species are calculated to be less compressible. This is largely due to a common set of amino acid sites (bovRH# 159, 196, 213, 275) undergoing positive destabilizing selection in six of the twelve amino acid physiochemical properties that determine protein compressibility. This suggests a common evolutionary mechanism to reduce the adiabatic compressibility of opsin proteins. Intriguingly, the sites under selection are on the proteins' outer faces at locations known to be involved in opsin-opsin dimer interactions. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  8. Evolution and adaptation of marine annelids in interstitial and cave habitats

    DEFF Research Database (Denmark)

    Martinez Garcia, Alejandro

    The origin of anchialine and marine cave fauna is still a highly debated topic in Evolutionary Biology. Restricted and disjunct distribution and uncertain affinities of some marine cave endemic lineages have favored their interpretation as living fossils, surviving the extinction of their coastal...... relatives in cave subterranean ecological refugia. Active colonization and ecological speciation to particular cave niches has been alternatively suggested, but the evaluation of that scenario is obscured by the dominance of crustaceans in anchialine habitats, ecologically similar out and inside caves....... The main goal of this thesis is to explore the evolutionary processes behind colonization and adaptation to submarine cave ecosystems in the Atlantic Ocean using annelids as a model, mainly when they involved ancestrally interstitial forms. In order to do that, we studied selected lineages of annelids...

  9. Sequestration of plant-derived glycosides by leaf beetles: A model system for evolution and adaptation

    Directory of Open Access Journals (Sweden)

    Wilhelm Boland

    2015-12-01

    Full Text Available Leaf beetles have developed an impressive repertoire of toxins and repellents to defend themselves against predators. Upon attack, the larvae discharge small droplets from glandular reservoirs on their back. The reservoirs are “bioreactors” performing the late reactions of the toxin-production from plant-derived or de novo synthesised glucosides. The import of the glucosides into the bioreactor relies on a complex transport system. Physiological studies revealed a functional network of transporters guiding the glucosides through the larval body into the defensive system. The first of the involved transporters has been identified and characterised concerning selectivity, tissue distribution, and regulation. The development of a well-tuned transport system, perfectly adjusted to the compounds provided by the food plants, provides the functional basis for the leaf beetle defenses and their local adaptation to their host plants.

  10. Adaptation to toxic hosts as a factor in the evolution of insecticide resistance.

    Science.gov (United States)

    Alyokhin, Andrei; Chen, Yolanda H

    2017-06-01

    Insecticide resistance is a serious economic problem that jeopardizes sustainability of chemical control of herbivorous insects and related arthropods. It can be viewed as a specific case of adaptation to toxic chemicals, which has been driven in large part, but not exclusively, by the necessity for insect pests to tolerate defensive compounds produced by their host plants. Synthetic insecticides may simply change expression of specific sets of detoxification genes that have evolved due to ancestral associations with host plants. Feeding on host plants with more abundant or novel secondary metabolites has even been shown to prime insect herbivores to tolerate pesticides. Clear understanding of basic evolutionary processes is important for achieving lasting success in managing herbivorous arthropods. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Polyamine-Based Thiols in Trypanosomatids: Evolution, Protein Structural Adaptations, and Biological Functions.

    Science.gov (United States)

    Manta, Bruno; Bonilla, Mariana; Fiestas, Lucía; Sturlese, Mattia; Salinas, Gustavo; Bellanda, Massimo; Comini, Marcelo A

    2017-11-27

    Major pathogenic enterobacteria and protozoan parasites from the phylum Euglenozoa, such as trypanosomatids, are endowed with glutathione (GSH)-spermidine (Sp) derivatives that play important roles in signaling and metal and thiol-redox homeostasis. For some Euglenozoa lineages, the GSH-Sp conjugates represent the main redox cosubstrates around which entire new redox systems have evolved. Several proteins underwent molecular adaptations to synthesize and utilize the new polyamine-based thiols. Recent Advances: The genomes of closely related organisms have recently been sequenced, which allows mining and analysis of gene sequences that belong to these peculiar redox systems. Similarly, the three-dimensional structures of several of these proteins have been solved, which allows for comparison with their counterparts in classical redox systems that rely on GSH/glutaredoxin and thioredoxin. The evolutionary and structural aspects related to the emergence and use of GSH-Sp conjugates in Euglenozoa are reviewed focusing on unique structural specializations that proteins developed to use N1,N8-bisglutathionylspermidine (trypanothione) as redox cosubstrate. An updated overview on the biochemical and biological significance of the major enzymatic activities is also provided. A thiol-redox system strictly dependent on trypanothione is a feature unique to trypanosomatids. The physicochemical properties of the polyamine-GSH conjugates were a major driving force for structural adaptation of proteins that use these thiols as ligand and redox cofactor. In fact, the structural differences of indispensable components of this system can be exploited toward selective drug development. Future research should clarify whether additional cellular processes are regulated by the trypanothione system. Antioxid. Redox Signal. 00, 000-000.

  12. Groundwater nitrate concentration evolution under climate change and agricultural adaptation scenarios: Prince Edward Island, Canada

    Science.gov (United States)

    Paradis, Daniel; Vigneault, Harold; Lefebvre, René; Savard, Martine M.; Ballard, Jean-Marc; Qian, Budong

    2016-03-01

    Nitrate (N-NO3) concentration in groundwater, the sole source of potable water in Prince Edward Island (PEI, Canada), currently exceeds the 10 mg L-1 (N-NO3) health threshold for drinking water in 6 % of domestic wells. Increasing climatic and socio-economic pressures on PEI agriculture may further deteriorate groundwater quality. This study assesses how groundwater nitrate concentration could evolve due to the forecasted climate change and its related potential changes in agricultural practices. For this purpose, a tridimensional numerical groundwater flow and mass transport model was developed for the aquifer system of the entire Island (5660 km2). A number of different groundwater flow and mass transport simulations were made to evaluate the potential impact of the projected climate change and agricultural adaptation. According to the simulations for year 2050, N-NO3 concentration would increase due to two main causes: (1) the progressive attainment of steady-state conditions related to present-day nitrogen loadings, and (2) the increase in nitrogen loadings due to changes in agricultural practices provoked by future climatic conditions. The combined effects of equilibration with loadings, climate and agricultural adaptation would lead to a 25 to 32 % increase in N-NO3 concentration over the Island aquifer system. The change in groundwater recharge regime induced by climate change (with current agricultural practices) would only contribute 0 to 6 % of that increase for the various climate scenarios. Moreover, simulated trends in groundwater N-NO3 concentration suggest that an increased number of domestic wells (more than doubling) would exceed the nitrate drinking water criteria. This study underlines the need to develop and apply better agricultural management practices to ensure sustainability of long-term groundwater resources. The simulations also show that observable benefits from positive changes in agricultural practices would be delayed in time due to

  13. The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus.

    Science.gov (United States)

    Wu, Shan; Shamimuzzaman, Md; Sun, Honghe; Salse, Jerome; Sui, Xuelian; Wilder, Alan; Wu, Zujian; Levi, Amnon; Xu, Yong; Ling, Kai-Shu; Fei, Zhangjun

    2017-12-01

    Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring-spot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  14. Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of chemodiversity in Nature (2010 JGI User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Noel, Joseph

    2010-03-26

    Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  15. Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation.

    Science.gov (United States)

    Engelstädter, Jan; Moradigaravand, Danesh

    2014-01-22

    Natural transformation is a process whereby bacteria actively take up DNA from the surrounding environment and incorporate it into their genome. Natural transformation is widespread in bacteria, but its evolutionary significance is still debated. Here, we hypothesize that transformation may confer a fitness advantage in changing environments through a process we term 'genetic time travel': by taking up old genes that were retained in the environment, the bacteria may revert to a past genotypic state that proves advantageous in the present or a future environment. We scrutinize our hypothesis by means of a mathematical model involving two bacterial types (transforming and non-transforming), a single locus under natural selection and a free DNA pool. The two bacterial types were competed in environments with changing selection regimes. We demonstrate that for a wide range of parameter values for the DNA turnover rate, the transformation rate and the frequency of environmental change, the transforming type outcompetes the non-transforming type. We discuss the empirical plausibility of our hypothesis, as well as its relationship to other hypotheses for the evolution of transformation in bacteria and sex more generally, speculating that 'genetic time travel' may also be relevant in eukaryotes that undergo horizontal gene transfer.

  16. Convergent adaptation of cellular machineries in the evolution of large body masses and long life spans.

    Science.gov (United States)

    Croco, Eleonora; Marchionni, Silvia; Storci, Gianluca; Bonafè, Massimiliano; Franceschi, Claudio; Stamato, Thomas D; Sell, Christian; Lorenzini, Antonello

    2017-08-01

    In evolutionary terms, life on the planet has taken the form of independently living cells for the majority of time. In comparison, the mammalian radiation is a relatively recent event. The common mammalian ancestor was probably small and short-lived. The "recent" acquisition of an extended longevity and large body mass of some species of mammals present on the earth today suggests the possibility that similar cellular mechanisms have been influenced by the forces of natural selection to create a convergent evolution of longevity. Many cellular mechanisms are potentially relevant for extending longevity; in this assay, we review the literature focusing primarily on two cellular features: (1) the capacity for extensive cellular proliferation of differentiated cells, while maintaining genome stability; and (2) the capacity to detect DNA damage. We have observed that longevity and body mass are both positively linked to these cellular mechanisms and then used statistical tools to evaluate their relative importance. Our analysis suggest that the capacity for extensive cellular proliferation while maintaining sufficient genome stability, correlates to species body mass while the capacity to correctly identify the presence of DNA damage seems more an attribute of long-lived species. Finally, our data are in support of the idea that a slower development, allowing for better DNA damage detection and handling, should associate with longer life span.

  17. Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO2 Fixation in Cyanobacteria and Some Proteobacteria

    Science.gov (United States)

    Rae, Benjamin D.; Long, Benedict M.; Badger, Murray R.

    2013-01-01

    SUMMARY Cyanobacteria are the globally dominant photoautotrophic lineage. Their success is dependent on a set of adaptations collectively termed the CO2-concentrating mechanism (CCM). The purpose of the CCM is to support effective CO2 fixation by enhancing the chemical conditions in the vicinity of the primary CO2-fixing enzyme, d-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), to promote the carboxylase reaction and suppress the oxygenase reaction. In cyanobacteria and some proteobacteria, this is achieved by encapsulation of RubisCO within carboxysomes, which are examples of a group of proteinaceous bodies called bacterial microcompartments. Carboxysomes encapsulate the CO2-fixing enzyme within the selectively permeable protein shell and simultaneously encapsulate a carbonic anhydrase enzyme for CO2 supply from a cytoplasmic bicarbonate pool. These bodies appear to have arisen twice and undergone a process of convergent evolution. While the gross structures of all known carboxysomes are ostensibly very similar, with shared gross features such as a selectively permeable shell layer, each type of carboxysome encapsulates a phyletically distinct form of RubisCO enzyme. Furthermore, the specific proteins forming structures such as the protein shell or the inner RubisCO matrix are not identical between carboxysome types. Each type has evolutionarily distinct forms of the same proteins, as well as proteins that are entirely unrelated to one another. In light of recent developments in the study of carboxysome structure and function, we present this review to summarize the knowledge of the structure and function of both types of carboxysome. We also endeavor to cast light on differing evolutionary trajectories which may have led to the differences observed in extant carboxysomes. PMID:24006469

  18. Adaptive melanin response of the soil fungus Aspergillus niger to UV radiation stress at "Evolution Canyon", Mount Carmel, Israel.

    Directory of Open Access Journals (Sweden)

    Natarajan Singaravelan

    Full Text Available BACKGROUND: Adaptation is an evolutionary process in which traits in a population are tailored by natural selection to better meet the challenges presented by the local environment. The major discussion relating to natural selection concerns the portraying of the cause and effect relationship between a presumably adaptive trait and selection agents generating it. Therefore, it is necessary to identify trait(s that evolve in direct response to selection, enhancing the organism's fitness. "Evolution Canyon" (EC in Israel mirrors a microcosmic evolutionary system across life and is ideal to study natural selection and local adaptation under sharply, microclimatically divergent environments. The south-facing, tropical, sunny and xeric "African" slope (AS receives 200%-800% higher solar radiation than the north-facing, temperate, shady and mesic "European" slope (ES, 200 meters apart. Thus, solar ultraviolet radiation (UVR is a major selection agent in EC influencing the organism-environment interaction. Melanin is a trait postulated to have evolved for UV-screening in microorganisms. Here we investigate the cause and effect relationship between differential UVR on the opposing slopes of EC and the conidial melanin concentration of the filamentous soil fungus Aspergillus niger. We test the working hypothesis that the AS strains exhibit higher melanin content than strains from the ES resulting in higher UV resistance. METHODOLOGY/PRINCIPAL FINDINGS: We measured conidial melanin concentration of 80 strains from the EC using a spectrophotometer. The results indicated that mean conidial melanin concentration of AS strains were threefold higher than ES strains and the former resisted UVA irradiation better than the latter. Comparisons of melanin in the conidia of A. niger strains from sunny and shady microniches on the predominantly sunny AS and predominantly shady ES indicated that shady conditions on the AS have no influence on the selection on melanin

  19. New evidence for mammaliaform ear evolution and feeding adaptation in a Jurassic ecosystem

    Science.gov (United States)

    Luo, Zhe-Xi; Meng, Qing-Jin; Grossnickle, David M.; Liu, Di; Neander, April I.; Zhang, Yu-Guang; Ji, Qiang

    2017-08-01

    Stem mammaliaforms are forerunners to modern mammals, and they achieved considerable ecomorphological diversity in their own right. Recent discoveries suggest that eleutherodontids, a subclade of Haramiyida, were more species-rich during the Jurassic period in Asia than previously recognized. Here we report a new Jurassic eleutherodontid mammaliaform with an unusual mosaic of highly specialized characteristics, and the results of phylogenetic analyses that support the hypothesis that haramiyidans are stem mammaliaforms. The new fossil shows fossilized skin membranes that are interpreted to be for gliding and a mandibular middle ear with a unique character combination previously unknown in mammaliaforms. Incisor replacement is prolonged until well after molars are fully erupted, a timing pattern unique to most other mammaliaforms. In situ molar occlusion and a functional analysis reveal a new mode of dental occlusion: dual mortar-pestle occlusion of opposing upper and lower molars, probably for dual crushing and grinding. This suggests that eleutherodontids are herbivorous, and probably specialized for granivory or feeding on soft plant tissues. The inferred dietary adaptation of eleutherodontid gliders represents a remarkable evolutionary convergence with herbivorous gliders in Theria. These Jurassic fossils represent volant, herbivorous stem mammaliaforms associated with pre-angiosperm plants that appear long before the later, iterative associations between angiosperm plants and volant herbivores in various therian clades.

  20. Adaptation, Ecology, and Evolution of the Halophilic Stromatolite Archaeon Halococcus hamelinensis Inferred through Genome Analyses

    Directory of Open Access Journals (Sweden)

    Reema K. Gudhka

    2015-01-01

    Full Text Available Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67% of which were protein-coding genes with functional assignments and 954 (29.83% of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

  1. Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.

    Science.gov (United States)

    Gudhka, Reema K; Neilan, Brett A; Burns, Brendan P

    2015-01-01

    Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

  2. Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage.

    Science.gov (United States)

    Rosinski-Chupin, Isabelle; Sauvage, Elisabeth; Mairey, Barbara; Mangenot, Sophie; Ma, Laurence; Da Cunha, Violette; Rusniok, Christophe; Bouchier, Christiane; Barbe, Valérie; Glaser, Philippe

    2013-04-15

    During host specialization, inactivation of genes whose function is no more required is favored by changes in selective constraints and evolutionary bottlenecks. The Gram positive bacteria Streptococcus agalactiae (also called GBS), responsible for septicemia and meningitis in neonates also emerged during the seventies as a cause of severe epidemics in fish farms. To decipher the genetic basis for the emergence of these highly virulent GBS strains and of their adaptation to fish, we have analyzed the genomic sequence of seven strains isolated from fish and other poikilotherms. Comparative analysis shows that the two groups of GBS strains responsible for fish epidemic diseases are only distantly related. While strains belonging to the clonal complex 7 cannot be distinguished from their human CC7 counterparts according to their gene content, strains belonging to the ST260-261 types probably diverged a long time ago. In this lineage, specialization to the fish host was correlated with a massive gene inactivation and broad changes in gene expression. We took advantage of the low level of sequence divergence between GBS strains and of the emergence of sublineages to reconstruct the different steps involved in this process. Non-homologous recombination was found to have played a major role in the genome erosion. Our results show that the early phase of genome reduction during host specialization mostly involves accumulation of small and likely reversible indels, followed by a second evolutionary step marked by a higher frequency of large deletions.

  3. Digestive adaptation: A new surgical proposal to treat obesity based on physiology and evolution

    Directory of Open Access Journals (Sweden)

    Sérgio Santoro

    2003-06-01

    Full Text Available Objective: To report on a new surgical technique to treat obesity -Digestive Adaptation - and to present its preliminary results.Method: The technique includes a vertical (sleeve gastrectomy,omentectomy and enterectomy maintaining the initial 150-cmportionof the jejunum and the final 150-cm-portion of the ileum.The three first obese patients operated on are described. Results:With a minimum follow-up of 6 months, all patients refer earlysatiety, are free of symptoms and have a BMI <31 Kg/m2.Conclusions: This procedure does not use prostheses and doesnot cause exclusion of gastrointestinal segments. It does notcreate subocclusions neither malabsorption nor blind endoscopicareas and above all, it causes no harm to important digestivefunctions. Conversely, it aims at moderate restriction with earlysatiety by distension, and at interfering in the neuroendocrineprofile, resulting in slow gastric emptying, early and prolongedsatiety, as well as positive changes in the metabolic profile. Basedon recent physiological data, the procedure aims at decreasingthe production of ghrelin, plasminogen activator inhibitor-1 (PAI-1and resistin, and at raising the levels of glucagon-like peptide-1(GLP-1. The patients operated on do not need nutritional supportor to take drugs because of the procedure, which is easy and safeto perform.

  4. Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation.

    Directory of Open Access Journals (Sweden)

    Sarah A Palmer

    Full Text Available BACKGROUND: Archaeobotanical samples of barley (Hordeum vulgare L. found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. METHODOLOGY AND FINDINGS: We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. CONCLUSIONS: The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.

  5. Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution.

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    Cheong Xin Chan

    Full Text Available Membrane transporters (MTs facilitate the movement of molecules between cellular compartments. The evolutionary history of these key components of eukaryote genomes remains unclear. Many photosynthetic microbial eukaryotes (e.g., diatoms, haptophytes, and dinoflagellates appear to have undergone serial endosymbiosis and thereby recruited foreign genes through endosymbiotic/horizontal gene transfer (E/HGT. Here we used the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum as models to examine the evolutionary origin of MTs in this important group of marine primary producers. Using phylogenomics, we used 1,014 diatom MTs as query against a broadly sampled protein sequence database that includes novel genome data from the mesophilic red algae Porphyridium cruentum and Calliarthron tuberculosum, and the stramenopile Ectocarpus siliculosus. Our conservative approach resulted in 879 maximum likelihood trees of which 399 genes show a non-lineal history between diatoms and other eukaryotes and prokaryotes (at the bootstrap value ≥70%. Of the eukaryote-derived MTs, 172 (ca. 25% of 697 examined phylogenies have members of both red/green algae as sister groups, with 103 putatively arising from green algae, 19 from red algae, and 50 have an unresolved affiliation to red and/or green algae. We used topology tests to analyze the most convincing cases of non-lineal gene history in which red and/or green algae were nested within stramenopiles. This analysis showed that ca. 6% of all trees (our most conservative estimate support an algal origin of MTs in stramenopiles with the majority derived from green algae. Our findings demonstrate the complex evolutionary history of photosynthetic eukaryotes and indicate a reticulate origin of MT genes in diatoms. We postulate that the algal-derived MTs acquired via E/HGT provided diatoms and other related microbial eukaryotes the ability to persist under conditions of fluctuating ocean chemistry, likely

  6. Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

    Science.gov (United States)

    Dunn, Barbara; Paulish, Terry; Stanbery, Alison; Piotrowski, Jeff; Koniges, Gregory; Kroll, Evgueny; Louis, Edward J.; Liti, Gianni; Sherlock, Gavin; Rosenzweig, Frank

    2013-01-01

    Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in

  7. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression.

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    Barbara Dunn

    2013-03-01

    Full Text Available Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ~1-kb region of chromosome 14, and all producing an "interspecific fusion junction" within the MEP2 gene coding sequence, such that the 5' portion derives from S. cerevisiae and the 3' portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a

  8. Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution.

    Science.gov (United States)

    Tang, Xian-Chun; Agnihothram, Sudhakar S; Jiao, Yongjun; Stanhope, Jeremy; Graham, Rachel L; Peterson, Eric C; Avnir, Yuval; Tallarico, Aimee St Clair; Sheehan, Jared; Zhu, Quan; Baric, Ralph S; Marasco, Wayne A

    2014-05-13

    The newly emerging Middle East Respiratory Syndrome coronavirus (MERS-CoV) causes a Severe Acute Respiratory Syndrome-like disease with ∼43% mortality. Given the recent detection of virus in dromedary camels, zoonotic transfer of MERS-CoV to humans is suspected. In addition, little is known about the role of human neutralizing Ab (nAb) pressure as a driving force in MERS-CoV adaptive evolution. Here, we used a well-characterized nonimmune human Ab-phage library and a panning strategy with proteoliposomes and cells to identify seven human nAbs against the receptor-binding domain (RBD) of the MERS-CoV Spike protein. These nAbs bind to three different epitopes in the RBD and human dipeptidyl peptidase 4 (hDPP4) interface with subnanomolar/nanomolar binding affinities and block the binding of MERS-CoV Spike protein with its hDPP4 receptor. Escape mutant assays identified five amino acid residues that are critical for neutralization escape. Despite the close proximity of the three epitopes on the RBD interface, escape from one epitope did not have a major impact on neutralization with Abs directed to a different epitope. Importantly, the majority of escape mutations had negative impacts on hDPP4 receptor binding and viral fitness. To our knowledge, these results provide the first report on human nAbs against MERS-CoV that may contribute to MERS-CoV clearance and evolution. Moreover, in the absence of a licensed vaccine or antiviral for MERS, this panel of nAbs offers the possibility of developing human mAb-based immunotherapy, especially for health-care workers.

  9. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

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    Andrew B Allison

    2014-11-01

    Full Text Available Canine parvovirus (CPV emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV, a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that>95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR, the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range.

  10. Adaptive evolution of Escherichia coli to an α-peptide/β-peptoid peptidomimetic induces stable resistance.

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    Line Hein-Kristensen

    Full Text Available Antimicrobial peptides (AMPs and synthetic analogues thereof target conserved structures of bacterial cell envelopes and hence, development of resistance has been considered an unlikely event. However, recently bacterial resistance to AMPs has been observed, and the aim of the present study was to determine whether bacterial resistance may also evolve against synthetic AMP analogues, e.g. α-peptide/β-peptoid peptidomimetics. E. coli ATCC 25922 was exposed to increasing concentrations of a peptidomimetic (10 lineages, polymyxin B (10 lineages, or MilliQ water (4 lineages in a re-inoculation culturing setup covering approx. 500 generations. All 10 lineages exposed to the peptidomimetic adapted to 32 × MIC while this occurred for 8 out of 10 of the polymyxin B-exposed lineages. All lineages exposed to 32 × MIC of either the peptidomimetic or polymyxin B had a significantly increased MIC (16-32 × to the selection agent. Five transfers (≈ 35 generations in unsupplemented media did not abolish resistance indicating that resistance was heritable. Single isolates from peptidomimetic-exposed lineage populations displayed MICs against the peptidomimetic from wild-type MIC to 32 × MIC revealing heterogeneous populations. Resistant isolates showed no cross-resistance against a panel of membrane-active AMPs. These isolates were highly susceptible to blood plasma antibacterial activity and were killed when plasma concentrations exceeded ≈ 30%. Notably, MIC of the peptidomimetic against resistant isolates returned to wild-type level upon addition of 25% plasma. Whole-genome sequencing of twenty isolates from four resistant lineages revealed mutations, in murein transglycosylase D (mltD and outer-membrane proteins, which were conserved within and between lineages. However, no common resistance-conferring mutation was identified. We hypothesise that alterations in cell envelope structure result in peptidomimetic resistance, and that this may occur via

  11. [Population: evolution of Rwandan attitudes or the adaptation of the Rwanda population to population growth].

    Science.gov (United States)

    Ngendakumana, M

    1988-04-01

    A consequence of the increasing pressure on Rwanda's ecosystem resulting from population growth has been that demographic factors have played a significant role in modifying attitudes and beliefs of the population. The history of Rwanda demonstrates a constant struggle for survival in the face of increasing population pressure. Migration, colonization of new agricultural lands, adoption of new crops and new forms of animal husbandry have been responses to population pressures. Recent unprecedented population growth has exceeded the capacity of older systems of cultivation and combinations of agricultural and animal husbandry to support the population. Smaller animals have largely replaced the cattle that once roamed freely in extensive pastures, and new techniques of stabling animals, use of organic or chemical fertilizers, and new tools adapted to the shrinking size of farm plots have represented responses to the new demographic realities. The concept of the family is likewise undergoing modification in the face of population growth and modernization. Children, who once were valued as a source of labor and constrained to conform to the wishes of the parents in return for the eventual inheritance of the goods and livelihood, now increasingly look beyond the household for education and employment. Family land holdings have become too small to support all the members with a claim on them. The greater distances between family members inevitably mean that relations between them lose closeness. The choice of a marriage partner is increasingly assumed by the young people themselves and not by their families. Old traditions of food sharing and hospitality have been curtailed because of the increasing scarcity of food. Despite the changes engendered by increasing population pressure, pronatalist sentiments are still widespread. But the desire to assure the future of each child rather than to await his services, a new conception of women less dependent on their reproductive

  12. TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Y; Lee, CG [University of Toronto, Toronto, ON (Canada); Chan, TCY [University of Toronto, Toronto, ON (Canada); Techna Institute for the Advancement of Technology for Health, Toronto, ON (Canada); Cho, YB; Islam, MK [University of Toronto, Toronto, ON (Canada); Princess Margaret Hospital, Toronto, ON (Canada); Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) (Canada)

    2014-06-15

    Purpose: To develop mathematical models of tumor geometry changes under radiotherapy that may support future adaptive paradigms. Methods: A total of 29 cervical patients were scanned using MRI, once for planning and weekly thereafter for treatment monitoring. Using the tumor volumes contoured by a radiologist, three mathematical models were investigated based on the assumption of a stochastic process of tumor evolution. The “weekly MRI” model predicts tumor geometry for the following week from the last two consecutive MRI scans, based on the voxel transition probability. The other two models use only the first pair of consecutive MRI scans, and the transition probabilities were estimated via tumor type classified from the entire data set. The classification is based on either measuring the tumor volume (the “weekly volume” model), or implementing an auxiliary “Markov chain” model. These models were compared to a constant volume approach that represents the current clinical practice, using various model parameters; e.g., the threshold probability β converts the probability map into a tumor shape (larger threshold implies smaller tumor). Model performance was measured using volume conformity index (VCI), i.e., the union of the actual target and modeled target volume squared divided by product of these two volumes. Results: The “weekly MRI” model outperforms the constant volume model by 26% on average, and by 103% for the worst 10% of cases in terms of VCI under a wide range of β. The “weekly volume” and “Markov chain” models outperform the constant volume model by 20% and 16% on average, respectively. They also perform better than the “weekly MRI” model when β is large. Conclusion: It has been demonstrated that mathematical models can be developed to predict tumor geometry changes for cervical cancer undergoing radiotherapy. The models can potentially support adaptive radiotherapy paradigm by reducing normal tissue dose. This research

  13. The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity.

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    Chris A Kieslich

    Full Text Available The interaction between complement fragment C3d and complement receptor 2 (CR2 is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of -1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic "hot-spots". Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic "hot-spots" at the two functional sites of C3d, while the surface of CR2 lacks electrostatic "hot-spots" despite its excessively positive nature. We propose that the electrostatic "hot-spots" of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2, which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3

  14. The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity.

    Science.gov (United States)

    Kieslich, Chris A; Morikis, Dimitrios

    2012-01-01

    The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of -1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic "hot-spots". Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic "hot-spots" at the two functional sites of C3d, while the surface of CR2 lacks electrostatic "hot-spots" despite its excessively positive nature. We propose that the electrostatic "hot-spots" of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3d, after the

  15. Adaptive Response to DNA-Damaging Agents in Natural Saccharomyces cerevisiae Populations from “Evolution Canyon”, Mt. Carmel, Israel

    Science.gov (United States)

    Lidzbarsky, Gabriel A.; Shkolnik, Tamar; Nevo, Eviatar

    2009-01-01

    Background Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the “Evolution Canyon” microsite (Nahal Oren, Mt. Carmel, Israel). The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%–800% more on the “African” slope) caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid “African” environment while the north-facing slope is represented by temperate, “European” forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS) in order to evaluate the interslope effect on the strains' ability to withstand DNA-damaging agents. Methodology/Principal Findings We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the “African” slope were more resilient to both UVA and MMS than the strains from the “European” slope. In contrast, we found that there was almost no difference between strains (with similar ploidy) from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the “African” strains are more adapted to higher solar radiation than the “European” strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation. Conclusions/Significance Our results and the results of parallel studies with

  16. pSum-SaDE: A Modified p-Median Problem and Self-Adaptive Differential Evolution Algorithm for Text Summarization

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    Rasim M. Alguliev

    2011-01-01

    Full Text Available Extractive multidocument summarization is modeled as a modified p-median problem. The problem is formulated with taking into account four basic requirements, namely, relevance, information coverage, diversity, and length limit that should satisfy summaries. To solve the optimization problem a self-adaptive differential evolution algorithm is created. Differential evolution has been proven to be an efficient and robust algorithm for many real optimization problems. However, it still may converge toward local optimum solutions, need to manually adjust the parameters, and finding the best values for the control parameters is a consuming task. In the paper is proposed a self-adaptive scaling factor in original DE to increase the exploration and exploitation ability. This paper has found that self-adaptive differential evolution can efficiently find the best solution in comparison with the canonical differential evolution. We implemented our model on multi-document summarization task. Experiments have shown that the proposed model is competitive on the DUC2006 dataset.

  17. Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation

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    Zhiqian Yi

    2015-09-01

    Full Text Available Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced