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Sample records for australia adaptive evolution

  1. Adaptability and evolution.

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    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.

  2. 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.

  3. Adaptive evolution of molecular phenotypes

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    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-01-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak. (paper)

  4. Evolution of stone management in Australia.

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    Lee, Ming-Chak; Bariol, Simon Virgil

    2011-11-01

    What's known on the subject? and What does the study add? There is very little contemporary data regarding stone management in Australia. This study assesses the impact of technological advances on stone management practises, and raises questions as to why there is an increasing rate of intervention for stone disease in Australia. Knowledge of management trends as demonstrated in this paper give individual surgeons a guideline for contemporary practise in this country. • To examine trends in the operative management of upper urinary tract stone disease in Australia over the past 15 years. • The Medicare Australia and Australian Institute of Health and Welfare databases were used to determine the annual number of renal colic presentations and procedural interventions undertaken for stone disease. • In Australia over the past 15 years, the annual number of procedural interventions for upper urinary tract stones has increased, primarily due to the rising number of endoscopic procedures performed. • During this period, shock wave lithotripsy numbers have remained steady whilst open and percutaneous procedures have been in decline. • The introduction of and subsequent preference for less invasive techniques has changed the management pathway of patients presenting with stone disease in Australia. • Further studies are necessary to determine whether this escalation in endoscopic procedures is due to an increase in the incidence of stone disease, earlier detection, a lower intervention threshold or a higher retreatment rate. © 2011 THE AUTHORS. BJU INTERNATIONAL © 2011 BJU INTERNATIONAL.

  5. Molecular evolution and thermal adaptation

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    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  6. Adaptive Evolution of Signaling Partners

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    Urano, Daisuke; Dong, Taoran; Bennetzen, Jeffrey L.; Jones, Alan M.

    2015-01-01

    Proteins that interact coevolve their structures. When mutation disrupts the interaction, compensation by the partner occurs to restore interaction otherwise counterselection occurs. We show in this study how a destabilizing mutation in one protein is compensated by a stabilizing mutation in its protein partner and their coevolving path. The pathway in this case and likely a general principle of coevolution is that the compensatory change must tolerate both the original and derived structures with equivalence in function and activity. Evolution of the structure of signaling elements in a network is constrained by specific protein pair interactions, by requisite conformational changes, and by catalytic activity. The heterotrimeric G protein-coupled signaling is a paragon of this protein interaction/function complexity and our deep understanding of this pathway in diverse organisms lends itself to evolutionary study. Regulators of G protein Signaling (RGS) proteins accelerate the intrinsic GTP hydrolysis rate of the Gα subunit of the heterotrimeric G protein complex. An important RGS-contact site is a hydroxyl-bearing residue on the switch I region of Gα subunits in animals and most plants, such as Arabidopsis. The exception is the grasses (e.g., rice, maize, sugarcane, millets); these plants have Gα subunits that replaced the critical hydroxyl-bearing threonine with a destabilizing asparagine shown to disrupt interaction between Arabidopsis RGS protein (AtRGS1) and the grass Gα subunit. With one known exception (Setaria italica), grasses do not encode RGS genes. One parsimonious deduction is that the RGS gene was lost in the ancestor to the grasses and then recently acquired horizontally in the lineage S. italica from a nongrass monocot. Like all investigated grasses, S. italica has the Gα subunit with the destabilizing asparagine residue in the protein interface but, unlike other known grass genomes, still encodes an expressed RGS gene, SiRGS1. SiRGS1

  7. 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.

  8. 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...

  9. Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

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    Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

    2016-09-21

    In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Adaptation, plant evolution, and the fossil record

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    Knoll, A. H.; Niklas, K. J.

    1987-01-01

    The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases

  11. Country, climate change adaptation and colonisation: insights from an Indigenous adaptation planning process, Australia.

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    Nursey-Bray, Melissa; Palmer, Robert

    2018-03-01

    Indigenous peoples are going to be disproportionately affected by climate change. Developing tailored, place based, and culturally appropriate solutions will be necessary. Yet finding cultural and institutional 'fit' within and between competing values-based climate and environmental management governance regimes remains an ongoing challenge. This paper reports on a collaborative research project with the Arabana people of central Australia, that resulted in the production of the first Indigenous community-based climate change adaptation strategy in Australia. We aimed to try and understand what conditions are needed to support Indigenous driven adaptation initiatives, if there are any cultural differences that need accounting for and how, once developed they be integrated into existing governance arrangements. Our analysis found that climate change adaptation is based on the centrality of the connection to 'country' (traditional land), it needs to be aligned with cultural values, and focus on the building of adaptive capacity. We find that the development of climate change adaptation initiatives cannot be divorced from the historical context of how the Arabana experienced and collectively remember colonisation. We argue that in developing culturally responsive climate governance for and with Indigenous peoples, that that the history of colonisation and the ongoing dominance of entrenched Western governance regimes needs acknowledging and redressing into contemporary environmental/climate management.

  12. Adaptive Evolution of Gene Expression in Drosophila.

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    Nourmohammad, Armita; Rambeau, Joachim; Held, Torsten; Kovacova, Viera; Berg, Johannes; Lässig, Michael

    2017-08-08

    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. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

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    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.

  14. 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.

  15. Adaptive evolution of transcription factor binding sites

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    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  16. Evolution of Genetic Variance during Adaptive Radiation.

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    Walter, Greg M; Aguirre, J David; Blows, Mark W; Ortiz-Barrientos, Daniel

    2018-04-01

    Genetic correlations between traits can concentrate genetic variance into fewer phenotypic dimensions that can bias evolutionary trajectories along the axis of greatest genetic variance and away from optimal phenotypes, constraining the rate of evolution. If genetic correlations limit adaptation, rapid adaptive divergence between multiple contrasting environments may be difficult. However, if natural selection increases the frequency of rare alleles after colonization of new environments, an increase in genetic variance in the direction of selection can accelerate adaptive divergence. Here, we explored adaptive divergence of an Australian native wildflower by examining the alignment between divergence in phenotype mean and divergence in genetic variance among four contrasting ecotypes. We found divergence in mean multivariate phenotype along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed divergence in the level of genetic variance in individual traits and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with divergence in genetic variance, with much of the divergence in phenotype among ecotypes associated with changes in trait combinations containing substantial levels of genetic variance. Overall, our results suggest that natural selection can alter the distribution of genetic variance underlying phenotypic traits, increasing the amount of genetic variance in the direction of natural selection and potentially facilitating rapid adaptive divergence during an adaptive radiation.

  17. Metallogenic relationships to tectonic evolution - the Lachlan Orogen, Australia

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    Bierlein, Frank P.; Gray, David R.; Foster, David A.

    2002-08-01

    Placing ore formation within the overall tectonic framework of an evolving orogenic system provides important constraints for the development of plate tectonic models. Distinct metallogenic associations across the Palaeozoic Lachlan Orogen in SE Australia are interpreted to be the manifestation of interactions between several microplates and three accretionary complexes in an oceanic back-arc setting. In the Ordovician, significant orogenic gold deposits formed within a developing accretionary wedge along the Pacific margin of Gondwana. At the same time, major porphyry Cu-Au systems formed in an oceanic island arc outboard of an evolved magmatic arc that, in turn, gave rise to granite-related Sn-W deposits in the Early Silurian. During the ongoing evolution of the orogen in the Late Silurian to Early Devonian, sediment-hosted Cu-Au and Pb-Zn deposits formed in short-lived intra-arc basins, whereas a developing fore-arc system provided the conditions for the formation of several volcanogenic massive sulphide deposits. Inversion of these basins and accretion to the Australian continental margin triggered another pulse of orogenic gold mineralisation during the final consolidation of the orogenic belt in the Middle to Late Devonian.

  18. 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.

  19. Epistatic adaptive evolution of human color vision.

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    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.

  20. Evolution of Cooperation in Adaptive Social Networks

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    Segbroeck, Sven Van; Santos, Francisco C.; Traulsen, Arne; Lenaerts, Tom; Pacheco, Jorge M.

    Humans are organized in societies, a phenomenon that would never have been possible without the evolution of cooperative behavior. Several mechanisms that foster this evolution have been unraveled over the years, with population structure as a prominent promoter of cooperation. Modern networks of exchange and cooperation are, however, becoming increasingly volatile, and less and less based on long-term stable structure. Here, we address how this change of paradigm aspects the evolution of cooperation. We discuss analytical and numerical models in which individuals can break social ties and create new ones. Interactions are modeled as two-player dilemmas of cooperation. Once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rates. This individual capacity of forming new links or severing inconvenient ones can effectively change the nature of the game. We address random formation of new links and local linking rules as well as different individual capacities to maintain social interactions. We conclude by discussing how adaptive social networks can become an important step towards more realistic models of cultural dynamics.

  1. 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.

  2. Pervasive Adaptive Evolution in Primate Seminal Proteins.

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    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.

  3. Improving cellulase production by Aspergillus niger using adaptive evolution

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

    OBJECTIVES: To evaluate the potential of adaptive evolution as a tool in generating strains with an improved production of plant biomass degrading enzymes. RESULTS: An Aspergillus niger cellulase mutant was obtained by adaptive evolution. Physiological properties of this mutant revealed a five times

  4. Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

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    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.

  5. Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes

    Science.gov (United States)

    Christie, Joshua R.; Beekman, Madeleine

    2017-01-01

    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. PMID:28025277

  6. Evolution of Mosquito-Based Arbovirus Surveillance Systems in Australia

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    Andrew F. van den Hurk

    2012-01-01

    Full Text Available Control of arboviral disease is dependent on the sensitive and timely detection of elevated virus activity or the identification of emergent or exotic viruses. The emergence of Japanese encephalitis virus (JEV in northern Australia revealed numerous problems with performing arbovirus surveillance in remote locations. A sentinel pig programme detected JEV activity, although there were a number of financial, logistical, diagnostic and ethical limitations. A system was developed which detected viral RNA in mosquitoes collected by solar or propane powered CO2-baited traps. However, this method was hampered by trap-component malfunction, microbial contamination and large mosquito numbers which overwhelmed diagnostic capabilities. A novel approach involves allowing mosquitoes within a box trap to probe a sugar-baited nucleic-acid preservation card that is processed for expectorated arboviruses. In a longitudinal field trial, both Ross River and Barmah Forest viruses were detected numerous times from multiple traps over different weeks. Further refinements, including the development of unpowered traps and use of yeast-generated CO2, could enhance the applicability of this system to remote locations. New diagnostic technology, such as next generation sequencing and biosensors, will increase the capacity for recognizing emergent or exotic viruses, while cloud computing platforms will facilitate rapid dissemination of data.

  7. A model of adaptation of overseas nurses: exploring the experiences of Japanese nurses working in Australia.

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    Kishi, Yuka; Inoue, Kumiyo; Crookes, Patrick; Shorten, Allison

    2014-04-01

    The purpose of the study was to investigate the experiences of Japanese nurses and their adaptation to their work environment in Australia. Using a qualitative research method and semistructured interviews, the study aimed to discover, describe, and analyze the experiences of 14 Japanese nurses participating in the study. A qualitative study. Fourteen Japanese registered nurses working in Australian hospitals participated in the study. Individual semistructured interviews were conducted from April to June in 2008. Thematic analysis was used to identify themes within the data. Analysis of qualitative open-ended questions revealed the participants' adaptation process. It consists of three themes or phases: seeking (S), acclimatizing (A), and settling (S), subsequently named the S.A.S. model. The conceptual model of the adaptation processes of 14 Japanese nurses working in Australia includes the seeking, acclimatizing, and settling phases. Although these phases are not mutually exclusive and the process is not necessarily uniformly linear, all participants in this study passed through this S.A.S. model in order to adapt to their new environment. The S.A.S. model of adaptation helps to describe the experiences of Japanese overseas qualified nurses working in Australian hospitals. Future research is needed to examine whether this model can be applied to nurses from other countries and in other settings outside Australia.

  8. Ultra-hot Mesoproterozoic evolution of intracontinental central Australia

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    Weronika Gorczyk

    2015-01-01

    Full Text Available The Musgrave Province developed at the nexus of the North, West and South Australian cratons and its Mesoproterozoic evolution incorporates a 100 Ma period of ultra-high temperature (UHT metamorphism from ca. 1220 to ca. 1120 Ma. This was accompanied by high-temperature A-type granitic magmatism over an 80 Ma period, sourced in part from mantle-derived components and emplaced as a series of pulsed events that also coincide with peaks in UHT metamorphism. The tectonic setting for this thermal event (the Musgrave Orogeny is thought to have been intracontinental and the lithospheric architecture of the region is suggested to have had a major influence on the thermal evolution. We use a series of two dimensional, fully coupled thermo-mechanical-petrological numerical models to investigate the plausibility of initiating and prolonging UHT conditions under model setup conditions appropriate to the inferred tectonic setting and lithospheric architecture of the Musgrave Province. The results support the inferred tectonic framework for the Musgrave Orogeny, predicting periods of UHT metamorphism of up to 70 Ma, accompanied by thin crust and extensive magmatism derived from both crustal and mantle sources. The results also appear to be critically dependent upon the specific location of the Musgrave Province, constrained between thicker cratonic masses.

  9. 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

  10. 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

  11. A bizarre new toothed mysticete (Cetacea) from Australia and the early evolution of baleen whales

    OpenAIRE

    Fitzgerald, Erich M.G

    2006-01-01

    Extant baleen whales (Cetacea, Mysticeti) are all large filter-feeding marine mammals that lack teeth as adults, instead possessing baleen, and feed on small marine animals in bulk. The early evolution of these superlative mammals, and their unique feeding method, has hitherto remained enigmatic. Here, I report a new toothed mysticete from the Late Oligocene of Australia that is more archaic than any previously described. Unlike all other mysticetes, this new whale was small, had enormous eye...

  12. 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

  13. 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.

  14. 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.

  15. Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima.

    Science.gov (United States)

    Kearns, Anna M; Joseph, Leo; Toon, Alicia; Cook, Lyn G

    2014-05-30

    A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.

  16. Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

    Science.gov (United States)

    Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

    2014-10-01

    Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  17. Harmony Search Based Parameter Ensemble Adaptation for Differential Evolution

    Directory of Open Access Journals (Sweden)

    Rammohan Mallipeddi

    2013-01-01

    Full Text Available In differential evolution (DE algorithm, depending on the characteristics of the problem at hand and the available computational resources, different strategies combined with a different set of parameters may be effective. In addition, a single, well-tuned combination of strategies and parameters may not guarantee optimal performance because different strategies combined with different parameter settings can be appropriate during different stages of the evolution. Therefore, various adaptive/self-adaptive techniques have been proposed to adapt the DE strategies and parameters during the course of evolution. In this paper, we propose a new parameter adaptation technique for DE based on ensemble approach and harmony search algorithm (HS. In the proposed method, an ensemble of parameters is randomly sampled which form the initial harmony memory. The parameter ensemble evolves during the course of the optimization process by HS algorithm. Each parameter combination in the harmony memory is evaluated by testing them on the DE population. The performance of the proposed adaptation method is evaluated using two recently proposed strategies (DE/current-to-pbest/bin and DE/current-to-gr_best/bin as basic DE frameworks. Numerical results demonstrate the effectiveness of the proposed adaptation technique compared to the state-of-the-art DE based algorithms on a set of challenging test problems (CEC 2005.

  18. 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 in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794...... through drastic depletion of phosphorus-containing biomass components but also through network-wide reductions in phosphate-reaction participation and the loss of a key enzyme, succinate dehydrogenase. These alterations occur despite the stringency of having relatively few pathway redundancies...

  19. 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 ...

  20. Adaptive evolution and effective population size in wild house mice

    Czech Academy of Sciences Publication Activity Database

    Phifer-Rixey, M.; Bonhomme, F.; Boursot, P.; Churchill, G. A.; Piálek, Jaroslav; Tucker, P.; Nachman, M.

    2012-01-01

    Roč. 29, č. 10 (2012), s. 2949-2955 ISSN 0737-4038 R&D Projects: GA ČR GA206/08/0640 Institutional support: RVO:68081766 Keywords : substitution * adaptation * evolution * effective population size * house mouse Subject RIV: EG - Zoology Impact factor: 10.353, year: 2012

  1. The rule of declining adaptability in microbial evolution experiments

    Science.gov (United States)

    Couce, Alejandro; Tenaillon, Olivier A.

    2015-01-01

    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 these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research. PMID:25815007

  2. Adaptive evolution of plastron shape in emydine turtles.

    Science.gov (United States)

    Angielczyk, Kenneth D; Feldman, Chris R; Miller, Gretchen R

    2011-02-01

    Morphology reflects ecological pressures, phylogeny, and genetic and biophysical constraints. Disentangling their influence is fundamental to understanding selection and trait evolution. Here, we assess the contributions of function, phylogeny, and habitat to patterns of plastron (ventral shell) shape variation in emydine turtles. We quantify shape variation using geometric morphometrics, and determine the influence of several variables on shape using path analysis. Factors influencing plastron shape variation are similar between emydine turtles and the more inclusive Testudinoidea. We evaluate the fit of various evolutionary models to the shape data to investigate the selective landscape responsible for the observed morphological patterns. The presence of a hinge on the plastron accounts for most morphological variance, but phylogeny and habitat also correlate with shape. The distribution of shape variance across emydine phylogeny is most consistent with an evolutionary model containing two adaptive zones--one for turtles with kinetic plastra, and one for turtles with rigid plastra. Models with more complex adaptive landscapes often fit the data only as well as the null model (purely stochastic evolution). The adaptive landscape of plastron shape in Emydinae may be relatively simple because plastral kinesis imposes overriding mechanical constraints on the evolution of form. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  3. Camelid genomes reveal evolution and adaptation to desert environments.

    Science.gov (United States)

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-10-21

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

  4. 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.

  5. Differential Evolution Algorithm with Self-Adaptive Population Resizing Mechanism

    Directory of Open Access Journals (Sweden)

    Xu Wang

    2013-01-01

    Full Text Available A differential evolution (DE algorithm with self-adaptive population resizing mechanism, SapsDE, is proposed to enhance the performance of DE by dynamically choosing one of two mutation strategies and tuning control parameters in a self-adaptive manner. More specifically, more appropriate mutation strategies along with its parameter settings can be determined adaptively according to the previous status at different stages of the evolution process. To verify the performance of SapsDE, 17 benchmark functions with a wide range of dimensions, and diverse complexities are used. Nonparametric statistical procedures were performed for multiple comparisons between the proposed algorithm and five well-known DE variants from the literature. Simulation results show that SapsDE is effective and efficient. It also exhibits much more superiorresultsthan the other five algorithms employed in the comparison in most of the cases.

  6. 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.

  7. 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.

  8. Pollinator adaptation and the evolution of floral nectar sugar composition.

    Science.gov (United States)

    Abrahamczyk, S; Kessler, M; Hanley, D; Karger, D N; Müller, M P J; Knauer, A C; Keller, F; Schwerdtfeger, M; Humphreys, A M

    2017-01-01

    A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse ~ 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  9. Adapting to Climate Change: Lessons from Farmers and Peri-Urban Fringe Residents in South Australia

    Directory of Open Access Journals (Sweden)

    Guy M. Robinson

    2018-03-01

    Full Text Available This paper reports on results from two major research projects conducted in South Australia. The first investigates adaptation to climate change in two of the state’s major grain and sheep farming regions, using semi-structured interviews and focus groups. The second uses a postal questionnaire and an internet-based survey of residents in the peri-urban fringes of Adelaide, the state capital, to examine knowledge of and attitudes to climate change and resulting adaptations, especially in the context of increasing risk of wildfires. The research on adaptation to climate change in agriculture focused on formal institutions (e.g., government agencies and communities of practice (e.g., farm systems groups. Both groups noted that farmers autonomously adapt to various risks, including those induced by climate variability. The types and levels of adaptation varied among individuals partly because of barriers to adaptation, which included limited communication and engagement processes established between formal institutions and communities of practice. The paper discusses possibilities for more effective transfers of knowledge and information on climate change among formal institutions, communities of practice, trusted individual advisors and farmers. Research in the peri-urban fringe revealed that actions taken by individuals to mitigate and/or adapt to climate change were linked to the nature of environmental values held (or ecological worldview and place attachment. Individuals with a strong place attachment to the study area (the Adelaide Hills who possessed knowledge of and/or beliefs in climate change were most likely to take mitigating actions. This was also linked to previous experience of major risk from wildfires. The paper concludes by discussing prospects for developing co-management for reducing the impact of climate change across multiple groups in rural and peri-urban areas.

  10. Increased tolerance towards serine obtained by adaptive laboratory evolution

    DEFF Research Database (Denmark)

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

    2014-01-01

    The amino acid serine has previously been identified as one of the top 30 candidates of value added chemicals, making the production of serine from glucose attractive. Production of serine have previously been attempted in E. coli and C. glutamicum, however, titers sufficient for commercial...... 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....... During the evolution experiment, the serine tolerance was increased substantially. Genome re-sequencing was subsequently used to analyze the genotype of a number of selected strains. These results reveal insights towards the adaptation process as well as the mechanism of serine tolerance....

  11. An Efficient Binary Differential Evolution with Parameter Adaptation

    Directory of Open Access Journals (Sweden)

    Dongli Jia

    2013-04-01

    Full Text Available Differential Evolution (DE has been applied to many scientific and engineering problems for its simplicity and efficiency. However, the standard DE cannot be used in a binary search space directly. This paper proposes an adaptive binary Differential Evolution algorithm, or ABDE, that has a similar framework as the standard DE but with an improved binary mutation strategy in which the best individual participates. To further enhance the search ability, the parameters of the ABDE are slightly disturbed in an adaptive manner. Experiments have been carried out by comparing ABDE with two binary DE variants, normDE and BDE, and the most used binary search technique, GA, on a set of 13 selected benchmark functions and the classical 0-1 knapsack problem. Results show that the ABDE performs better than, or at least comparable to, the other algorithms in terms of search ability, convergence speed, and solution accuracy.

  12. 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...... autotrophically and reducing CO2 into acetate more efficiently. Strains developed via this ALE method were also used to gain knowledge on the autotrophic metabolism of S. ovata as well as other acetogenic bacteria....

  13. Adaptive evolution of facial colour patterns in Neotropical primates

    OpenAIRE

    Santana, Sharlene E.; Lynch Alfaro, Jessica; Alfaro, Michael E.

    2012-01-01

    The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial co...

  14. Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

    Science.gov (United States)

    Lenski, Richard E

    2017-10-01

    Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

  15. Sex speeds adaptation by altering the dynamics of molecular evolution.

    Science.gov (United States)

    McDonald, Michael J; Rice, Daniel P; Desai, Michael M

    2016-03-10

    Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

  16. 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...... to humans, we find that purifying selection is stronger on the X chromosome than on the autosomes in chimpanzees. We therefore conclude that most adaptive mutations are recessive. We also document dramatically reduced synonymous diversity in the chimpanzee X chromosome relative to autosomes and stronger...... purifying selection than for the human X chromosome. If similar processes were operating in the human-chimpanzee ancestor as in central chimpanzees today, our results therefore provide an explanation for the much-discussed reduction in the human-chimpanzee divergence at the X chromosome....

  17. Gene expression and adaptive noncoding changes during human evolution.

    Science.gov (United States)

    Babbitt, Courtney C; Haygood, Ralph; Nielsen, William J; Wray, Gregory A

    2017-06-05

    Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

  18. How can general practitioners establish 'place attachment' in Australia's Northern Territory? Adjustment trumps adaptation.

    Science.gov (United States)

    Auer, K; Carson, D

    2010-01-01

    Retention of GPs in the more remote parts of Australia remains an important issue in workforce planning. The Northern Territory of Australia experiences very high rates of staff turnover. This research examined how the process of forming 'place attachment' between GP and practice location might influence prospects for retention. It examines whether GPs use 'adjustment' (short term trade-offs between work and lifestyle ambitions) or 'adaptation' (attempts to change themselves and their environment to fulfil lifestyle ambitions) strategies to cope with the move to new locations. 19 semi-structured interviews were conducted mostly with GPs who had been in the Northern Territory for less than 3 years. Participants were asked about the strategies they used in an attempt to establish place attachment. Strategies could be structural (work related), personal, social or environmental. There were strong structural motivators for GPs to move to the Northern Territory. These factors were seen as sufficiently attractive to permit the setting aside of other lifestyle ambitions for a short period of time. Respondents found the environmental aspects of life in remote areas to be the most satisfying outside work. Social networks were temporary and the need to re-establish previous networks was the primary driver of out migration. GPs primarily use adjustment strategies to temporarily secure their position within their practice community. There were few examples of adaptation strategies that would facilitate a longer term match between the GPs' overall life ambitions and the characteristics of the community. While this suggests that lengths of stay will continue to be short, better adjustment skills might increase the potential for repeat service and limit the volume of unplanned early exits.

  19. Trans gene regulation in adaptive evolution: a genetic algorithm model.

    Science.gov (United States)

    Behera, N; Nanjundiah, V

    1997-09-21

    This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate-"plastic"-loci, where a plastic locus had a finite probability in each generation of functioning (being switched "on") or not functioning (being switched "off"). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation. Copyright 1997 Academic Press Limited.

  20. A Self Adaptive Differential Evolution Algorithm for Global Optimization

    Science.gov (United States)

    Kumar, Pravesh; Pant, Millie

    This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

  1. 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

  2. Managing urban water crises: adaptive policy responses to drought and flood in Southeast Queensland, Australia

    Directory of Open Access Journals (Sweden)

    Brian W. Head

    2014-06-01

    Full Text Available In this case study, I examine the quality of decision-making under conditions of rapidly evolving urban water crises, and the adaptive policy challenges of building regional resilience in response to both drought and flood. Like other regions of Australia, Southeast Queensland has been subject to substantial cycles of drought and flood. I draw on resilience literature concerning sustainability, together with governance literature on policy change, to explain the changing awareness of urban water crises and the strategic options available for addressing these crises in this case study. The problem of resilience thinking opens up a number of important questions about the efficacy and adaptability of the policy system. The case provides insights into the interplay between the ways in which problems are framed, the knowledge bases required for planning and decision-making, the collaborative governance processes required for managing complex and rapidly evolving issues, and the overall capacity for policy learning over time. Regional resilience was proclaimed as a policy goal by government, but the practices remained largely anchored in traditional technical frameworks. Centralized investment decisions and governance restructures provoked conflict between levels of government, undermining the capacity of stakeholders to create more consensual approaches to problem-solving and limiting the collective learning that could have emerged.

  3. Simulating the evolution of glyphosate resistance in grains farming in northern Australia.

    Science.gov (United States)

    Thornby, David F; Walker, Steve R

    2009-09-01

    The evolution of resistance to herbicides is a substantial problem in contemporary agriculture. Solutions to this problem generally consist of the use of practices to control the resistant population once it evolves, and/or to institute preventative measures before populations become resistant. Herbicide resistance evolves in populations over years or decades, so predicting the effectiveness of preventative strategies in particular relies on computational modelling approaches. While models of herbicide resistance already exist, none deals with the complex regional variability in the northern Australian sub-tropical grains farming region. For this reason, a new computer model was developed. The model consists of an age- and stage-structured population model of weeds, with an existing crop model used to simulate plant growth and competition, and extensions to the crop model added to simulate seed bank ecology and population genetics factors. Using awnless barnyard grass (Echinochloa colona) as a test case, the model was used to investigate the likely rate of evolution under conditions expected to produce high selection pressure. Simulating continuous summer fallows with glyphosate used as the only means of weed control resulted in predicted resistant weed populations after approx. 15 years. Validation of the model against the paddock history for the first real-world glyphosate-resistant awnless barnyard grass population shows that the model predicted resistance evolution to within a few years of the real situation. This validation work shows that empirical validation of herbicide resistance models is problematic. However, the model simulates the complexities of sub-tropical grains farming in Australia well, and can be used to investigate, generate and improve glyphosate resistance prevention strategies.

  4. 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.

  5. A problem-oriented approach to understanding adaptation: lessons learnt from Alpine Shire, Victoria Australia.

    Science.gov (United States)

    Roman, Carolina

    2010-05-01

    Climate change is gaining attention as a significant strategic issue for localities that rely on their business sectors for economic viability. For businesses in the tourism sector, considerable research effort has sought to characterise the vulnerability to the likely impacts of future climate change through scenarios or ‘end-point' approaches (Kelly & Adger, 2000). Whilst useful, there are few demonstrable case studies that complement such work with a ‘start-point' approach that seeks to explore contextual vulnerability (O'Brien et al., 2007). This broader approach is inclusive of climate change as a process operating within a biophysical system and allows recognition of the complex interactions that occur in the coupled human-environmental system. A problem-oriented and interdisciplinary approach was employed at Alpine Shire, in northeast Victoria Australia, to explore the concept of contextual vulnerability and adaptability to stressors that include, but are not limited to climatic change. Using a policy sciences approach, the objective was to identify factors that influence existing vulnerabilities and that might consequently act as barriers to effective adaptation for the Shire's business community involved in the tourism sector. Analyses of results suggest that many threats, including the effects climate change, compete for the resources, strategy and direction of local tourism management bodies. Further analysis of conditioning factors revealed that many complex and interacting factors define the vulnerability and adaptive capacity of the Shire's tourism sector to the challenges of global change, which collectively have more immediate implications for policy and planning than long-term future climate change scenarios. An approximation of the common interest, i.e. enhancing capacity in business acumen amongst tourism operators, would facilitate adaptability and sustainability through the enhancement of social capital in this business community. Kelly, P

  6. Mechanisms of adaptive evolution. Darwinism and Lamarckism restated.

    Science.gov (United States)

    Aboitiz, F

    1992-07-01

    This article discusses the conceptual basis of the different mechanisms of adaptive evolution. It is argued that only two such mechanisms may conceivably exist, Lamarckism and Darwinism. Darwinism is the fundamental process generating the diversity of species. Some aspects of the gene-centered approach to Darwinism are questioned, since they do not account for the generation of biological diversity. Diversity in biological design must be explained in relation to the diversity of interactions of organisms (or other higher-level units) with their environment. This aspect is usually overlooked in gene-centered views of evolution. A variant of the gene-selectionist approach has been proposed to account for the spread of cultural traits in human societies. Alternatively, I argue that social evolution is rather driven by what I call pseudo-Lamarckian inheritance. Finally, I argue that Lamarckian and pseudo-Lamarckian inheritance are just special cases of faithful replication which are found in the development of some higher-order units, such as multicellular organisms and human societies.

  7. On the Adaptive Design Rules of Biochemical Networks in Evolution

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2007-01-01

    Full Text Available Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.

  8. On the adaptivity and complexity embedded into differential evolution

    International Nuclear Information System (INIS)

    Senkerik, Roman; Pluhacek, Michal; Jasek, Roman; Zelinka, Ivan

    2016-01-01

    This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

  9. On the adaptivity and complexity embedded into differential evolution

    Science.gov (United States)

    Senkerik, Roman; Pluhacek, Michal; Zelinka, Ivan; Jasek, Roman

    2016-06-01

    This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

  10. On the adaptivity and complexity embedded into differential evolution

    Energy Technology Data Exchange (ETDEWEB)

    Senkerik, Roman; Pluhacek, Michal; Jasek, Roman [Tomas Bata University in Zlin, Faculty of Applied Informatics, Nam T.G. Masaryka 5555, 760 01 Zlin, Czech Republic, senkerik@fai.utb.cz,pluhacek@fai.utb.cz (Czech Republic); Zelinka, Ivan [Technical University of Ostrava, Faculty of Electrical Engineering and Computer Science, 17. listopadu 15,708 33 Ostrava-Poruba, Czech Republic, ivan.zelinka@vsb.cz (Czech Republic)

    2016-06-08

    This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

  11. 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

  12. Prolonged Adaptive Evolution of a Defensive Gene in the Solanaceae.

    Science.gov (United States)

    Rausher, Mark D; Huang, Jie

    2016-01-01

    Although plants and their natural enemies may coevolve for prolonged periods, little is known about how long individual plant defensive genes are involved in the coevolutionary process. We address this issue by examining patterns of selection on the defensive gene threonine deaminase (TD). Tomato (Solanum lycopersicum) has two copies of this gene. One performs the canonical housekeeping function in amino acid metabolism of catalyzing the first reaction in the conversion of threonine to isoleucine. The second copy functions as an antinutritive defense against lepidopteran herbivores by depleting threonine in the insect gut. Wild tobacco (Nicotiana attenuata) also contains a defensive copy. We show that a single copy of TD underwent two or three duplications near the base of the Solanaceae. One copy retains the housekeeping function, whereas a second copy evolved defensive functions. Positive selection occurred on the branch of the TD2 gene tree subtending the common ancestor of the Nicotianoideae and Solanoideae. It also occurred within the Solanoideae clade but not within the Nicotianoideae clade. Finally, it occurred on most branches leading from the common ancestor to S. lycopersicum. Based on recent calibrations of the Solanaceae phylogeny, TD2 experienced adaptive substitutions for a period of 30-50 My. We suggest that the most likely explanation for this result is fluctuating herbivore abundances: When herbivores are rare, relaxed selection increases the likelihood that slightly disadvantageous mutations will be fixed by drift; when herbivores are common, increased selection causes the evolution of compensatory adaptive mutations. Alternative explanations are also discussed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. THE EVOLUTION OF THE DESIGN AND CONSTRUCTION OF MASONRY BUILDINGS IN AUSTRALIA

    Directory of Open Access Journals (Sweden)

    Adrian Page

    2012-12-01

    Full Text Available Masonry is a construction material which is widely used in Australia in a number of forms (fired clay, concrete, calcium silicate, natural stone, autoclaved aerated concrete and in a wide range of both loadbearing and non-loadbearing applications. As such, it serves as the primary structural element in structures such as 3-4 story “walk up” apartment buildings or low rise commercial structures, or as a veneer or infill in housing or high rise framed construction. Despite its current widespread use, for masonry to remain a viable construction material in the future, design and construction practices need to be flexible, able to adapt to change and be receptive to innovation. This applies not only to advances in materials technology and the development of new products and building systems, but also an effective response to changes in the regulatory framework which have an increasing emphasis on thermal and acoustic performance, seismic resistance and sustainable practices. In this context, an overview of the Australian past, present and possible future masonry scene is given.

  14. Adaptive evolution of facial colour patterns in Neotropical primates.

    Science.gov (United States)

    Santana, Sharlene E; Lynch Alfaro, Jessica; Alfaro, Michael E

    2012-06-07

    The rich diversity of primate faces has interested naturalists for over a century. Researchers have long proposed that social behaviours have shaped the evolution of primate facial diversity. However, the primate face constitutes a unique structure where the diverse and potentially competing functions of communication, ecology and physiology intersect, and the major determinants of facial diversity remain poorly understood. Here, we provide the first evidence for an adaptive role of facial colour patterns and pigmentation within Neotropical primates. Consistent with the hypothesis that facial patterns function in communication and species recognition, we find that species living in smaller groups and in sympatry with a higher number of congener species have evolved more complex patterns of facial colour. The evolution of facial pigmentation and hair length is linked to ecological factors, and ecogeographical rules related to UV radiation and thermoregulation are met by some facial regions. Our results demonstrate the interaction of behavioural and ecological factors in shaping one of the most outstanding facial diversities of any mammalian lineage.

  15. Adaptive Evolution of CENP-A in Percid Fishes

    Directory of Open Access Journals (Sweden)

    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.

  16. Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

    Directory of Open Access Journals (Sweden)

    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

  17. CBCT-guided evolutive library for cervical adaptive IMRT.

    Science.gov (United States)

    Rigaud, Bastien; Simon, Antoine; Gobeli, Maxime; Lafond, Caroline; Leseur, Julie; Barateau, Anais; Jaksic, Nicolas; Castelli, Joël; Williaume, Danièle; Haigron, Pascal; De Crevoisier, Renaud

    2018-04-01

    In the context of adaptive radiation therapy (ART) for locally advanced cervical carcinoma (LACC), this study proposed an original cone-beam computed tomography (CBCT)-guided "Evolutive library" and evaluated it against four other known radiotherapy (RT) strategies. For 20 patients who underwent intensity-modulated radiation therapy (IMRT) for LACC, three planning CTs [with empty (EB), intermediate (IB), and full (FB) bladder volumes], a CT scan at 20 Gy and bi-weekly CBCTs for 5 weeks were performed. Five RT strategies were simulated for each patient: "Standard RT" was based on one IB planning CT; "internal target volume (ITV)-based RT" was an ITV built from the three planning CTs; "RT with one mid-treatment replanning (MidTtReplan)" corresponded to the standard RT with a replanning at 20 Gy; "Pretreatment library ART" using a planning library based on the three planning CTs; and the "Evolutive library ART", which was the "Pretreatment library ART" strategy enriched by including some CBCT anatomies into the library when the daily clinical target volume (CTV) shape differed from the ones in the library. Two planning target volume (PTV) margins of 7 and 10 mm were evaluated. All the strategies were geometrically compared in terms of the percentage of coverage by the PTV, for the CTV and the organs at risk (OAR) delineated on the CBCT. Inadequate coverage of the CTV and OARs by the PTV was also assessed using deformable image registration. The cumulated dose distributions of each strategy were likewise estimated and compared for one patient. The "Evolutive library ART" strategy involved a number of added CBCTs: 0 for 55%; 1 for 30%; 2 for 5%; and 3 for 10% of patients. Compared with the other four, this strategy provided the highest CTV geometric coverage by the PTV, with a mean (min-max) coverage of 98.5% (96.4-100) for 10 mm margins and 96.2% (93.0-99.7) for 7 mm margins (P < 0.05). Moreover, this strategy significantly decreased the geometric coverage of the bowel

  18. Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount Carmel, Israel.

    Science.gov (United States)

    Ben-Abu, Yuval; Beiles, Avigdor; Flom, Dvir; Nevo, Eviatar

    2018-01-01

    "Evolution Canyon" (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution-in-action, highlighting the evolutionary processes of biodiversity evolution, adaptation, and incipient sympatric speciation. A major model organism in ECI is the tetraploid wild emmer wheat, Triticum dicoccoides (TD), the progenitor of cultivated emmer and durum wheat. TD displays dramatic interslope adaptive evolutionary divergence on the tropical, savannoid-hot and dry south-facing, "African" slope (AS), and on the temperate, forested, cool and humid, north-facing, "European" slope (ES), separated on average by 250 m. From the perspective of chemical evolution and metabolomics, it is important to unravel interslope divergence in biologically relevant secondary metabolites between the abutting slope populations. Here, in TD we examined hydroxamic acid (Hx), which is a family of secondary cereal metabolites, and plays a major role in defending the plant against fungi, insects and weeds. Our examination revealed that higher concentrations of DIBOA and DIMBOA were found in seedlings growing in the same greenhouse from seeds collected from the cool and humid forested ES, whereas the seedlings of seeds collected from the savannoid AS (both in root and shoot tissues), showed no DIMBOA. Remarkably, only DIBOA appears in both shoots and roots of the AS seedlings. It rises to a peak and then decreases in both organs and in seedlings from both slopes. The DIMBOA, which appears only in the ES seedlings, rises to a peak and decreases in the shoot, but increased and remained in a plateau in the root, till the end of the experiment. The results suggest stronger genetic resistance of defense compounds DIBOA and DIMBOA against biotic stresses (fungi and other pathogens) by ES seedlings. However, AS seedlings responded earlier but were to the same biotic stresses. The genetic difference found in AS seedlings was caused by the main adaptive selection

  19. Adaptive evolution of benzoxazinoids in wild emmer wheat, Triticum dicoccoides, at "Evolution Canyon", Mount Carmel, Israel.

    Directory of Open Access Journals (Sweden)

    Yuval Ben-Abu

    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 evolutionary processes of biodiversity evolution, adaptation, and incipient sympatric speciation. A major model organism in ECI is the tetraploid wild emmer wheat, Triticum dicoccoides (TD, the progenitor of cultivated emmer and durum wheat. TD displays dramatic interslope adaptive evolutionary divergence on the tropical, savannoid-hot and dry south-facing, "African" slope (AS, and on the temperate, forested, cool and humid, north-facing, "European" slope (ES, separated on average by 250 m. From the perspective of chemical evolution and metabolomics, it is important to unravel interslope divergence in biologically relevant secondary metabolites between the abutting slope populations. Here, in TD we examined hydroxamic acid (Hx, which is a family of secondary cereal metabolites, and plays a major role in defending the plant against fungi, insects and weeds.Our examination revealed that higher concentrations of DIBOA and DIMBOA were found in seedlings growing in the same greenhouse from seeds collected from the cool and humid forested ES, whereas the seedlings of seeds collected from the savannoid AS (both in root and shoot tissues, showed no DIMBOA. Remarkably, only DIBOA appears in both shoots and roots of the AS seedlings. It rises to a peak and then decreases in both organs and in seedlings from both slopes. The DIMBOA, which appears only in the ES seedlings, rises to a peak and decreases in the shoot, but increased and remained in a plateau in the root, till the end of the experiment.The results suggest stronger genetic resistance of defense compounds DIBOA and DIMBOA against biotic stresses (fungi and other pathogens by ES seedlings. However, AS seedlings responded earlier but were to the same biotic stresses. The genetic difference found in AS seedlings was caused by the main adaptive

  20. How adaptive learning affects evolution: reviewing theory on the Baldwin effect

    NARCIS (Netherlands)

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

    2012-01-01

    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

  1. Light adaptation and the evolution of vertebrate photoreceptors.

    Science.gov (United States)

    Morshedian, Ala; Fain, Gordon L

    2017-07-15

    Lamprey are cyclostomes, a group of vertebrates that diverged from lines leading to jawed vertebrates (including mammals) in the late Cambrian, 500 million years ago. It may therefore be possible to infer properties of photoreceptors in early vertebrate progenitors by comparing lamprey to other vertebrates. We show that lamprey rods and cones respond to light much like rods and cones in amphibians and mammals. They operate over a similar range of light intensities and adapt to backgrounds and bleaches nearly identically. These correspondences are pervasive and detailed; they argue for the presence of rods and cones very early in the evolution of vertebrates with properties much like those of rods and cones in existing vertebrate species. The earliest vertebrates were agnathans - fish-like organisms without jaws, which first appeared near the end of the Cambrian radiation. One group of agnathans became cyclostomes, which include lamprey and hagfish. Other agnathans gave rise to jawed vertebrates or gnathostomes, the group including all other existing vertebrate species. Because cyclostomes diverged from other vertebrates 500 million years ago, it may be possible to infer some of the properties of the retina of early vertebrate progenitors by comparing lamprey to other vertebrates. We have previously shown that rods and cones in lamprey respond to light much like photoreceptors in other vertebrates and have a similar sensitivity. We now show that these affinities are even closer. Both rods and cones adapt to background light and to bleaches in a manner almost identical to other vertebrate photoreceptors. The operating range in darkness is nearly the same in lamprey and in amphibian or mammalian rods and cones; moreover background light shifts response-intensity curves downward and to the right over a similar range of ambient intensities. Rods show increment saturation at about the same intensity as mammalian rods, and cones never saturate. Bleaches decrease

  2. 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.

  3. Post-Palaeozoic uplift history of southeastern Australia revisited: results from a process-based mode of landscape evolution

    International Nuclear Information System (INIS)

    Van Der Beek, P.A.; Braun, J.; Lambeck, K.

    1999-01-01

    Developments over the last decade in the debate concerning the geomorphic evolution of the south-eastern Australian highlands are reviewed, taking as a starting point the model of passive denudation and isostatic rebound of a Palaeozoic mountain belt presented by Lambeck and Stephenson (1986). This model has been popular in the geomorphological community because it provides a quantitative framework to explain the very low rates of landscape evolution inferred from most geomorphological studies. The model has, however, also been criticised for its treatment of erosion as being linearly dependent on elevation, as well as for its predictions of regional uplift and denudation patterns that are not in accord with inferences from fission-track thermochronological data. Part of controversy stems from conceptual misunderstandings on the interpretation of data and from insufficient consideration of questions of spatial and temporal scale. First results of a new physical process-based model for large-scale long-term landscape evolution in the south-eastern highlands are presented. These show that the denudation history and drainage development of south-eastern Australia can be explained to a first order without invoking large-scale mid-Cretaceous or Tertiary uplift events. The model predicts drainage patterns in southeastern Australia to have evolved by rearrangement of an initially north-westerly directed drainage net, caused by drops in base-level during Mesozoic rifting along the southern and eastern margins of the study region. The geomorphology and available fission-track data in the Snowy Mountains region (and possibly also in the Bathurst - Blue Mountains region) do require renewed (mid Cretaceous?) uplift to have taken place. The model results are discussed in the light of recent controversies surrounding the southeastern highlands-their uplift history, denudation rates, depth of denudation of the coastal strip and inferred Mesozoic drainage patterns. Copyright (1999

  4. 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

  5. Adaptation strategies for health impacts of climate change in Western Australia: Application of a Health Impact Assessment framework

    International Nuclear Information System (INIS)

    Spickett, Jeffery T.; Brown, Helen L.; Katscherian, Dianne

    2011-01-01

    Climate change is one of the greatest challenges facing the globe and there is substantial evidence that this will result in a number of health impacts, regardless of the level of greenhouse gas mitigation. It is therefore apparent that a combined approach of mitigation and adaptation will be required to protect public health. While the importance of mitigation is recognised, this project focused on the role of adaptation strategies in addressing the potential health impacts of climate change. The nature and magnitude of these health impacts will be determined by a number of parameters that are dependent upon the location. Firstly, climate change will vary between regions. Secondly, the characteristics of each region in terms of population and the ability to adapt to changes will greatly influence the extent of the health impacts that are experienced now and into the future. Effective adaptation measures therefore need to be developed with these differences in mind. A Health Impact Assessment (HIA) framework was used to consider the implications of climate change on the health of the population of Western Australia (WA) and to develop a range of adaptive responses suited to WA. A broad range of stakeholders participated in the HIA process, providing informed input into developing an understanding of the potential health impacts and potential adaptation strategies from a diverse sector perspective. Potential health impacts were identified in relation to climate change predictions in WA in the year 2030. The risk associated with each of these impacts was assessed using a qualitative process that considered the consequences and the likelihood of the health impact occurring. Adaptations were then developed which could be used to mitigate the identified health impacts and provide responses which could be used by Government for future decision making. The periodic application of a HIA framework is seen as an ideal tool to develop appropriate adaptation strategies to

  6. Adaptive evolution of relish, a Drosophila NF-kappaB/IkappaB protein.

    OpenAIRE

    Begun, D J; Whitley, P

    2000-01-01

    NF-kappaB and IkappaB proteins have central roles in regulation of inflammation and innate immunity in mammals. Homologues of these proteins also play an important role in regulation of the Drosophila immune response. Here we present a molecular population genetic analysis of Relish, a Drosophila NF-kappaB/IkappaB protein, in Drosophila simulans and D. melanogaster. We find strong evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster. The adaptive evolution appear...

  7. Aspects of the structural and late thermal evolution of the Redbank Thrust system, central Australia: constraints from the Speares Metamorphics

    International Nuclear Information System (INIS)

    Biermeier, C.; Wiesinger, M.; Stuewe, K.; Foster, D.A.

    2003-01-01

    We present new data on the field geology and late thermal evolution of the Redbank Thrust system in the Arunta Block of central Australia. Geochronological and field data from the Speares Meta-morphics are also used to relate the thermal evolution of the Redbank Thrust system to the structural evolution of the region. We show that several stages in the evolution might be discerned. An originally sedimentary sequence was intruded by mafic intrusions and then deformed during partial melting to form the principal foliation observed in the region (D1). This sequence was then folded during D2 into upright folds with north- to northeast-plunging fold axes. These events are likely to correlate with the Strangways and/or Argilke and Chewings Orogenies known from previous studies. Subsequently, the Redbank Thrust was initiated during D3. This event is recognised by deflection of the host rocks into the shear zone and might therefore have been associated with a component of strike-slip motion. It occurred probably at or before 1500-1400 Ma. Subsequent north-over-south thrust motion in the Redbank Thrust formed the intense mylonitic fabric and folded the mylonitic fabric during D4 into asymmetric folds with shallow fold axes. New 40 Ar/ 39 Ar K-feldspar ages from three samples collected from variably deformed branches of the Redbank Thrust and undeformed rocks in the Speares Metamorphics suggest that most parts of the Redbank Thrust system cooled relatively slowly after metamorphism and deformation in the Mesoproterozoic so that the D4 thrusting might have been very long-lived. Minimum ages of the K-feldspar age spectra show that the entire region cooled below 200 deg C by approximately 300 Ma. Apatite fission track ages from nine samples show that cooling through the apatite partial annealing zone occurred during Cretaceous time (ca 150-70 Ma) and modelled cooling histories are consistent with the cooling rates obtained from the K-feldspar data. They indicate that final

  8. 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

  9. 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.

  10. Water scarcity and institutional change: lessons in adaptive governance from the drought experience of Perth, Western Australia.

    Science.gov (United States)

    Bettini, Y; Brown, R; de Haan, F J

    2013-01-01

    Urban water systems will be increasingly challenged under future climates and global pressures. Meeting challenges by reconfiguring water systems to integrate supplies and deliver multifunctional uses is technically well described. Adjusting the institutions that frame the management of these systems is not well operationalized in practice or conceptualized in theory. This study seeks to address this gap through an institutional analysis of Perth, Australia, a city where drought crisis has put under pressure both management practices and the institutional setting that underlies them. The study found that while trusted practices moderated water scarcity, the stability of the institutional setting may not facilitate a shift toward adaptable institutional configurations suited to future conditions. The results identified three key ingredients for a flexible institutional setting: (i) feedbacks in the system through better information management, (ii) reflexive dialogue and strategic use of projects to generate greater learning opportunities, and (iii) policy level support for sector-wide collaboration through progressive agendas, incentives for innovation and capacity building in stakeholder and community engagement. Further, the results suggest that a deeper understanding of institutional dynamics is needed to enable adaptive governance. The paper provides an analytical framework for diagnosing how greater adaptive capacity might be mobilized through influencing these dynamics.

  11. Time in Redox Adaptation Processes: From Evolution to Hormesis

    Directory of Open Access Journals (Sweden)

    Mireille M. J. P. E. Sthijns

    2016-09-01

    Full Text Available Life on Earth has to adapt to the ever changing environment. For example, due to introduction of oxygen in the atmosphere, an antioxidant network evolved to cope with the exposure to oxygen. The adaptive mechanisms of the antioxidant network, specifically the glutathione (GSH system, are reviewed with a special focus on the time. The quickest adaptive response to oxidative stress is direct enzyme modification, increasing the GSH levels or activating the GSH-dependent protective enzymes. After several hours, a hormetic response is seen at the transcriptional level by up-regulating Nrf2-mediated expression of enzymes involved in GSH synthesis. In the long run, adaptations occur at the epigenetic and genomic level; for example, the ability to synthesize GSH by phototrophic bacteria. Apparently, in an adaptive hormetic response not only the dose or the compound, but also time, should be considered. This is essential for targeted interventions aimed to prevent diseases by successfully coping with changes in the environment e.g., oxidative stress.

  12. Revolution then evolution: the advance of health economic evaluation in Australia.

    Science.gov (United States)

    Lopert, Ruth; Viney, Rosalie

    2014-01-01

    All governments face immense challenges in providing affordable healthcare for their citizens, and the diffusion of novel health technologies is a key driver of growth in expenditure for many. Although important methodological and process variations exist around the world, health economic evaluation is increasingly seen as an important tool to support decision-making around the introduction of new health technologies, interventions and programmes in countries of varying stages of economic development. In Australia, the assessment of the comparative cost-effectiveness of new medicines proposed for subsidy under the country's national drug subsidy programme, the Pharmaceutical Benefits Scheme, was introduced in the late 1980s and became mandatory in 1993, making Australia the first country to introduce such a requirement nationally. Since then the use of health economic evaluation has expanded and been applied to support decision-making across a broader range of health technologies, as well as to programmes in public health. Copyright © 2014. Published by Elsevier GmbH.

  13. 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...... 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...

  14. Charles Darwin in Australia; or How To Introduce Some Local Colour to the Teaching of Evolution, Geology, Meteorology, and the Determination of Longitude.

    Science.gov (United States)

    Nicholas, Frank W.

    The background to Charles Darwin's little-known visit to Australia, and the account of his experiences while here, provide some invaluable historical material for teaching evolution, geology, meteorology, and the determination of longitude. Indeed, by using his Australian experiences as a foundation, it is possible to explain the theory of…

  15. Adaptive evolution of sexual systems in pedunculate barnacles

    DEFF Research Database (Denmark)

    Yusa, Yoichi; Yoshikawa, Mai; Kitaura, Jun

    2012-01-01

    (androdioecy), and coexistence of dwarf males and females (dioecy). Here, we report the first phylogenetically controlled test of the hypothesis that the ultimate cause of the diverse sexual systems and presence of dwarf males in this group is limited mating opportunities for non-dwarf individuals, owing...... to mating in small groups. Within the pedunculate barnacle phylogeny, dwarf males and females have evolved repeatedly. Females are more likely to evolve in androdioecious than hermaphroditic populations, suggesting that evolution of dwarf males has preceded that of females in pedunculates. Both dwarf males...... and females are associated with a higher proportion of solitary individuals in the population, corroborating the hypothesis that limited mating opportunities have favoured evolution of these diverse sexual systems, which have puzzled biologists since Darwin....

  16. Land-surface evolution at the continental time-scale: An example from interior Western Australia

    Science.gov (United States)

    Mabbutt, J. A.

    1988-12-01

    The interior plateau of Western Australia in the Wiluna—Meekatharra area is in part an exhumed pre-Permian surface of low relief and to that extent of Gondwana age. A lateritic duricrust on interfluvial remnants of an Old Plateau surface is probably the outcome of several cycles of weathering and stripping, rather than of a single geomorphic episode. Landforms above the Old Plateau have maintained their relief during this circumdenudation and there is no regional evidence of their isolation by major escarpment retreat. A New Plateau surface has extended by stripping of saprolite and is an etchplain, as also is the Old Plateau under the genesis postulated. The New Plateau cycle was initiated by general drainage rejuvenation whilst lateritic weathering still continued, but its extension was halted through increasing climatic aridity, probably during the Miocene.

  17. 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...

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

    Science.gov (United States)

    Marvig, Rasmus Lykke; Sommer, Lea Mette; Molin, Søren; Johansen, Helle Krogh

    2015-01-01

    Little is known about how within-host evolution compares between genotypically different strains of the same pathogenic species. We sequenced the whole genomes of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young individuals with cystic 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.

  19. Evolution of the societal value of water resources for economic development versus environmental sustainability in Australia from 1843 to 2011

    Science.gov (United States)

    Wei, Y.; Wei, J., , Dr; Western, A. W.

    2017-12-01

    The scale of human activity in the last 200 years has reached a point where our actions are affecting the global biophysical environment to such a degree and at such a speed that irreversible effects are being observed. Societal values are generally seen as leading to changes in human decisions and actions, but have not been addressed adequately in current water management, which is blind to changes in the social drivers for, or societal responses to, management decisions. This paper describes the evolution of societal value of water resources in Australia over a period of 169 years. These values were classified into two groups: supporting economic development versus supporting environmental sustainability. The Sydney Morning Herald newspaper was used as the main data source to track the changes in the societal value of water resources. Content analysis was used to create a description of the evolution of these societal values. Mathematical regression analysis, in combination of transition theory, was used to determine the stages of transition of the societal value, and the co-evolved social-ecological framework was used to explain how the evolution of societal values interacted with water management policies/practices and droughts. Key findings included that the transition of the societal value of water resources fitted the sigmoid curve - a conceptual S curve for the transition of social systems. Also, the transition of societal value of water resources in Australia went through three stages: (1) pre-development (1900s-1960s), when the societal value of water resources was dominated by economic development; (2) take-off (1962-1980), when the societal value of water resources reflected the increasing awareness of the environment due to the outbreak of pollution events; (3) acceleration (1981-2011), when the environment-oriented societal value of water resources combined with the Millennium Drought to trigger a package of policy initiatives and management practices

  20. 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

    independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different......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...

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

    Science.gov (United States)

    2015-12-20

    IS150 mutation has a pleiotropic effect across environments: it is neutral in most of the PTS environments (mean ± SEM: 0.981 ± 0.015), but has...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 ...the mutations are likely to have a similar proximal basis of the benefit they confer: a shorter lag 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE

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

    Science.gov (United States)

    Barton, Robert A.

    2016-01-01

    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. PMID:27629025

  3. 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

  4. Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

    Science.gov (United States)

    Yunpeng, Liang; Li, Yu

    2015-01-01

    As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

  5. The evolution of the doctrine of restraint of trade in Australia: a law reform perspective

    OpenAIRE

    Cheng, John Wei-Ting

    2017-01-01

    This thesis examines the present state of the common law doctrine of restraint of trade from a law reform perspective. The doctrine was developed in England between the 1600s and mid-1800s and its evolution over the centuries has been a slow and ongoing process. The present state of the doctrine and its application in the Australian jurisdiction presents a challenging set of circumstances due to the difficulties faced by contracting parties when they wish to engage in restraint of trade. ...

  6. Localizing recent adaptive evolution in the human genome

    DEFF Research Database (Denmark)

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

    2007-01-01

    , 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...

  7. 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...

  8. 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.

  9. 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

  10. 'Newness-struggle-success' continuum: a qualitative examination of the cultural adaptation process experienced by overseas-qualified dentists in Australia.

    Science.gov (United States)

    Balasubramanian, Madhan; Brennan, David S; Spencer, A John; Short, Stephanie D

    2016-04-01

    Objectives Overseas-qualified dentists constitute a significant proportion of the Australian dental workforce (approximately one in four). The aim of the present study was to provide a better understanding of the cultural adaptation process of overseas-qualified dentists in Australia, so as to facilitate their integration into the Australian way of life and improve their contribution to Australian healthcare, economy and society. Methods Life stories of 49 overseas-qualified dentists from 22 countries were analysed for significant themes and patterns. We focused on their settlement experience, which relates to their social and cultural experience in Australia. This analysis was consistent with a hermeneutic phenomenological approach to qualitative social scientific research. Results Many participants noted that encounters with 'the Australian accent' and 'slang' influenced their cultural experience in Australia. Most of the participants expressed 'fascination' with the people and lifestyle in Australia, primarily with regard to the relaxed way of life, cultural diversity and the freedom one usually experiences living in Australia. Few participants expressed 'shock' at not being able to find a community of similar religious faith in Australia, as they are used to in their home countries. These issues were analysed in two themes; (1) language and communication; and (2) people, religion and lifestyle. The cultural adaptation process of overseas-qualified dentists in Australia is described as a continuum or superordinate theme, which we have entitled the 'newness-struggle-success' continuum. This overarching theme supersedes and incorporates all subthemes. Conclusion Family, friends, community and organisational structures (universities and public sector) play a vital role in the cultural learning process, affecting overseas-qualified dentist's ability to progress successfully through the cultural continuum. What is known about the topic? Australia is a popular host

  11. Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses.

    Science.gov (United States)

    Pievani, Telmo; Serrelli, Emanuele

    2011-01-01

    Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.

  12. 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...

  13. Evolution of Alternative Adaptive Immune Systems in Vertebrates.

    Science.gov (United States)

    Boehm, Thomas; Hirano, Masayuki; Holland, Stephen J; Das, Sabyasachi; Schorpp, Michael; Cooper, Max D

    2018-04-26

    Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.

  14. 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

  15. 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.

  16. 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.

  17. Adaptive evolution in locomotor performance: How selective pressures and functional relationships produce diversity.

    Science.gov (United States)

    Scales, Jeffrey A; Butler, Marguerite A

    2016-01-01

    Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored the evolution of locomotor performance in lizards in relation to possible selective pressures using the Ornstein-Uhlenbeck process. Here, we show that a combination of selection based on foraging mode and predator escape is required to explain variation in performance phenotypes. Surprisingly, habitat use contributed little explanatory power. We find that it is possible to evolve very different abilities in performance which were previously thought to be tightly correlated, supporting a growing literature that explores the many-to-one mapping of morphological design. Although we generally find the expected trade-off between maximal exertion and speed, this relationship surprisingly disappears when species experience selection for both performance types. We conclude that functional integration need not limit adaptive potential, and that an integrative approach considering multiple major influences on a phenotype allows a more complete understanding of adaptation and the evolution of diversity. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  18. 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.

  19. Surface evolution and carbon sequestration in disturbed and undisturbed wetland soils of the Hunter estuary, southeast Australia

    Science.gov (United States)

    Howe, A. J.; Rodríguez, J. F.; Saco, P. M.

    2009-08-01

    The aim of this work was to quantify the soil carbon storage and sequestration rates of undisturbed natural wetlands and disturbed wetlands subject to restriction of tidal flow and subsequent rehabilitation in an Australian estuary. Disturbed and undisturbed estuarine wetlands of the Hunter estuary, New South Wales, Australia were selected as the study sites for this research. Vertical accretion rates of estuarine substrates were combined with soil carbon concentrations and bulk densities to determine the carbon store and carbon sequestration rates of the substrates tested. Relationships between estuary water level, soil evolution and vertical accretion were also examined. The carbon sequestration rate of undisturbed wetlands was lower (15% for mangrove and 55% for saltmarsh) than disturbed wetlands, but the carbon store was higher (65% for mangrove and 60% for saltmarsh). The increased carbon sequestration rate of the disturbed wetlands was driven by substantially higher rates of vertical accretion (95% for mangrove and 345% for saltmarsh). Estuarine wetland carbon stores were estimated at 700-1000 Gg C for the Hunter estuary and 3900-5600 Gg C for New South Wales. Vertical accretion and carbon sequestration rates of estuarine wetlands in the Hunter are at the lower end of the range reported in the literature. The comparatively high carbon sequestration rates reported for the disturbed wetlands in this study indicate that wetland rehabilitation has positive benefits for regulation of atmospheric carbon concentrations, in addition to more broadly accepted ecosystem services.

  20. Decline, Adaptation or Transformation:New Perspectives on Demographic Change in Resource Peripheries in Australia and Sweden

    Directory of Open Access Journals (Sweden)

    Dean B. Carson

    2016-01-01

    Full Text Available Many sparsely populated resource peripheries in developed countries are perceived to suffer from periods of demographic decline due to loss of employment opportunities and services, youth out-migration and population ageing. While these trends tend to apply at broad regional scales and for particular time periods, diverse patterns of demographic change may be apparent if different spatial, temporal and social scales of analysis are taken into consideration. Comparing the experiences of two case study regions in northern Sweden and inland South Australia, this paper proposes an alternative conceptual framework to the “discourse of decline”, which could be used to examine the nuances of demographic change within resource peripheries. The framework includes spatial scale considerations that contrast broader regional demographic patterns with the experiences of sub-regions and individual settlements. It also includes temporal scale aspects, examining demographic change over different time periods to understand the pace, duration and frequency of population growth and decline. The framework finally includes social unit considerations, emphasising that demographic change affects different social groups in different ways. The results of the case studies suggest that considering demographic change as adaptation or transformation rather than decline may be more useful for identifying new – and qualitatively different – demographic pathways that emerge over time.

  1. Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects.

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    Snigdhadip Dey

    2016-02-01

    Full Text Available All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging, are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia-anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia-anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to

  2. Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.

    Directory of Open Access Journals (Sweden)

    Pep Charusanti

    Full Text Available Adaptation is normally viewed as the enemy of the antibiotic discovery and development process because adaptation among pathogens to antibiotic exposure leads to resistance. We present a method here that, in contrast, exploits the power of adaptation among antibiotic producers to accelerate the discovery of antibiotics. A competition-based adaptive laboratory evolution scheme is presented whereby an antibiotic-producing microorganism is competed against a target pathogen and serially passed over time until the producer evolves the ability to synthesize a chemical entity that inhibits growth of the pathogen. When multiple Streptomyces clavuligerus replicates were adaptively evolved against methicillin-resistant Staphylococcus aureus N315 in this manner, a strain emerged that acquired the ability to constitutively produce holomycin. In contrast, no holomycin could be detected from the unevolved wild-type strain. Moreover, genome re-sequencing revealed that the evolved strain had lost pSCL4, a large 1.8 Mbp plasmid, and acquired several single nucleotide polymorphisms in genes that have been shown to affect secondary metabolite biosynthesis. These results demonstrate that competition-based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well.

  3. Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel.

    Science.gov (United States)

    Yang, Zujun; Zhang, Tao; Bolshoy, Alexander; Beharav, Alexander; Nevo, Eviatar

    2009-05-01

    'Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum, the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the 'African' dry slope (AS) and the 'European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene (Dhn1) between the opposite slopes. We analysed 47 plants (genotypes), 4-10 individuals in each of seven stations (populations) in an area of 7000 m(2), for Dhn1 sequence diversity located in the 5' upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at 'Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force.

  4. 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...... natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches....

  5. Parameter identification of PEMFC model based on hybrid adaptive differential evolution algorithm

    International Nuclear Information System (INIS)

    Sun, Zhe; Wang, Ning; Bi, Yunrui; Srinivasan, Dipti

    2015-01-01

    In this paper, a HADE (hybrid adaptive differential evolution) algorithm is proposed for the identification problem of PEMFC (proton exchange membrane fuel cell). Inspired by biological genetic strategy, a novel adaptive scaling factor and a dynamic crossover probability are presented to improve the adaptive and dynamic performance of differential evolution algorithm. Moreover, two kinds of neighborhood search operations based on the bee colony foraging mechanism are introduced for enhancing local search efficiency. Through testing the benchmark functions, the proposed algorithm exhibits better performance in convergent accuracy and speed. Finally, the HADE algorithm is applied to identify the nonlinear parameters of PEMFC stack model. Through experimental comparison with other identified methods, the PEMFC model based on the HADE algorithm shows better performance. - Highlights: • We propose a hybrid adaptive differential evolution algorithm (HADE). • The search efficiency is enhanced in low and high dimension search space. • The effectiveness is confirmed by testing benchmark functions. • The identification of the PEMFC model is conducted by adopting HADE.

  6. 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.

  7. Queens and Workers Contribute Differently to Adaptive Evolution in Bumble Bees and Honey Bees.

    Science.gov (United States)

    Harpur, Brock A; Dey, Alivia; Albert, Jennifer R; Patel, Sani; Hines, Heather M; Hasselmann, Martin; Packer, Laurence; Zayed, Amro

    2017-09-01

    Eusociality represents a major transition in evolution and is typified by cooperative brood care and reproductive division of labor between generations. In bees, this division of labor allows queens and workers to phenotypically specialize. Worker traits associated with helping are thought to be crucial to the fitness of a eusocial lineage, and recent studies of honey bees (genus Apis) have found that adaptively evolving genes often have worker-biased expression patterns. It is unclear however if worker-biased genes are disproportionately acted on by strong positive selection in all eusocial insects. We undertook a comparative population genomics study of bumble bees (Bombus) and honey bees to quantify natural selection on queen- and worker-biased genes across two levels of social complexity. Despite sharing a common eusocial ancestor, genes, and gene groups with the highest levels of positive selection were often unique within each genus, indicating that life history and the environment, but not sociality per se, drives patterns of adaptive molecular evolution. We uncovered differences in the contribution of queen- and worker-biased genes to adaptive evolution in bumble bees versus honey bees. Unlike honey bees, where worker-biased genes are enriched for signs of adaptive evolution, genes experiencing positive selection in bumble bees were predominately expressed by reproductive foundresses during the initial solitary-founding stage of colonies. Our study suggests that solitary founding is a major selective pressure and that the loss of queen totipotency may cause a change in the architecture of selective pressures upon the social insect genome. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. 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.

  9. Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Alex Wong

    2012-09-01

    Full Text Available Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

  10. 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).

  11. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

    DEFF Research Database (Denmark)

    Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina

    2018-01-01

    Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary...... adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding...

  12. 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

    small differences. The large gap among the 11 TEs favored on the NFS was significant and supports our rejection of drift as the only explanation of the distribution of the slope differences. The gaps in the distribution of the differences separated the putative TEs with strong enough selection from those TEs that couldn't overrule the migration. The results are compared and contrasted with the directional effect of the frequencies of the same TEs in the study of global climatic comparisons across thousands of kilometers. From the 11 putative adaptive TEs in the local "Evolution Canyon," six differentiate in the same direction as in the continental comparisons and four in the opposite direction. One TE, FBti0019144, differentiated in EC in the same direction as in Australia and in the opposite direction to that of North America. We presume that the major divergent evolutionary driving force at the local EC microsite is natural selection overruling gene flow. Therefore, after we rejected drift as an explanation of all the large slope differences, we regarded them as putatively adaptive. In order to substantiate the individual TE adaptation, we need to increase the sample sizes and reveal the significant adaptive TEs. The comparison of local and global studies show only partial similarity in the adaptation of the TEs, because of the dryness of the ecologically tropical climate in EC, in contrast to the wet tropical climate in the global compared climates. Moreover, adaptation of a TE may be expressed only in part of the time and specific localities.

  13. Adaptive Patterns of Mitogenome Evolution Are Associated with the Loss of Shell Scutes in Turtles.

    Science.gov (United States)

    Escalona, Tibisay; Weadick, Cameron J; Antunes, Agostinho

    2017-10-01

    The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration. One prominent adaptation to a highly aquatic lifestyle in turtles is the secondary loss of keratenized shell scutes (i.e., soft-shells), which is associated with enhanced swimming ability and, in some species, cutaneous respiration. We used codon models to examine patterns of selection on mitochondrial protein-coding genes along the three turtle lineages that independently evolved soft-shells. We found strong evidence for positive selection along the branches leading to the pig-nosed turtle (Carettochelys insculpta) and the softshells clade (Trionychidae), but only weak evidence for the leatherback (Dermochelys coriacea) branch. Positively selected sites were found to be particularly prevalent in OXPHOS Complex I proteins, especially subunit ND2, along both positively selected lineages, consistent with convergent adaptive evolution. Structural analysis showed that many of the identified sites are within key regions or near residues involved in proton transport, indicating that positive selection may have precipitated substantial changes in mitochondrial function. Overall, our study provides evidence that physiological challenges associated with adaptation to a highly aquatic lifestyle have shaped the evolution of the turtle mitochondrial genome in a lineage-specific manner. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

    2015-09-30

    release; distribution is unlimited. Evolution of the Marginal Ice Zone: Adaptive Sampling with Autonomous Gliders Craig M. Lee, Luc Rainville and Jason I...missions in ice-covered waters , where they provide several unique capabilities. Ice-capable Seagliders can maintain persistent (many months) sampling ...irradiance. Careful calibration casts, including water sampling , were conducted during both the deployment and recovery cruises. An example of a

  15. Dancing to a Different Tune: Adaptive Evolution Fine-Tunes Protein Dynamics

    Science.gov (United States)

    2015-09-01

    efficiency at low temperatures when the enzymes from mesophilic bacteria were evolved to have stabilities as high as their thermophilic homologs. The work...wild-type enzyme . This unfolding temperature is relatively high for a non- thermophilic enzyme ,15 as mesophilic enzymes typically unfold below 60 °C...The work described in this thesis provides a case study exploring the molecular changes underlying adaptive evolution in a key allosteric enzyme . It

  16. Parameter extraction of different fuel cell models with transferred adaptive differential evolution

    International Nuclear Information System (INIS)

    Gong, Wenyin; Yan, Xuesong; Liu, Xiaobo; Cai, Zhihua

    2015-01-01

    To improve the design and control of FC (fuel cell) models, it is important to extract their unknown parameters. Generally, the parameter extraction problems of FC models can be transformed as nonlinear and multi-variable optimization problems. To extract the parameters of different FC models exactly and fast, in this paper, we propose a transferred adaptive DE (differential evolution) framework, in which the successful parameters of the adaptive DE solving previous problems are properly transferred to solve new optimization problems in the similar problem-domains. Based on this framework, an improved adaptive DE method (TRADE, in short) is presented as an illustration. To verify the performance of our proposal, TRADE is used to extract the unknown parameters of two types of fuel cell models, i.e., PEMFC (proton exchange membrane fuel cell) and SOFC (solid oxide fuel cell). The results of TRADE are also compared with those of other state-of-the-art EAs (evolutionary algorithms). Even though the modification is very simple, the results indicate that TRADE can extract the parameters of both PEMFC and SOFC models exactly and fast. Moreover, the V–I characteristics obtained by TRADE agree well with the simulated and experimental data in all cases for both types of fuel cell models. Also, it improves the performance of the original adaptive DE significantly in terms of both the quality of final solutions and the convergence speed in all cases. Additionally, TRADE is able to provide better results compared with other EAs. - Highlights: • A framework of transferred adaptive differential evolution is proposed. • Based on the framework, an improved differential evolution (TRADE) is presented. • TRADE obtains very promising results to extract the parameters of PEMFC and SOFC models

  17. Evolution of regulatory networks towards adaptability and stability in a changing environment

    Science.gov (United States)

    Lee, Deok-Sun

    2014-11-01

    Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

  18. 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.

  19. 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.

  20. Chewing on the trees: Constraints and adaptation in the evolution of the primate mandible.

    Science.gov (United States)

    Meloro, Carlo; Cáceres, Nilton Carlos; Carotenuto, Francesco; Sponchiado, Jonas; Melo, Geruza Leal; Passaro, Federico; Raia, Pasquale

    2015-07-01

    Chewing on different food types is a demanding biological function. The classic assumption in studying the shape of feeding apparatuses is that animals are what they eat, meaning that adaptation to different food items accounts for most of their interspecific variation. Yet, a growing body of evidence points against this concept. We use the primate mandible as a model structure to investigate the complex interplay among shape, size, diet, and phylogeny. We find a weak but significant impact of diet on mandible shape variation in primates as a whole but not in anthropoids and catarrhines as tested in isolation. These clades mainly exhibit allometric shape changes, which are unrelated to diet. Diet is an important factor in the diversification of strepsirrhines and platyrrhines and a phylogenetic signal is detected in all primate clades. Peaks in morphological disparity occur during the Oligocene (between 37 and 25 Ma) supporting the notion that an adaptive radiation characterized the evolution of South American monkeys. In all primate clades, the evolution of mandible size is faster than its shape pointing to a strong effect of allometry on ecomorphological diversification in this group. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

    Science.gov (United States)

    Voloch, Carolina M; Capellão, Renata T; Mello, Beatriz; Schrago, Carlos G

    2014-11-19

    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 body size subject to indirect effect in trophic cascade system.

    Science.gov (United States)

    Wang, Xin; Fan, Meng; Hao, Lina

    2017-09-01

    Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective

  4. 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.

  5. 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

    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...... 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...... of evolved strains via a number of different data types revealed the various genetic and phenotypic changes implemented in pursuit of growth optimality and how these differed across the different growth substrates and switching protocols. This work not only helps to establish general principles of adaptation...

  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

    , 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...... 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. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses.

    Science.gov (United States)

    Huang, Lin; Raats, Dina; Sela, Hanan; Klymiuk, Valentina; Lidzbarsky, Gabriel; Feng, Lihua; Krugman, Tamar; Fahima, Tzion

    2016-08-04

    The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.

  8. Adaptive evolution of the mitochondrial ND6 gene in the domestic horse.

    Science.gov (United States)

    Ning, T; Xiao, H; Li, J; Hua, S; Zhang, Y P

    2010-01-26

    Mitochondria play a crucial role in energy metabolism through oxidative phosphorylation. Organisms living at high altitudes are potentially influenced by oxygen deficits and cold temperatures. The severe environmental conditions can impact on metabolism and direct selection of mitochondrial DNA. As a wide-ranging animal, the domestic horse (Equus caballus) has developed various morphological and physiological characteristics for adapting to different altitudes. Thus, this is a good species for studying adaption to high altitudes at a molecular level. We sequenced the complete NADH dehydrogenase 6 gene (ND6) of 509 horses from 24 sampling locations. By comparative analysis of three horse populations living at different altitudes (>2200 m, 1200-1700 m, and horses was found distributed on the selected branches. We conclude that the high-altitude environment has directed adaptive evolution of the mitochondrial ND6 gene in the plateau horse.

  9. Accelerated evolution of innate immunity proteins in social insects: adaptive evolution or relaxed constraint?

    Science.gov (United States)

    Harpur, Brock A; Zayed, Amro

    2013-07-01

    The genomes of eusocial insects have a reduced complement of immune genes-an unusual finding considering that sociality provides ideal conditions for disease transmission. The following three hypotheses have been invoked to explain this finding: 1) social insects are attacked by fewer pathogens, 2) social insects have effective behavioral or 3) novel molecular mechanisms for combating pathogens. At the molecular level, these hypotheses predict that canonical innate immune pathways experience a relaxation of selective constraint. A recent study of several innate immune genes in ants and bees showed a pattern of accelerated amino acid evolution, which is consistent with either positive selection or a relaxation of constraint. We studied the population genetics of innate immune genes in the honey bee Apis mellifera by partially sequencing 13 genes from the bee's Toll pathway (∼10.5 kb) and 20 randomly chosen genes (∼16.5 kb) sequenced in 43 diploid workers. Relative to the random gene set, Toll pathway genes had significantly higher levels of amino acid replacement mutations segregating within A. mellifera and fixed between A. mellifera and A. cerana. However, levels of diversity and divergence at synonymous sites did not differ between the two gene sets. Although we detect strong signs of balancing selection on the pathogen recognition gene pgrp-sa, many of the genes in the Toll pathway show signatures of relaxed selective constraint. These results are consistent with the reduced complement of innate immune genes found in social insects and support the hypothesis that some aspect of eusociality renders canonical innate immunity superfluous.

  10. 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.

  11. Adaptive evolution of cooperation through Darwinian dynamics in Public Goods games.

    Science.gov (United States)

    Deng, Kuiying; Chu, Tianguang

    2011-01-01

    The linear or threshold Public Goods game (PGG) is extensively accepted as a paradigmatic model to approach the evolution of cooperation in social dilemmas. Here we explore the significant effect of nonlinearity of the structures of public goods on the evolution of cooperation within the well-mixed population by adopting Darwinian dynamics, which simultaneously consider the evolution of populations and strategies on a continuous adaptive landscape, and extend the concept of evolutionarily stable strategy (ESS) as a coalition of strategies that is both convergent-stable and resistant to invasion. Results show (i) that in the linear PGG contributing nothing is an ESS, which contradicts experimental data, (ii) that in the threshold PGG contributing the threshold value is a fragile ESS, which cannot resist the invasion of contributing nothing, and (iii) that there exists a robust ESS of contributing more than half in the sigmoid PGG if the return rate is relatively high. This work reveals the significant effect of the nonlinearity of the structures of public goods on the evolution of cooperation, and suggests that, compared with the linear or threshold PGG, the sigmoid PGG might be a more proper model for the evolution of cooperation within the well-mixed population.

  12. 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.

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

    Science.gov (United States)

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

    2006-01-01

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

  14. Natural Selection Causes Adaptive Genetic Resistance in Wild Emmer Wheat against Powdery Mildew at ?Evolution Canyon? Microsite, Mt. Carmel, Israel

    OpenAIRE

    Yin, Huayan; Ben-Abu, Yuval; Wang, Hongwei; Li, Anfei; Nevo, Eviatar; Kong, Lingrang

    2015-01-01

    Background ?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), sep...

  15. 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.

    2015-01-01

    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. PMID:26170282

  16. Biological adaptations for functional features of language in the face of cultural evolution.

    Science.gov (United States)

    Christiansen, Morten H; Reali, Florencia; Chater, Nick

    2011-04-01

    Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

  17. 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.

  18. 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.

  19. 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.

  20. Evolution dynamics of a model for gene duplication under adaptive conflict

    Science.gov (United States)

    Ancliff, Mark; Park, Jeong-Man

    2014-06-01

    We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

  1. 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

    2012-12-07

    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.

  2. 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

  3. 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.

  4. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

    DEFF Research Database (Denmark)

    Zepeda Mendoza, M. Lisandra; Xiong, Zijun; Escalera-Zamudio, Marina

    2018-01-01

    Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary...... integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis...

  5. A Self-Adaptive Evolutionary Approach to the Evolution of Aesthetic Maps for a RTS Game

    OpenAIRE

    Lara-Cabrera, Raúl; Cotta, Carlos; Fernández-Leiva, Antonio J.

    2014-01-01

    Procedural content generation (PCG) is a research eld on the rise,with numerous papers devoted to this topic. This paper presents a PCG method based on a self-adaptive evolution strategy for the automatic generation of maps for the real-time strategy (RTS) game PlanetWars. These maps are generated in order to ful ll the aesthetic preferences of the user, as implied by her assessment of a collection of maps used as training set. A topological approach is used for the characterization of th...

  6. Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.

    Science.gov (United States)

    Kelleher, Philip; Bottacini, Francesca; Mahony, Jennifer; Kilcawley, Kieran N; van Sinderen, Douwe

    2017-03-29

    Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.

  7. Design of 2-D Recursive Filters Using Self-adaptive Mutation Differential Evolution Algorithm

    Directory of Open Access Journals (Sweden)

    Lianghong Wu

    2011-08-01

    Full Text Available This paper investigates a novel approach to the design of two-dimensional recursive digital filters using differential evolution (DE algorithm. The design task is reformulated as a constrained minimization problem and is solved by an Self-adaptive Mutation DE algorithm (SAMDE, which adopts an adaptive mutation operator that combines with the advantages of the DE/rand/1/bin strategy and the DE/best/2/bin strategy. As a result, its convergence performance is improved greatly. Numerical experiment results confirm the conclusion. The proposedSAMDE approach is effectively applied to test a numerical example and is compared with previous design methods. The computational experiments show that the SAMDE approach can obtain better results than previous design methods.

  8. 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.

  9. 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.

  10. Evolution of the Gondwanaland Archaean Shield: ion microprobe zircon dating and southwestern Australia/Wilkes Land, Antartica

    International Nuclear Information System (INIS)

    Lovering, J.F.; Comaford, D.J.

    1979-01-01

    The ion microprobe has been used to study 207 Pb/ 206 Pb ages on 20μm-sized sites on single zircon grains from coastal rocks on either side of the rift in the Gondwanaland Archaean Shield between southwestern Australia and Wilkes Land, Antarctica. The ages on individual sites on zircon grains from a variety of rock types from southwestern Australia show a range from 1600 m.y. to about 3400 m.y., with an inverse dependence on the uranium abundance at each site. Ages of zircons from rocks from the Antartic region show a range from 1600 m.y. to 3100 m.y

  11. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.

    Science.gov (United States)

    Lyu, Haomin; He, Ziwen; Wu, Chung-I; Shi, Suhua

    2018-01-01

    Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  12. 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.

  13. An adaptive left–right eigenvector evolution algorithm for vibration isolation control

    International Nuclear Information System (INIS)

    Wu, T Y

    2009-01-01

    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

  14. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation.

    Science.gov (United States)

    Lande, Russell

    2009-07-01

    Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

  15. 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.

  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. 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.

  18. 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.

  19. 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.

    2013-01-01

    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 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. PMID:24297900

  20. A Bayesian Network Based Adaptability Design of Product Structures for Function Evolution

    Directory of Open Access Journals (Sweden)

    Shaobo Li

    2018-03-01

    Full Text Available Structure adaptability design is critical for function evolution in product families, in which many structural and functional design factors are intertwined together with manufacturing cost, customer satisfaction, and final market sales. How to achieve a delicate balance among all of these factors to maximize the market performance of the product is too complicated to address based on traditional domain experts’ knowledge or some ad hoc heuristics. Here, we propose a quantitative product evolution design model that is based on Bayesian networks to model the dynamic relationship between customer needs and product structure design. In our model, all of the structural or functional features along with customer satisfaction, manufacturing cost, sale price, market sales, and indirect factors are modeled as random variables denoted as nodes in the Bayesian networks. The structure of the Bayesian model is then determined based on the historical data, which captures the dynamic sophisticated relationship of customer demands of a product, structural design, and market performance. Application of our approach to an electric toothbrush product family evolution design problem shows that our model allows for designers to interrogate with the model and obtain theoretical and decision support for dynamic product feature design process.

  1. The evolution model of Uppsala in light of the complex adaptive systems approach

    Directory of Open Access Journals (Sweden)

    Rennaly Alves da Silva

    2013-11-01

    Full Text Available The behavioral approach to the internationalization of companies explains that the movements toward external markets occur in accordance with the increasing commitment of resources to mitigate the effects of uncertainty and reduce the perception of risk. Evidence indicates that the theories and practices developed in the domestic market may not be able to explain the reality of companies that operate in international markets. Thus, the Paradigm of Complexity presents itself as a comprehensive alternative to realize the relationships within organizations and markets. Accordingly, the aim of this theoretical paper is to analyze the evolution of the Uppsala Model between years 1975 and 2010 with the understanding of the companies in the process of internationalization as Complex Adaptive Systems, in accordance with the Model Kelly and Allison (1998. Four propositions are presented that show the links between the approaches. The most surprising is the perception that the conceptual evolution of the Uppsala Model seems to accompany the evolution of complexity levels, presented in Model Kelly and Allison.

  2. Adaptive Evolution of the Myo6 Gene in Old World Fruit Bats (Family: Pteropodidae)

    Science.gov (United States)

    Shen, Bin; Han, Xiuqun; Jones, Gareth; Rossiter, Stephen J.; Zhang, Shuyi

    2013-01-01

    Myosin VI (encoded by the Myo6 gene) is highly expressed in the inner and outer hair cells of the ear, retina, and polarized epithelial cells such as kidney proximal tubule cells and intestinal enterocytes. The Myo6 gene is thought to be involved in a wide range of physiological functions such as hearing, vision, and clathrin-mediated endocytosis. Bats (Chiroptera) represent one of the most fascinating mammal groups for molecular evolutionary studies of the Myo6 gene. A diversity of specialized adaptations occur among different bat lineages, such as echolocation and associated high-frequency hearing in laryngeal echolocating bats, large eyes and a strong dependence on vision in Old World fruit bats (Pteropodidae), and specialized high-carbohydrate but low-nitrogen diets in both Old World and New World fruit bats (Phyllostomidae). To investigate what role(s) the Myo6 gene might fulfill in bats, we sequenced the coding region of the Myo6 gene in 15 bat species and used molecular evolutionary analyses to detect evidence of positive selection in different bat lineages. We also conducted real-time PCR assays to explore the expression levels of Myo6 in a range of tissues from three representative bat species. Molecular evolutionary analyses revealed that the Myo6 gene, which was widely considered as a hearing gene, has undergone adaptive evolution in the Old World fruit bats which lack laryngeal echolocation and associated high-frequency hearing. Real-time PCR showed the highest expression level of the Myo6 gene in the kidney among ten tissues examined in three bat species, indicating an important role for this gene in kidney function. We suggest that Myo6 has undergone adaptive evolution in Old World fruit bats in relation to receptor-mediated endocytosis for the preservation of protein and essential nutrients. PMID:23620821

  3. Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes.

    Science.gov (United States)

    Torres-Dowdall, Julián; Pierotti, Michele E R; Härer, Andreas; Karagic, Nidal; Woltering, Joost M; Henning, Frederico; Elmer, Kathryn R; Meyer, Axel

    2017-10-01

    Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only a few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted toward shorter wavelengths compared with the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding.

    Science.gov (United States)

    Shenoi, V N; Ali, S Z; Prasad, N G

    2016-02-01

    In holometabolous animals such as Drosophila melanogaster, larval crowding can affect a wide range of larval and adult traits. Adults emerging from high larval density cultures have smaller body size and increased mean life span compared to flies emerging from low larval density cultures. Therefore, adaptation to larval crowding could potentially affect adult longevity as a correlated response. We addressed this issue by studying a set of large, outbred populations of D. melanogaster, experimentally evolved for adaptation to larval crowding for 83 generations. We assayed longevity of adult flies from both selected (MCUs) and control populations (MBs) after growing them at different larval densities. We found that MCUs have evolved increased mean longevity compared to MBs at all larval densities. The interaction between selection regime and larval density was not significant, indicating that the density dependence of mean longevity had not evolved in the MCU populations. The increase in longevity in MCUs can be partially attributed to their lower rates of ageing. It is also noteworthy that reaction norm of dry body weight, a trait probably under direct selection in our populations, has indeed evolved in MCU populations. To the best of our knowledge, this is the first report of the evolution of adult longevity as a correlated response of adaptation to larval crowding. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  5. Genetic evolution, plasticity, and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: A quantitative genetic model.

    Science.gov (United States)

    Tufto, Jarle

    2015-08-01

    Adaptive responses to autocorrelated environmental fluctuations through evolution in mean reaction norm elevation and slope and an independent component of the phenotypic variance are analyzed using a quantitative genetic model. Analytic approximations expressing the mutual dependencies between all three response modes are derived and solved for the joint evolutionary outcome. Both genetic evolution in reaction norm elevation and plasticity are favored by slow temporal fluctuations, with plasticity, in the absence of microenvironmental variability, being the dominant evolutionary outcome for reasonable parameter values. For fast fluctuations, tracking of the optimal phenotype through genetic evolution and plasticity is limited. If residual fluctuations in the optimal phenotype are large and stabilizing selection is strong, selection then acts to increase the phenotypic variance (bet-hedging adaptive). Otherwise, canalizing selection occurs. If the phenotypic variance increases with plasticity through the effect of microenvironmental variability, this shifts the joint evolutionary balance away from plasticity in favor of genetic evolution. If microenvironmental deviations experienced by each individual at the time of development and selection are correlated, however, more plasticity evolves. The adaptive significance of evolutionary fluctuations in plasticity and the phenotypic variance, transient evolution, and the validity of the analytic approximations are investigated using simulations. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  6. Phases and Actions of the Evolution of the Concept of Quality in Canada and Australia – A Theoretical Modelling of the Development of Knowledge in Business Performance in the XXI Century - The Approach to Excellence

    Directory of Open Access Journals (Sweden)

    Cristina Raluca Popescu

    2015-05-01

    Full Text Available In the paper “Phases and Actions of the Evolution of the Concept of Quality in Canada and Australia – A Theoretical Modelling of the Development of Knowledge in Business Performance in the XXI Century - The Approach to Excellence” the authors present the basic features of the phases and actions of the evolution of the concept of quality in Canada and Australia, as a theoretical modelling of the development of knowledge in business performance in the XXI century in order to improve the organizational processes so that excellence can be achieved.

  7. 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......, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically...... dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known...

  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 eunuch phenomenon: adaptive evolution of genital emasculation in sexually dimorphic spiders.

    Science.gov (United States)

    Kuntner, Matjaž; Agnarsson, Ingi; Li, Daiqin

    2015-02-01

    Under natural and sexual selection traits often evolve that secure paternity or maternity through self-sacrifice to predators, rivals, offspring, or partners. Emasculation-males removing their genitals-is an unusual example of such behaviours. Known only in insects and spiders, the phenomenon's adaptiveness is difficult to explain, yet its repeated origins and association with sexual size dimorphism (SSD) and sexual cannibalism suggest an adaptive significance. In spiders, emasculation of paired male sperm-transferring organs - secondary genitals - (hereafter, palps), results in 'eunuchs'. This behaviour has been hypothesized to be adaptive because (i) males plug female genitals with their severed palps (plugging hypothesis), (ii) males remove their palps to become better fighters in male-male contests (better-fighter hypothesis), perhaps reaching higher agility due to reduced total body mass (gloves-off hypothesis), and (iii) males achieve prolonged sperm transfer through severed genitals (remote-copulation hypothesis). Prior research has provided evidence in support of these hypotheses in some orb-weaving spiders but these explanations are far from general. Seeking broad macroevolutionary patterns of spider emasculation, we review the known occurrences, weigh the evidence in support of the hypotheses in each known case, and redefine more precisely the particular cases of emasculation depending on its timing in relation to maturation and mating: 'pre-maturation', 'mating', and 'post-mating'. We use a genus-level spider phylogeny to explore emasculation evolution and to investigate potential evolutionary linkage between emasculation, SSD, lesser genital damage (embolic breakage), and sexual cannibalism (females consuming their mates). We find a complex pattern of spider emasculation evolution, all cases confined to Araneoidea: emasculation evolved at least five and up to 11 times, was lost at least four times, and became further modified at least once. We also find

  10. 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.

  11. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes.

    Science.gov (United States)

    Koonin, Eugene V; Makarova, Kira S

    2013-05-01

    The CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR-associated genes) is an adaptive immunity system in bacteria and archaea that functions via a distinct self-non-self recognition mechanism that is partially analogous to the mechanism of eukaryotic RNA interference (RNAi). The CRISPR-Cas system incorporates fragments of virus or plasmid DNA into the CRISPR repeat cassettes and employs the processed transcripts of these spacers as guide RNAs to cleave the cognate foreign DNA or RNA. The Cas proteins, however, are not homologous to the proteins involved in RNAi and comprise numerous, highly diverged families. The majority of the Cas proteins contain diverse variants of the RNA recognition motif (RRM), a widespread RNA-binding domain. Despite the fast evolution that is typical of the cas genes, the presence of diverse versions of the RRM in most Cas proteins provides for a simple scenario for the evolution of the three distinct types of CRISPR-cas systems. In addition to several proteins that are directly implicated in the immune response, the cas genes encode a variety of proteins that are homologous to prokaryotic toxins that typically possess nuclease activity. The predicted toxins associated with CRISPR-Cas systems include the essential Cas2 protein, proteins of COG1517 that, in addition to a ligand-binding domain and a helix-turn-helix domain, typically contain different nuclease domains and several other predicted nucleases. The tight association of the CRISPR-Cas immunity systems with predicted toxins that, upon activation, would induce dormancy or cell death suggests that adaptive immunity and dormancy/suicide response are functionally coupled. Such coupling could manifest in the persistence state being induced and potentially providing conditions for more effective action of the immune system or in cell death being triggered when immunity fails.

  12. Trickle-down evolution: an approach to getting major evolutionary adaptive changes into textbooks and curricula.

    Science.gov (United States)

    Padian, Kevin

    2008-08-01

    Although contemporary high school and college textbooks of biology generally cover the principles and data of microevolution (genetic and populational change) and speciation rather well, coverage of what is known of the major changes in evolution (macroevolution), and how the evidence is understood is generally poor to nonexistent. It is critical to improve this because acceptance of evolution by the American public rests on the understanding of how we know what we know about the emergence of major new taxonomic groups, and about their adaptations, behaviors, and ecologies in geologic time. An efficient approach to this problem is to improve the illustrations in college textbooks to show the consilience of different lines of fossil, morphological, and molecular evidence mapped on phylogenies. Such "evograms" will markedly improve traditional illustrations of phylogenies, "menageries," and "companatomies." If "evograms" are installed at the college level, the basic principles and evidence of macroevolution will be more likely taught in K-12, thus providing an essential missing piece in biological education.

  13. Evolution of phenotypic clusters through competition and local adaptation along an environmental gradient.

    Science.gov (United States)

    Leimar, Olof; Doebeli, Michael; Dieckmann, Ulf

    2008-04-01

    We have analyzed the evolution of a quantitative trait in populations that are spatially extended along an environmental gradient, with gene flow between nearby locations. In the absence of competition, there is stabilizing selection toward a locally best-adapted trait that changes gradually along the gradient. According to traditional ideas, gradual spatial variation in environmental conditions is expected to lead to gradual variation in the evolved trait. A contrasting possibility is that the trait distribution instead breaks up into discrete clusters. Doebeli and Dieckmann (2003) argued that competition acting locally in trait space and geographical space can promote such clustering. We have investigated this possibility using deterministic population dynamics for asexual populations, analyzing our model numerically and through an analytical approximation. We examined how the evolution of clusters is affected by the shape of competition kernels, by the presence of Allee effects, and by the strength of gene flow along the gradient. For certain parameter ranges clustering was a robust outcome, and for other ranges there was no clustering. Our analysis shows that the shape of competition kernels is important for clustering: the sign structure of the Fourier transform of a competition kernel determines whether the kernel promotes clustering. Also, we found that Allee effects promote clustering, whereas gene flow can have a counteracting influence. In line with earlier findings, we could demonstrate that phenotypic clustering was favored by gradients of intermediate slope.

  14. Evolution of vertebrate adaptive immunity: immune cells and tissues, and AID/APOBEC cytidine deaminases.

    Science.gov (United States)

    Hirano, Masayuki

    2015-08-01

    All surviving jawed vertebrate representatives achieve diversity in immunoglobulin-based B and T cell receptors for antigen recognition through recombinatorial rearrangement of V(D)J segments. However, the extant jawless vertebrates, lampreys and hagfish, instead generate three types of variable lymphocyte receptors (VLRs) through a template-mediated combinatorial assembly of different leucine-rich repeat (LRR) sequences. The clonally diverse VLRB receptors are expressed by B-like lymphocytes, while the VLRA and VLRC receptors are expressed by lymphocyte lineages that resemble αβ and γδ T lymphocytes, respectively. These findings suggest that three basic types of lymphocytes, one B-like and two T-like, are an essential feature of vertebrate adaptive immunity. Around 500 million years ago, a common ancestor of jawed and jawless vertebrates evolved a genetic program for the development of prototypic lymphoid cells as a foundation for an adaptive immune system. This acquisition preceded the convergent evolution of alternative types of clonally diverse receptors for antigens in all vertebrates, as reviewed in this article. © 2015 WILEY Periodicals, Inc.

  15. Genome-wide signatures of complex introgression and adaptive evolution in the big cats

    Science.gov (United States)

    Figueiró, Henrique V.; Li, Gang; Trindade, Fernanda J.; Assis, Juliana; Pais, Fabiano; Fernandes, Gabriel; Santos, Sarah H. D.; Hughes, Graham M.; Komissarov, Aleksey; Antunes, Agostinho; Trinca, Cristine S.; Rodrigues, Maíra R.; Linderoth, Tyler; Bi, Ke; Silveira, Leandro; Azevedo, Fernando C. C.; Kantek, Daniel; Ramalho, Emiliano; Brassaloti, Ricardo A.; Villela, Priscilla M. S.; Nunes, Adauto L. V.; Teixeira, Rodrigo H. F.; Morato, Ronaldo G.; Loska, Damian; Saragüeta, Patricia; Gabaldón, Toni; Teeling, Emma C.; O’Brien, Stephen J.; Nielsen, Rasmus; Coutinho, Luiz L.; Oliveira, Guilherme; Murphy, William J.; Eizirik, Eduardo

    2017-01-01

    The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. PMID:28776029

  16. Adaptive evolution of defense ability leads to diversification of prey species.

    Science.gov (United States)

    Zu, Jian; Wang, Jinliang; Du, Jianqiang

    2014-06-01

    In this paper, by using the adaptive dynamics approach, we investigate how the adaptive evolution of defense ability promotes the diversity of prey species in an initial one-prey-two-predator community. We assume that the prey species can evolve to a safer strategy such that it can reduce the predation risk, but a prey with a high defense ability for one predator may have a low defense ability for the other and vice versa. First, by using the method of critical function analysis, we find that if the trade-off is convex in the vicinity of the evolutionarily singular strategy, then this singular strategy is a continuously stable strategy. However, if the trade-off is weakly concave near the singular strategy and the competition between the two predators is relatively weak, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the prey strategy, if the trade-off curve is globally concave, then the prey species might eventually evolve into two specialists, each caught by only one predator species. However, if the trade-off curve is convex-concave-convex, the prey species might eventually branch into two partial specialists, each being caught by both of the two predators and they can stably coexist on the much longer evolutionary timescale.

  17. Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

    Science.gov (United States)

    Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

    2015-06-01

    Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

  18. The ALICE-HMPID Detector Control System: Its evolution towards an expert and adaptive system

    Science.gov (United States)

    De Cataldo, G.; Franco, A.; Pastore, C.; Sgura, I.; Volpe, G.

    2011-05-01

    The High Momentum Particle IDentification (HMPID) detector is a proximity focusing Ring Imaging Cherenkov (RICH) for charged hadron identification. The HMPID is based on liquid C 6F 14 as the radiator medium and on a 10 m 2 CsI coated, pad segmented photocathode of MWPCs for UV Cherenkov photon detection. To ensure full remote control, the HMPID is equipped with a detector control system (DCS) responding to industrial standards for robustness and reliability. It has been implemented using PVSS as Slow Control And Data Acquisition (SCADA) environment, Programmable Logic Controller as control devices and Finite State Machines for modular and automatic command execution. In the perspective of reducing human presence at the experiment site, this paper focuses on DCS evolution towards an expert and adaptive control system, providing, respectively, automatic error recovery and stable detector performance. HAL9000, the first prototype of the HMPID expert system, is then presented. Finally an analysis of the possible application of the adaptive features is provided.

  19. The ALICE-HMPID Detector Control System: Its evolution towards an expert and adaptive system

    International Nuclear Information System (INIS)

    De Cataldo, G.; Franco, A.; Pastore, C.; Sgura, I.; Volpe, G.

    2011-01-01

    The High Momentum Particle IDentification (HMPID) detector is a proximity focusing Ring Imaging Cherenkov (RICH) for charged hadron identification. The HMPID is based on liquid C 6 F 14 as the radiator medium and on a 10 m 2 CsI coated, pad segmented photocathode of MWPCs for UV Cherenkov photon detection. To ensure full remote control, the HMPID is equipped with a detector control system (DCS) responding to industrial standards for robustness and reliability. It has been implemented using PVSS as Slow Control And Data Acquisition (SCADA) environment, Programmable Logic Controller as control devices and Finite State Machines for modular and automatic command execution. In the perspective of reducing human presence at the experiment site, this paper focuses on DCS evolution towards an expert and adaptive control system, providing, respectively, automatic error recovery and stable detector performance. HAL9000, the first prototype of the HMPID expert system, is then presented. Finally an analysis of the possible application of the adaptive features is provided.

  20. 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.

  1. 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 c...... targets for additional ameliorating mutations. Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future implementation of ALE as a tool for scientific research and engineering....

  2. Future Scenarios as a Research Tool: Investigating Climate Change Impacts, Adaptation Options and Outcomes for the Great Barrier Reef, Australia.

    Science.gov (United States)

    Evans, Louisa S; Hicks, Christina C; Fidelman, Pedro; Tobin, Renae C; Perry, Allison L

    2013-01-01

    Climate change is a significant future driver of change in coastal social-ecological systems. Our knowledge of impacts, adaptation options, and possible outcomes for marine environments and coastal industries is expanding, but remains limited and uncertain. Alternative scenarios are a way to explore potential futures under a range of conditions. We developed four alternative future scenarios for the Great Barrier Reef and its fishing and tourism industries positing moderate and more extreme (2-3 °C above pre-industrial temperatures) warming for 2050 and contrasting 'limited' and 'ideal' ecological and social adaptation. We presented these scenarios to representatives of key stakeholder groups to assess the perceived viability of different social adaptation options to deliver desirable outcomes under varied contexts.

  3. 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...

  4. Geodynamic evolution of the West and Central Pilbara Craton in Western Australia : a mid-Archaean active continental margin

    NARCIS (Netherlands)

    Beintema, K.A.

    2003-01-01

    The Archaean era lasted for about one third of the Earth's history, from ca 4.0 until 2.5 billion years ago. Because the Archaean spans such a long time, knowledge about this era is for understanding the evolution of the Earth until the present day, especially because it is the time offormation of

  5. Geodynamic evolution of the West and Central Pilbara Craton in Western Australia : a mid-Archaean active continental margin

    NARCIS (Netherlands)

    Beintema, K.A.

    2003-01-01

    The Archaean era lasted for about one third of the Earth's history, from ca 4.0 until 2.5 billion years ago. Because the Archaean spans such a long time, knowledge about this era is for understanding the evolution of the Earth until the present day, especially because it is the time

  6. Adaptive laboratory evolution of ethanologenic Zymomonas mobilis strain tolerant to furfural and acetic acid inhibitors.

    Science.gov (United States)

    Shui, Zong-Xia; Qin, Han; Wu, Bo; Ruan, Zhi-yong; Wang, Lu-shang; Tan, Fu-Rong; Wang, Jing-Li; Tang, Xiao-Yu; Dai, Li-Chun; Hu, Guo-Quan; He, Ming-Xiong

    2015-07-01

    Furfural and acetic acid from lignocellulosic hydrolysates are the prevalent inhibitors to Zymomonas mobilis during cellulosic ethanol production. Developing a strain tolerant to furfural or acetic acid inhibitors is difficul by using rational engineering strategies due to poor understanding of their underlying molecular mechanisms. In this study, strategy of adaptive laboratory evolution (ALE) was used for development of a furfural and acetic acid-tolerant strain. After three round evolution, four evolved mutants (ZMA7-2, ZMA7-3, ZMF3-2, and ZMF3-3) that showed higher growth capacity were successfully obtained via ALE method. Based on the results of profiling of cell growth, glucose utilization, ethanol yield, and activity of key enzymes, two desired strains, ZMA7-2 and ZMF3-3, were achieved, which showed higher tolerance under 7 g/l acetic acid and 3 g/l furfural stress condition. Especially, it is the first report of Z. mobilis strain that could tolerate higher furfural. The best strain, Z. mobilis ZMF3-3, has showed 94.84% theoretical ethanol yield under 3-g/l furfural stress condition, and the theoretical ethanol yield of ZM4 is only 9.89%. Our study also demonstrated that ALE method might also be used as a powerful metabolic engineering tool for metabolic engineering in Z. mobilis. Furthermore, the two best strains could be used as novel host for further metabolic engineering in cellulosic ethanol or future biorefinery. Importantly, the two strains may also be used as novel-tolerant model organisms for the genetic mechanism on the "omics" level, which will provide some useful information for inverse metabolic engineering.

  7. 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

  8. Evolution of motion uncertainty in rectal cancer: implications for adaptive radiotherapy

    Science.gov (United States)

    Kleijnen, Jean-Paul J. E.; van Asselen, Bram; Burbach, Johannes P. M.; Intven, Martijn; Philippens, Marielle E. P.; Reerink, Onne; Lagendijk, Jan J. W.; Raaymakers, Bas W.

    2016-01-01

    Reduction of motion uncertainty by applying adaptive radiotherapy strategies depends largely on the temporal behavior of this motion. To fully optimize adaptive strategies, insight into target motion is needed. The purpose of this study was to analyze stability and evolution in time of motion uncertainty of both the gross tumor volume (GTV) and clinical target volume (CTV) for patients with rectal cancer. We scanned 16 patients daily during one week, on a 1.5 T MRI scanner in treatment position, prior to each radiotherapy fraction. Single slice sagittal cine MRIs were made at the beginning, middle, and end of each scan session, for one minute at 2 Hz temporal resolution. GTV and CTV motion were determined by registering a delineated reference frame to time-points later in time. The 95th percentile of observed motion (dist95%) was taken as a measure of motion. The stability of motion in time was evaluated within each cine-MRI separately. The evolution of motion was investigated between the reference frame and the cine-MRIs of a single scan session and between the reference frame and the cine-MRIs of several days later in the course of treatment. This observed motion was then converted into a PTV-margin estimate. Within a one minute cine-MRI scan, motion was found to be stable and small. Independent of the time-point within the scan session, the average dist95% remains below 3.6 mm and 2.3 mm for CTV and GTV, respectively 90% of the time. We found similar motion over time intervals from 18 min to 4 days. When reducing the time interval from 18 min to 1 min, a large reduction in motion uncertainty is observed. A reduction in motion uncertainty, and thus the PTV-margin estimate, of 71% and 75% for CTV and tumor was observed, respectively. Time intervals of 15 and 30 s yield no further reduction in motion uncertainty compared to a 1 min time interval.

  9. 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.

  10. 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 Δ mutS lesion was repaired in representative L. casei 12A and ATCC 334 Δ mutS 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 Δ mutS derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the L. casei 12A-adapted Δ mutS 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 Δ mutS 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

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

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    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

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

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    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

  13. 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

    2018-04-01

    We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 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 10 3 and 10 5 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.

  14. Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes).

    Science.gov (United States)

    Arbour, J H; López-Fernández, H

    2014-11-01

    Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  15. Environmental tracers as indicators of groundwater flow and evolution in a fractured rock aquifer, Clare Valley, South Australia

    International Nuclear Information System (INIS)

    Love, A.J.; Cook, P.G.; Herczeg, A.L.; Simmons, C.T.

    1999-01-01

    Environmental tracers, chemistry and hydraulic data have been used to develop a conceptual model for groundwater flow in a fractured rock aquifer, at Clare, South Australia. In the upper 36 m there is relatively high horizontal flow, closely spaced fractures and large apertures. Below 36 m, horizontal flow rates are less and apertures become smaller. A sub horizontal fracture at 36 m separates the upper system from flow systems below. There is minimum vertical connection of groundwater above and below 36 m as indicated by low hydraulic conductivity and a steep 14 C concentration gradient. The observed linear trends in chemistry and isotope data are a result of mixing between old saline water and relatively younger fresh water. Greater mixing has occurred in the upper 36 m, with the amount of mixing diminishing with depth. We propose that this mixing is a recent process that has been triggered as a result of increased recharge to the system since the clearing of native vegetation approximately 100 years ago. Increased recharge of lower salinity water has resulted in the establishment of concentration gradients between the matrix and the fractures. This has resulted in diffusion of relatively immobile water in the matrix into relatively fast moving water in the fractures. Greater flushing has occurred in the upper 36 m due greater fracture density and larger apertures and higher horizontal flow rates. (author)

  16. 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.

    2015-01-01

    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. PMID:25548182

  17. 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.

  18. Evolution of static allometries: adaptive change in allometric slopes of eye span in stalk-eyed flies.

    Science.gov (United States)

    Voje, Kjetil L; Hansen, Thomas F

    2013-02-01

    Julian Huxley showed that within-species (static) allometric (power-law) relations can arise from proportional growth regulation with the exponent in the power law equaling the factor of proportionality. Allometric exponents may therefore be hard to change and act as constraints on the independent evolution of traits. In apparent contradiction to this, many empirical studies have concluded that static allometries are evolvable. Many of these studies have been based, however, on a broad definition of allometry that includes any monotonic shape change with size, and do not falsify the hypothesis of constrained narrow-sense allometry. Here, we present the first phylogenetic comparative study of narrow-sense allometric exponents based on a reanalysis of data on eye span and body size in stalk-eyed flies (Diopsidae). Consistent with a role in sexual selection, we found strong evidence that male slopes were tracking "optima" based on sexual dimorphism and relative male trait size. This tracking was slow, however, with estimated times of 2-3 million years for adaptation to exceed ancestral influence on the trait. Our results are therefore consistent with adaptive evolution on million-year time scales, but cannot rule out that static allometry may act as a constraint on eye-span adaptation at shorter time scales. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  19. Adaptive evolution of a key gene affecting queen and worker traits in the honey bee, Apis mellifera.

    Science.gov (United States)

    Kent, Clement F; Issa, Amer; Bunting, Alexandra C; Zayed, Amro

    2011-12-01

    The vitellogenin egg yolk precursor protein represents a well-studied case of social pleiotropy in the model organism Apis mellifera. Vitellogenin is associated with fecundity in queens and plays a major role in controlling division of labour in workers, thereby affecting both individual and colony-level fitness. We studied the molecular evolution of vitellogenin and seven other genes sequenced in a large population panel of Apis mellifera and several closely related species to investigate the role of social pleiotropy on adaptive protein evolution. We found a significant excess of nonsynonymous fixed differences between A. mellifera, A. cerana and A. florea relative to synonymous sites indicating high rates of adaptive evolution at vitellogenin. Indeed, 88% of amino acid changes were fixed by selection in some portions of the gene. Further, vitellogenin exhibited hallmark signatures of selective sweeps in A. mellifera, including a significant skew in the allele frequency spectrum, extreme levels of genetic differentiation and linkage disequilibrium. Finally, replacement polymorphisms in vitellogenin were significantly enriched in parts of the protein involved in binding lipid, establishing a link between the gene's structure, function and effects on fitness. Our case study provides unequivocal evidence of historical and ongoing bouts of adaptive evolution acting on a key socially pleiotropic gene in the honey bee. © 2011 Blackwell Publishing Ltd.

  20. Adaptation and convergent evolution within the Jamesonia-Eriosorus complex in high-elevation biodiverse Andean hotspots.

    Science.gov (United States)

    Sánchez-Baracaldo, Patricia; Thomas, Gavin H

    2014-01-01

    The recent uplift of the tropical Andes (since the late Pliocene or early Pleistocene) provided extensive ecological opportunity for evolutionary radiations. We test for phylogenetic and morphological evidence of adaptive radiation and convergent evolution to novel habitats (exposed, high-altitude páramo habitats) in the Andean fern genera Jamesonia and Eriosorus. We construct time-calibrated phylogenies for the Jamesonia-Eriosorus clade. We then use recent phylogenetic comparative methods to test for evolutionary transitions among habitats, associations between habitat and leaf morphology, and ecologically driven variation in the rate of morphological evolution. Páramo species (Jamesonia) display morphological adaptations consistent with convergent evolution in response to the demands of a highly exposed environment but these adaptations are associated with microhabitat use rather than the páramo per se. Species that are associated with exposed microhabitats (including Jamesonia and Eriorsorus) are characterized by many but short pinnae per frond whereas species occupying sheltered microhabitats (primarily Eriosorus) have few but long pinnae per frond. Pinnae length declines more rapidly with altitude in sheltered species. Rates of speciation are significantly higher among páramo than non-páramo lineages supporting the hypothesis of adaptation and divergence in the unique Páramo biodiversity hotspot.

  1. 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 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.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.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.

  2. Hydrochemical evolution and groundwater flow processes in the Galilee and Eromanga basins, Great Artesian Basin, Australia: a multivariate statistical approach.

    Science.gov (United States)

    Moya, Claudio E; Raiber, Matthias; Taulis, Mauricio; Cox, Malcolm E

    2015-03-01

    The Galilee and Eromanga basins are sub-basins of the Great Artesian Basin (GAB). In this study, a multivariate statistical approach (hierarchical cluster analysis, principal component analysis and factor analysis) is carried out to identify hydrochemical patterns and assess the processes that control hydrochemical evolution within key aquifers of the GAB in these basins. The results of the hydrochemical assessment are integrated into a 3D geological model (previously developed) to support the analysis of spatial patterns of hydrochemistry, and to identify the hydrochemical and hydrological processes that control hydrochemical variability. In this area of the GAB, the hydrochemical evolution of groundwater is dominated by evapotranspiration near the recharge area resulting in a dominance of the Na-Cl water types. This is shown conceptually using two selected cross-sections which represent discrete groundwater flow paths from the recharge areas to the deeper parts of the basins. With increasing distance from the recharge area, a shift towards a dominance of carbonate (e.g. Na-HCO3 water type) has been observed. The assessment of hydrochemical changes along groundwater flow paths highlights how aquifers are separated in some areas, and how mixing between groundwater from different aquifers occurs elsewhere controlled by geological structures, including between GAB aquifers and coal bearing strata of the Galilee Basin. The results of this study suggest that distinct hydrochemical differences can be observed within the previously defined Early Cretaceous-Jurassic aquifer sequence of the GAB. A revision of the two previously recognised hydrochemical sequences is being proposed, resulting in three hydrochemical sequences based on systematic differences in hydrochemistry, salinity and dominant hydrochemical processes. The integrated approach presented in this study which combines different complementary multivariate statistical techniques with a detailed assessment of the

  3. 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.

  4. Growth, water use efficiency, and adaptive features of the tree legume tagasaste (Chamaecytisus proliferus Link.) on deep sands in south-western Australia

    International Nuclear Information System (INIS)

    Lefroy, E. C.; Pate, J. S.

    2001-01-01

    Four-year-old tagasaste trees in dense plantation and wide-spaced alley cropping layouts at Moora, Western Australia, were cut back to 0.6 m high and their patterns of coppice regrowth and water use monitored over 3 years. Trees reached a permanent fresh watertable at 5 m depth by means of deeply penetrating sinker roots. Dry matter (DM) accumulation and transpiration loss were closely similar at the 2 planting densities despite higher soil water contents in alley plots. Yearly transpiration at plantation density amounted to 0.55 and 0.63 of Penman-Montieth potential evapotranspiration (E 0 ) in the second and third years, respectively. Mean water use efficiency over the 3 years was 247 L/kg DM, compared with values in the range 186-320 L/kg for younger pot-and column-grown trees. Using a combination of neutron moisture metre (NMM) assays of soil moisture and deuterium: hydrogen ratios of groundwater and xylem water of tagasaste and annual weeds, it was shown that trees became increasingly dependent on groundwater over time and had the capacity to switch rapidly between soil and groundwater sources. Seasonal changes in carbon isotope composition of new shoot tip dry matter indicated that plantation trees were less stressed than alley trees by the third summer as they adapted to heavy dependence on groundwater. In the third season, when plantation trees were transpiring at rates equivalent to 2.3 times annual rainfall, NMM profiles and time domain reflectometry (TDR) assays indicated that no free drainage occurred and that trees were capable of hydraulically lifting groundwater to near surface soil in the dry season. Additional adaptive features of importance to this environment included heat stress induced leaf shedding, development of perennial root nodules on lower parts of tap roots, and an ability to respond in summer to artificial irrigation or a seasonal rainfall by rapidly increasing transpiration 2-3-fold to values equalling E 0 . Copyright (2001) CSIRO

  5. Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus.

    Science.gov (United States)

    Kamath, Pauline L; Getz, Wayne M

    2011-05-18

    Major Histocompatibility Complex (MHC) genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens. This hypothesis has been supported by observations of extremely high polymorphism, elevated nonsynonymous to synonymous base pair substitution rates and trans-species polymorphisms at these loci. In equids, the organization and variability of this gene family has been described, however the full extent of diversity and selection is unknown. As selection is not expected to act uniformly on a functional gene, maximum likelihood codon-based models of selection that allow heterogeneity in selection across codon positions can be valuable for examining MHC gene evolution and the molecular basis for species adaptations. We investigated the evolution of two class II MHC genes of the Equine Lymphocyte Antigen (ELA), DRA and DQA, in the genus Equus with the addition of novel alleles identified in plains zebra (E. quagga, formerly E. burchelli). We found that both genes exhibited a high degree of polymorphism and inter-specific sharing of allele lineages. To our knowledge, DRA allelic diversity was discovered to be higher than has ever been observed in vertebrates. Evidence was also found to support a duplication of the DQA locus. Selection analyses, evaluated in terms of relative rates of nonsynonymous to synonymous mutations (dN/dS) averaged over the gene region, indicated that the majority of codon sites were conserved and under purifying selection (dN

  6. Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus

    Directory of Open Access Journals (Sweden)

    Getz Wayne M

    2011-05-01

    Full Text Available Abstract Background Major Histocompatibility Complex (MHC genes are central to vertebrate immune response and are believed to be under balancing selection by pathogens. This hypothesis has been supported by observations of extremely high polymorphism, elevated nonsynonymous to synonymous base pair substitution rates and trans-species polymorphisms at these loci. In equids, the organization and variability of this gene family has been described, however the full extent of diversity and selection is unknown. As selection is not expected to act uniformly on a functional gene, maximum likelihood codon-based models of selection that allow heterogeneity in selection across codon positions can be valuable for examining MHC gene evolution and the molecular basis for species adaptations. Results We investigated the evolution of two class II MHC genes of the Equine Lymphocyte Antigen (ELA, DRA and DQA, in the genus Equus with the addition of novel alleles identified in plains zebra (E. quagga, formerly E. burchelli. We found that both genes exhibited a high degree of polymorphism and inter-specific sharing of allele lineages. To our knowledge, DRA allelic diversity was discovered to be higher than has ever been observed in vertebrates. Evidence was also found to support a duplication of the DQA locus. Selection analyses, evaluated in terms of relative rates of nonsynonymous to synonymous mutations (dN/dS averaged over the gene region, indicated that the majority of codon sites were conserved and under purifying selection (dN dS. However, the most likely evolutionary codon models allowed for variable rates of selection across codon sites at both loci and, at the DQA, supported the hypothesis of positive selection acting on specific sites. Conclusions Observations of elevated genetic diversity and trans-species polymorphisms supported the conclusion that balancing selection may be acting on these loci. Furthermore, at the DQA, positive selection was

  7. 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.

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

    Science.gov (United States)

    Pereira, Joana; Johnson, Warren E; O'Brien, Stephen J; Jarvis, Erich D; Zhang, Guojie; Gilbert, M Thomas P; Vasconcelos, Vitor; Antunes, Agostinho

    2014-01-01

    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.

  9. Evolution and Adaptation of Phytoplankton Photosynthetic Pathways to perturbations of the geological carbon system

    Science.gov (United States)

    Rickaby, R. E.; Young, J. N.; Hermoso, M.; Heureux, A.; McCLelland, H.; Lee, R.; Eason Hubbard, M.

    2012-12-01

    The ocean and atmosphere carbon system has varied greatly over geological history both in response to initial evolutionary innovation, and as a driver of adaptive change. Here we establish that positive selection in Rubisco, the most abundant enzyme on the Earth responsible for all photosynthetic carbon fixation, occurred early in Earth's history, and basal to the radiation of the modern marine algal groups. Our signals of positive selection appear to be triggered by changing intracellular concentrations of carbon dioxide (CO2) due to the emergence of carbon concentrating mechanisms between 1.56 and 0.41 Ba in response to declining atmospheric CO2 . We contend that, at least in terms of carbon, phytoplankton generally were well poised to manage subsequent abrupt carbon cycle perturbations. The physiological pathways for optimising carbon acquisition across a wide range of ambient carbon dioxide concentrations had already been established and were genetically widespread across open ocean phytoplankton groups. We will further investigate some case studies from the Mesozoic and Cenozoic abrupt carbon cycle excursions using isotopic tools to probe the community photosynthetic response and demonstrate the flexibility of phytoplankton photosynthesis in the face of major perturbations. In particular, an unprecedented resolution record across the Toarcian (Early Jurassic) carbon isotope excursion in the Paris Basin reveals a selection and evolution towards a community reliant solely on diffusive carbon dioxide supply for photosynthesis at the height of the excursion at 1500-2500 ppm CO2. The continued flourishing of the phytoplankton biological pump throughout this excursion was able to remove the excess carbon injected into the water column in less than 45 kyrs.

  10. 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

  11. Interacting proteins on human spermatozoa: adaptive evolution of the binding of semenogelin I to EPPIN.

    Directory of Open Access Journals (Sweden)

    Erick J R Silva

    Full Text Available Semenogelin I (SEMG1 is found in human semen coagulum and on the surface of spermatozoa bound to EPPIN. The physiological significance of the SEMG1/EPPIN interaction on the surface of spermatozoa is its capacity to modulate sperm progressive motility. The present study investigates the hypothesis that the interacting surface of SEMG1 and EPPIN co-evolved within the Hominoidea time scale, as a result of adaptive pressures applied by their roles in sperm protection and reproductive fitness. Our results indicate that some amino acid residues of SEMG1 and EPPIN possess a remarkable deficiency of variation among hominoid primates. We observe a distinct residue change unique to humans within the EPPIN sequence containing a SEMG1 interacting surface, namely His92. In addition, Bayes Empirical Bayes analysis for positive selection indicates that the SEMG1 Cys239 residue underwent positive selection in humans, probably as a consequence of its role in increasing the binding affinity of these interacting proteins. We confirm the critical role of Cys239 residue for SEMG1 binding to EPPIN and inhibition of sperm motility by showing that recombinant SEMG1 mutants in which Cys239 residue was changed to glycine, aspartic acid, histidine, serine or arginine have reduced capacity to interact to EPPIN and to inhibit human sperm motility in vitro. In conclusion, our results indicate that EPPIN and SEMG1 rapidly co-evolved in primates due to their critical role in the modulation of sperm motility in the semen coagulum, providing unique insights into the molecular co-evolution of sperm surface interacting proteins.

  12. Testing Biological Hypotheses with Embodied Robots: Adaptations, Accidents, and By-Products in the Evolution of Vertebrates

    OpenAIRE

    Roberts, Sonia F.; Hirokawa, Jonathan; Rosenblum, Hannah G.; Sakhtah, Hassan; Gutierrez, Andres A.; Porter, Marianne E.; Long, John H.

    2014-01-01

    Evolutionary robotics allows biologists to test hypotheses about extinct animals. In our case, we modeled some of the first vertebrates, jawless fishes, in order to study the evolution of the trait after which vertebrates are named: vertebrae. We tested the hypothesis that vertebrae are an adaptation for enhanced feeding and fleeing performance. We created a population of autonomous embodied robots, Preyro, in which the number of vertebrae, N, were free to evolve. In addition, two other trait...

  13. Multi-objective optimization of p-xylene oxidation process using an improved self-adaptive differential evolution algorithm

    Institute of Scientific and Technical Information of China (English)

    Lili Tao; Bin Xu; Zhihua Hu; Weimin Zhong

    2017-01-01

    The rise in the use of global polyester fiber contributed to strong demand of the Terephthalic acid (TPA). The liquid-phase catalytic oxidation of p-xylene (PX) to TPA is regarded as a critical and efficient chemical process in industry [1]. PX oxidation reaction involves many complex side reactions, among which acetic acid combustion and PX combustion are the most important. As the target product of this oxidation process, the quality and yield of TPA are of great concern. However, the improvement of the qualified product yield can bring about the high energy consumption, which means that the economic objectives of this process cannot be achieved simulta-neously because the two objectives are in conflict with each other. In this paper, an improved self-adaptive multi-objective differential evolution algorithm was proposed to handle the multi-objective optimization prob-lems. The immune concept is introduced to the self-adaptive multi-objective differential evolution algorithm (SADE) to strengthen the local search ability and optimization accuracy. The proposed algorithm is successfully tested on several benchmark test problems, and the performance measures such as convergence and divergence metrics are calculated. Subsequently, the multi-objective optimization of an industrial PX oxidation process is carried out using the proposed immune self-adaptive multi-objective differential evolution algorithm (ISADE). Optimization results indicate that application of ISADE can greatly improve the yield of TPA with low combustion loss without degenerating TA quality.

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

    Science.gov (United States)

    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.

  15. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    DEFF Research Database (Denmark)

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

  16. Forage-based dairying in a water-limited future: use of models to investigate farming system adaptation in southern Australia.

    Science.gov (United States)

    Chapman, D F; Dassanayake, K; Hill, J O; Cullen, B R; Lane, N

    2012-07-01

    The irrigated dairy industry in southern Australia has experienced significant restrictions in irrigation water allocations since 2005, consistent with climate change impact predictions for the region. Simulation models of pasture growth (DairyMod), crop yield (Agricultural Production Systems Simulator, APSIM), and dairy system management and production (UDDER) were used in combination to investigate a range of forage options that may be capable of sustaining dairy business profitability under restricted water-allocation scenarios in northern Victoria, Australia. A total of 23 scenarios were simulated and compared with a base farm system (100% of historical water allocations, grazed perennial ryegrass pasture with supplements; estimated operating surplus $A2,615/ha at a milk price of $A4.14/kg of milk solids). Nine simulations explored the response of the base farm to changes in stocking rate or the implementation of a double cropping rotation on 30% of farm area, or both. Five simulations explored the extreme scenario of dairying without any irrigation water. Two general responses to water restrictions were investigated in a further 9 simulations. Annual ryegrass grazed pasture, complemented by a double cropping rotation (maize grown in summer for silage, followed by either brassica forage crop and annual ryegrass for silage in winter and spring) on 30% of farm area, led to an estimated operating surplus of $A1746/ha at the same stocking rate as the base farm when calving was moved to autumn (instead of late winter, as in the base system). Estimated total irrigation water use was 2.7ML/ha compared with 5.4ML/ha for the base system. Summer-dormant perennial grass plus double cropping (30% of farm area) lifted operating surplus by a further $A100/ha if associated with autumn calving (estimated total irrigation water use 3.1ML/ha). Large shifts in the forage base of dairy farms could sustain profitability in the face of lower, and fluctuating, water allocations

  17. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica.

    Science.gov (United States)

    Sosa, Victoria; Ornelas, Juan Francisco; Ramírez-Barahona, Santiago; Gándara, Etelvina

    2016-01-01

    Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant

  18. Adaptation.

    Science.gov (United States)

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  19. Adaptive radiation versus 'radiation' and 'explosive diversification': why conceptual distinctions are fundamental to understanding evolution.

    Science.gov (United States)

    Givnish, Thomas J

    2015-07-01

    Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within a lineage. Recently, some researchers have begun to use 'adaptive radiation' or 'radiation' as synonymous with 'explosive species diversification'. This essay aims to clarify distinctions between these concepts, and the related ideas of geographic speciation, sexual selection, key innovations, key landscapes and ecological keys. Several examples are given to demonstrate that adaptive radiation and explosive diversification are not the same phenomenon, and that focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some 'radiations' involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of 'adaptive radiation' appear to involve effects driven partly by geographic speciation, species' dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  20. Adaptive evolution of Escherichia coli to Ciprofloxacin in controlled stress environments: emergence of tolerance in spatial and temporal gradients

    Science.gov (United States)

    Deng, J.; Sanford, R. A.; Dong, Y.; Shechtman, L. A.; Zhou, L.; Alcalde, R.; Werth, C. J.; Fouke, B. W.

    2016-12-01

    Microorganisms in nature have evolved in response to a variety of environmental stresses, including gradients of temperature, pH, substrate availability and aqueous chemistry. While environmental stresses are considered to be the driving forces of adaptive evolution, the impact and extent of any specific stress needed to drive such changes has not been well characterized. In this study, the antibiotic Ciprofloxacin was used as a stressor and systematically applied to E. coli st. 307 cells via a spatial gradient in a microfluidic pore network and a temporal gradient in batch cultures. The microfluidic device facilitated in vitro real-time tracking of bacterial abundances and dynamic spatial distributions in response to the gradients of both the antibiotic and nutrients. Cells collected from the microfluidic device showed growth on plates containing up to 10-times the original minimum inhibition concentration (MIC). In batch systems, Ciprofloxacin was used to evaluate adaptive responses via temporal gradients, in which the stressor concentration was incrementally increased over time with each transfer of the culture after 24 hours of growth. Responses of E. coli 307 to these stress patterns were measured by quantifying changes in the MIC for Ciprofloxacin. Over a period of 18 days of step-wise concentration increments, bacterial cells were observed to acquire tolerance gradually and eventually adapt to a 28-fold increase in the original MIC. Samples at different stages within the temporal Ciprofloxacin gradient treatment show different extents of resistance. All samples exhibited resistance exceeding the highest exposure stress concentration. In combination with the spatial and temporal gradient systems, this work provides the first comprehensive measure of the dynamic resistance of E. coli in response to Ciprofloxacin concentration gradients. These will provide invaluable insights to understand the effects of antibiotic stresses on bacterial adaptive evolution in

  1. Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

    DEFF Research Database (Denmark)

    LaCroix, Ryan A.; Sandberg, Troy E.; O'Brien, Edward J.

    2015-01-01

    Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes and their combinatorial effects is challenging...

  2. Adaptation

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

    building skills, knowledge or networks on adaptation, ... the African partners leading the AfricaAdapt network, together with the UK-based Institute of Development Studies; and ... UNCCD Secretariat, Regional Coordination Unit for Africa, Tunis, Tunisia .... 26 Rural–urban Cooperation on Water Management in the Context of.

  3. Adaptive Management of Environmental Flows: Using Irrigation Infrastructure to Deliver Environmental Benefits During a Large Hypoxic Blackwater Event in the Southern Murray-Darling Basin, Australia

    Science.gov (United States)

    Watts, Robyn J.; Kopf, R. Keller; McCasker, Nicole; Howitt, Julia A.; Conallin, John; Wooden, Ian; Baumgartner, Lee

    2018-03-01

    Widespread flooding in south-eastern Australia in 2010 resulted in a hypoxic (low dissolved oxygen, DO) blackwater (high dissolved carbon) event affecting 1800 kilometres of the Murray-Darling Basin. There was concern that prolonged low DO would result in death of aquatic biota. Australian federal and state governments and local stakeholders collaborated to create refuge areas by releasing water with higher DO from irrigation canals via regulating structures (known as `irrigation canal escapes') into rivers in the Edward-Wakool system. To determine if these environmental flows resulted in good environmental outcomes in rivers affected by hypoxic blackwater, we evaluated (1) water chemistry data collected before, during and after the intervention, from river reaches upstream and downstream of the three irrigation canal escapes used to deliver the environmental flows, (2) fish assemblage surveys undertaken before and after the blackwater event, and (3) reports of fish kills from fisheries officers and local citizens. The environmental flows had positive outcomes; mean DO increased by 1-2 mg L-1 for at least 40 km downstream of two escapes, and there were fewer days when DO was below the sub-lethal threshold of 4 mg L-1 and the lethal threshold of 2 mg L-1 at which fish are known to become stressed or die, respectively. There were no fish deaths in reaches receiving environmental flows, whereas fish deaths were reported elsewhere throughout the system. This study demonstrates that adaptive management of environmental flows can occur through collaboration and the timely provision of monitoring results and local knowledge.

  4. A brief history of adaptation: conceptual evolution across the IPCC reports (1990-2014)

    International Nuclear Information System (INIS)

    Simonet, Guillaume

    2015-01-01

    In the past decade, work on the concepts of vulnerability, resilience and adaptation became central in climate change literature. At the same time a growing number of studies have focussed on the influence of cognitive factors on decision-making processes, such as interpreting elusive concepts such as adaptation. Comprehension of adaptation has evolved considerably since its recognition as a response to climate change in the 90's by the Intergovernmental Panel on Climate Change (IPCC). Currently protecting systems from weather events (the 'adjustment adaptation' approach) is still the prevailing view in climate policies. Nevertheless, a shift toward a 'transformation adaptation' approach is being observed. This position would take better account of the complexity of existing systems and allow reexamining their mechanisms (institutional, technical, financial). This paper aims to analyze conceptual advances on adaptation across the five IPCC reports from 1990 to 2014. This contribution attempts to show that the prominence given to adaptation in the latest report (2014) reflects the cognitive difficulty of conceiving this concept, responds to the growing demand to facilitate its operationalization and confirms its relevance for a better understanding of the underlying complexity of climate change and the global environmental change issue. Pursuing reflection on the adaptation concept should certainly contribute to the emergence of a promising and interdisciplinary field of research

  5. 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.

  6. 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....... 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...... 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...

  7. Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

    Science.gov (United States)

    Engsontia, Patamarerk; Sangket, Unitsa; Chotigeat, Wilaiwan; Satasook, Chutamas

    2014-08-01

    Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis. A limited number of cases of large lineage-specific gene expansion are observed (except in the P. xylostella lineage), possibly due to selection against tandem gene duplication. There has been strong purifying selection during the evolution of both lepidopteran odorant and gustatory genes, as shown by the low ω values estimated through CodeML analysis, ranging from 0.0093 to 0.3926. However, purifying selection has been relaxed on some amino acid sites in these receptors, leading to sequence divergence, which is a precursor of positive selection on these sequences. Signatures of positive selection were detected only in a few loci from the lineage-specific analysis. Estimation of gene gains and losses suggests that the common ancestor of the Lepidoptera had fewer Or genes compared to extant species and an even more reduced number of Gr genes, particularly within the bitter receptor clade. Multiple gene gains and a few gene losses occurred during the evolution of Lepidoptera. Gene family expansion may be associated with the adaptation of lepidopteran species to plant hosts, especially after angiosperm radiation. Phylogenetic analysis of the moth sex pheromone receptor genes suggested that chromosomal translocations have occurred several times. New sex pheromone receptors have arisen through tandem gene duplication. Positive selection was detected at some amino acid sites predicted to be

  8. 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

    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...... of evolved strains, which exhibited a significant increase in the specific growth rate and a higher glycerol consumption rate, were isolated. The best performing strains were further analyzed by classical genetics and whole genome re-sequencing in order to understand the molecular basis of glycerol...

  9. 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

    the within-host evolution of the transmissible P. aeruginosa DK2 lineage. We found positive selection for promoter mutations leading to increased expression of the phu system. By mimicking conditions of the CF airways in vitro, we experimentally demonstrate that increased expression of phuR confers a growth...... 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...... might therefore be a promising strategy for the treatment of P. aeruginosa infections in CF patients. IMPORTANCE Most bacterial pathogens depend on scavenging iron within their hosts, which makes the battle for iron between pathogens and hosts a hallmark of infection. Accordingly, the ability...

  10. Water Recycling in Australia

    Directory of Open Access Journals (Sweden)

    Ross Young

    2011-09-01

    Full Text Available Australia is the driest inhabited continent on earth and, more importantly, experiences the most variable rainfall of all the continents on our planet. The vast majority of Australians live in large cities on the coast. Because wastewater treatments plants were all located near the coast, it was thought that large scale recycling would be problematic given the cost of infrastructure and pumping required to establish recycled water schemes. This all changed when Australia experienced a decade of record low rainfall and water utilities were given aggressive targets to increase the volume of water recycled. This resulted in recycled water being accepted as a legitimate source of water for non-drinking purposes in a diversified portfolio of water sources to mitigate climate risk. To ensure community support for recycled water, Australia lead the world in developing national guidelines for the various uses of recycled water to ensure the protection of public health and the environment. Australia now provides a great case study of the developments in maximizing water recycling opportunities from policy, regulatory and technological perspectives. This paper explores the evolution in thinking and how approaches to wastewater reuse has changed over the past 40 years from an effluent disposal issue to one of recognizing wastewater as a legitimate and valuable resource. Despite recycled water being a popular choice and being broadly embraced, the concept of indirect potable reuse schemes have lacked community and political support across Australia to date.

  11. Evolution of competitive ability: an adaptation speed vs. accuracy tradeoff rooted in gene network size.

    Science.gov (United States)

    Malcom, Jacob W

    2011-04-25

    Ecologists have increasingly come to understand that evolutionary change on short time-scales can alter ecological dynamics (and vice-versa), and this idea is being incorporated into community ecology research programs. Previous research has suggested that the size and topology of the gene network underlying a quantitative trait should constrain or facilitate adaptation and thereby alter population dynamics. Here, I consider a scenario in which two species with different genetic architectures compete and evolve in fluctuating environments. An important trade-off emerges between adaptive accuracy and adaptive speed, driven by the size of the gene network underlying the ecologically-critical trait and the rate of environmental change. Smaller, scale-free networks confer a competitive advantage in rapidly-changing environments, but larger networks permit increased adaptive accuracy when environmental change is sufficiently slow to allow a species time to adapt. As the differences in network characteristics increase, the time-to-resolution of competition decreases. These results augment and refine previous conclusions about the ecological implications of the genetic architecture of quantitative traits, emphasizing a role of adaptive accuracy. Along with previous work, in particular that considering the role of gene network connectivity, these results provide a set of expectations for what we may observe as the field of ecological genomics develops.

  12. Adapt

    Science.gov (United States)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

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

    DEFF Research Database (Denmark)

    Madsen Sommer, Lea Mette

    of natural environments, the primary obstacle is re-sampling of the samepopulation over time, especially if the population is small.Nevertheless, it has been accomplished: Chronic airway infections of cystic fibrosis (CF) patients have offered a unique view into the adaptationand evolution of Pseudomonas...... to the CF airways. From this analysis we found common clonal lineages among the patients, evidence of patient-to-patient transmission, historic contingencies, and convergent evolution of 52 candidate pathoadaptive genes. By further genome sequencing 26 P. aeruginosa isolates from four Italian CF patients...

  14. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

    Directory of Open Access Journals (Sweden)

    Victoria Sosa

    2016-11-01

    Full Text Available Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from

  15. Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.

    Science.gov (United States)

    Fricke, W Florian; Mammel, Mark K; McDermott, Patrick F; Tartera, Carmen; White, David G; Leclerc, J Eugene; Ravel, Jacques; Cebula, Thomas A

    2011-07-01

    Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks.

  16. 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.

  17. 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.

  18. Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago

    Directory of Open Access Journals (Sweden)

    Ronfort Joëlle

    2007-11-01

    Full Text Available Abstract 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.

  19. Natural selection causes adaptive genetic resistance in wild emmer wheat against powdery mildew at "Evolution Canyon" microsite, Mt. Carmel, Israel.

    Science.gov (United States)

    Yin, Huayan; Ben-Abu, Yuval; Wang, Hongwei; Li, Anfei; Nevo, Eviatar; Kong, Lingrang

    2015-01-01

    "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.

  20. 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.

  1. Physiological and comparative evidence fails to confirm an adaptive role for aging in evolution.

    Science.gov (United States)

    Cohen, Alan A

    2015-01-01

    The longstanding debate about whether aging may have evolved for some adaptive reason is generally considered to pit evolutionary theory against empirical observations consistent with aging as a programmed aspect of organismal biology, in particular conserved aging genes. Here I argue that the empirical evidence on aging mechanisms does not support a view of aging as a programmed phenomenon, but rather supports a view of aging as the dysregulation of complex networks that maintain organismal homeostasis. The appearance of programming is due largely to the inadvertent activation of existing pathways during the process of dysregulation. It is argued that aging differs markedly from known programmed biological phenomena such as apoptosis in that it is (a) very heterogeneous in how it proceeds, and (b) much slower than it would need to be. Furthermore, the taxonomic distribution of aging across species does not support any proposed adaptive theories of aging, which would predict that aging rate would vary on a finer taxonomic scale depending on factors such as population density. Thus, while there are problems with the longstanding non-adaptive paradigm, current evidence does not support the notion that aging is programmed or that it may have evolved for adaptive reasons.

  2. Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions

    Directory of Open Access Journals (Sweden)

    Afonnikov Dmitry A

    2009-12-01

    Full Text Available Abstract Background Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions. Results Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain. Conclusions The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P

  3. A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

    Directory of Open Access Journals (Sweden)

    Satoshi Uchida

    2018-02-01

    Full Text Available Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”. In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

  4. A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

    Science.gov (United States)

    Uchida, Satoshi; Yamamoto, Hitoshi; Okada, Isamu; Sasaki, Tatsuya

    2018-02-01

    Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”). In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

  5. Evolution of spatio-temporal drought characteristics: validation, projections and effect of adaptation scenarios

    Science.gov (United States)

    Vidal, J.-P.; Martin, E.; Kitova, N.; Najac, J.; Soubeyroux, J.-M.

    2012-08-01

    Drought events develop in both space and time and they are therefore best described through summary joint spatio-temporal characteristics, such as mean duration, mean affected area and total magnitude. This paper addresses the issue of future projections of such characteristics of drought events over France through three main research questions: (1) Are downscaled climate projections able to simulate spatio-temporal characteristics of meteorological and agricultural droughts in France over a present-day period? (2) How such characteristics will evolve over the 21st century? (3) How to use standardized drought indices to represent theoretical adaptation scenarios? These questions are addressed using the Isba land surface model, downscaled climate projections from the ARPEGE General Circulation Model under three emissions scenarios, as well as results from a previously performed 50-yr multilevel and multiscale drought reanalysis over France. Spatio-temporal characteristics of meteorological and agricultural drought events are computed using the Standardized Precipitation Index and the Standardized Soil Wetness Index, respectively, and for time scales of 3 and 12 months. Results first show that the distributions of joint spatio-temporal characteristics of observed events are well simulated by the downscaled hydroclimate projections over a present-day period. All spatio-temporal characteristics of drought events are then found to dramatically increase over the 21st century, with stronger changes for agricultural droughts. Two theoretical adaptation scenarios are eventually built based on hypotheses of adaptation to evolving climate and hydrological normals, either retrospective or prospective. The perceived spatio-temporal characteristics of drought events derived from these theoretical adaptation scenarios show much reduced changes, but they call for more realistic scenarios at both the catchment and national scale in order to accurately assess the combined effect of

  6. 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.

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

    OpenAIRE

    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.

    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 ...

  8. 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.

  9. 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

  10. Model-Based Evolution of a Fast Hybrid Fuzzy Adaptive Controller for a Pneumatic Muscle Actuator

    Directory of Open Access Journals (Sweden)

    Alexander Hošovský

    2012-07-01

    Full Text Available Pneumatic artificial muscle-based robotic systems usually necessitate the use of various nonlinear control techniques in order to improve their performance. Their robustness to parameter variation, which is generally difficult to predict, should also be tested. Here a fast hybrid adaptive control is proposed, where a conventional PD controller is placed into the feedforward branch and a fuzzy controller is placed into the adaptation branch. The fuzzy controller compensates for the actions of the PD controller under conditions of inertia moment variation. The fuzzy controller of Takagi-Sugeno type is evolved through a genetic algorithm using the dynamic model of a pneumatic muscle actuator. The results confirm the capability of the designed system to provide robust performance under the conditions of varying inertia.

  11. Introduction to a Special Issue Dialectical Behavior Therapy: Evolution and Adaptations in the 21(st) Century.

    Science.gov (United States)

    Miller, Alec L

    2015-01-01

    Born from the randomized controlled trial by Linehan and colleagues in 1991, dialectical behavior therapy (DBT) has become the gold standard for treatment of individuals who are suicidal and have borderline personality disorder. In this special issue, we begin with a historical review of DBT provided by the treatment developer herself. We then introduce readers to new, 21(st) century adaptations developed of this treatment modality. In this issue we explore the use of DBT for suicidal adolescents with one paper focusing on Latina teens and their parents, and one focused on the more recently developed walking the middle path skills module. Other papers in this issue include unique adaptations of DBT for eating disorders, and disorders of over-control, as well as trauma in incarcerated male adolescents. We also look at transdiagnostic applications of DBT and finally a comparison of DBT with mentalization-based treatment.

  12. 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

    to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature...... is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition....... This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased...

  13. Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

    OpenAIRE

    Jobson, Richard W.; Nielsen, Rasmus; Laakkonen, Liisa; Wikström, Mårten; Albert, Victor A.

    2004-01-01

    Much recent attention in the study of adaptation of organismal form has centered on developmental regulation. As such, the highly conserved respiratory machinery of eukaryotic cells might seem an unlikely target for selection supporting novel morphologies. We demonstrate that a dramatic molecular evolutionary rate increase in subunit I of cytochrome c oxidase (COX) from an active-trapping lineage of carnivorous plants is caused by positive Darwinian selection. Bladderworts (Utricularia) trap ...

  14. Seismic communication in a blind subterranean mammal: a major somatosensory mechanism in adaptive evolution underground.

    OpenAIRE

    Nevo, E; Heth, G; Pratt, H

    1991-01-01

    Seismic communication, through low-frequency and patterned substrate-borne vibrations that are generated by head thumping, and which travel long distances underground, is important in the nonvisual communication of subterranean mole rats of the Spalax ehrenbergi superspecies (2n = 52, 54, 58, and 60) in Israel. This importance pertains both intraspecifically in adaptation and interspecifically in speciation. Neurophysiologic, behavioral, and anatomic findings in this study suggest that the me...

  15. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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.

  18. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss.

    Science.gov (United States)

    Morris, J Jeffrey; Lenski, Richard E; Zinser, Erik R

    2012-01-01

    Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.

  19. 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.

  20. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses.

    Science.gov (United States)

    Caspeta, Luis; Nielsen, Jens

    2015-07-21

    A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40 °C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes. Yeast thermotolerance can significantly reduce the production costs of biomass

  1. 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.

  2. Characterizing semantic mappings adaptation via biomedical KOS evolution: a case study investigating SNOMED CT and ICD.

    Science.gov (United States)

    Dos Reis, Julio Cesar; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

    2013-01-01

    Mappings established between Knowledge Organization Systems (KOS) increase semantic interoperability between biomedical information systems. However, biomedical knowledge is highly dynamic and changes affecting KOS entities can potentially invalidate part or the totality of existing mappings. Understanding how mappings evolve and what the impacts of KOS evolution on mappings are is therefore crucial for the definition of an automatic approach to maintain mappings valid and up-to-date over time. In this article, we study variations of a specific KOS complex change (split) for two biomedical KOS (SNOMED CT and ICD-9-CM) through a rigorous method of investigation for identifying and refining complex changes, and for selecting representative cases. We empirically analyze and explain their influence on the evolution of associated mappings. Results point out the importance of considering various dimensions of the information described in KOS, like the semantic structure of concepts, the set of relevant information used to define the mappings and the change operations interfering with this set of information.

  3. 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

  4. 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

    2011-02-10

    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.

  5. The evolution of resource adaptation: how generalist and specialist consumers evolve.

    Science.gov (United States)

    Ma, Junling; Levin, Simon A

    2006-07-01

    Why and how specialist and generalist strategies evolve are important questions in evolutionary ecology. In this paper, with the method of adaptive dynamics and evolutionary branching, we identify conditions that select for specialist and generalist strategies. Generally, generalist strategies evolve if there is a switching benefit; specialists evolve if there is a switching cost. If the switching cost is large, specialists always evolve. If the switching cost is small, even though the consumer will first evolve toward a generalist strategy, it will eventually branch into two specialists.

  6. 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

    between cirral setation and feeding mode. The species studied comprise both pedunculate and sessile forms and represent a wide range of marine habitats as well as morphologies, viz., Ibla cumingi, Octolasmis warwickii, Capitulum mitella, Pollicipes polymerus, Tetraclita japonica japonica and Megabalanus...... 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...

  7. How to Survive the Anthropocene: Adaptive Atheism and the Evolution of Homo deiparensis

    Directory of Open Access Journals (Sweden)

    F. LeRon Shults

    2015-06-01

    Full Text Available Why is it so easy to ignore the ecological and economic crises of the Anthropocene? This article unveils some of the religious biases whose covert operation facilitates the repression or rejection of warnings about the consequences of extreme climate change and excessive capitalist consumption. The evolved defaults that are most relevant for our purposes here have to do with mental credulity toward religious content (beliefs about supernatural agents and with social congruity in religious contexts (behaviors shaped by supernatural rituals. Learning how to contest these phylogenetically inherited and culturally fortified biases may be a necessary condition for adapting to and altering our current natural and social environments in ways that will enhance the chances for the survival (and flourishing of Homo sapiens and other sentient species. I outline a conceptual framework, derived from empirical findings and theoretical developments in the bio-cultural sciences of religion, which can help clarify why and how gods are imaginatively conceived and nurtured by ritually engaged believers. Finally, I discuss the role that “adaptive atheism” might play in responding to the crises of the Anthropocene.

  8. 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.

  9. 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.

  10. Linearized Flux Evolution (LiFE): A technique for rapidly adapting fluxes from full-physics radiative transfer models

    Science.gov (United States)

    Robinson, Tyler D.; Crisp, David

    2018-05-01

    Solar and thermal radiation are critical aspects of planetary climate, with gradients in radiative energy fluxes driving heating and cooling. Climate models require that radiative transfer tools be versatile, computationally efficient, and accurate. Here, we describe a technique that uses an accurate full-physics radiative transfer model to generate a set of atmospheric radiative quantities which can be used to linearly adapt radiative flux profiles to changes in the atmospheric and surface state-the Linearized Flux Evolution (LiFE) approach. These radiative quantities describe how each model layer in a plane-parallel atmosphere reflects and transmits light, as well as how the layer generates diffuse radiation by thermal emission and by scattering light from the direct solar beam. By computing derivatives of these layer radiative properties with respect to dynamic elements of the atmospheric state, we can then efficiently adapt the flux profiles computed by the full-physics model to new atmospheric states. We validate the LiFE approach, and then apply this approach to Mars, Earth, and Venus, demonstrating the information contained in the layer radiative properties and their derivatives, as well as how the LiFE approach can be used to determine the thermal structure of radiative and radiative-convective equilibrium states in one-dimensional atmospheric models.

  11. Adaptive co-evolution of strategies and network leading to optimal cooperation level in spatial prisoner's dilemma game

    International Nuclear Information System (INIS)

    Han-Shuang, Chen; Zhong-Huai, Hou; Hou-Wen, Xin; Ji-Qian, Zhang

    2010-01-01

    We study evolutionary prisoner's dilemma game on adaptive networks where a population of players co-evolves with their interaction networks. During the co-evolution process, interacted players with opposite strategies either rewire the link between them with probability p or update their strategies with probability 1 – p depending on their payoffs. Numerical simulation shows that the final network is either split into some disconnected communities whose players share the same strategy within each community or forms a single connected network in which all nodes are in the same strategy. Interestingly, the density of cooperators in the final state can be maximised in an intermediate range of p via the competition between time scale of the network dynamics and that of the node dynamics. Finally, the mean-field analysis helps to understand the results of numerical simulation. Our results may provide some insight into understanding the emergence of cooperation in the real situation where the individuals' behaviour and their relationship adaptively co-evolve. (general)

  12. 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.

  13. Unsettling Australia

    DEFF Research Database (Denmark)

    Jensen, Lars

    This book is a critical intervention into debates on Australia's cultural history. The book demonstrates the interconnectedness of themes commonly seen as separate discursive formations, and shows the fruitfulness of bringing a combined cultural studies and postcolonial approach to bear on a number...

  14. 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

  15. 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

    2009-06-01

    Full Text Available 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.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.Our results and the results of parallel studies with several other organisms, suggest that natural selection appears to select, at a

  16. Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease

    Science.gov (United States)

    Gomez, Felicia; Hirbo, Jibril; Tishkoff, Sarah A.

    2014-01-01

    Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent. PMID:24984772

  17. 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...

  18. 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.

  19. Evolution and adaptation of marine annelids in interstitial and cave habitats

    DEFF Research Database (Denmark)

    Martinez Garcia, Alejandro

    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...... with cave and interstitial representatives, mainly the families Protodrilidae, Nerillidae, Saccocirridae and Scalibregmatidae. The studies combined the characterization of ancestral and cave habitats, with morphological investigations and phylogenetic analyses founded on extensive taxon coverage...

  20. 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

  1. Many-Objective Optimization Using Adaptive Differential Evolution with a New Ranking Method

    Directory of Open Access Journals (Sweden)

    Xiaoguang He

    2014-01-01

    Full Text Available Pareto dominance is an important concept and is usually used in multiobjective evolutionary algorithms (MOEAs to determine the nondominated solutions. However, for many-objective problems, using Pareto dominance to rank the solutions even in the early generation, most obtained solutions are often the nondominated solutions, which results in a little selection pressure of MOEAs toward the optimal solutions. In this paper, a new ranking method is proposed for many-objective optimization problems to verify a relatively smaller number of representative nondominated solutions with a uniform and wide distribution and improve the selection pressure of MOEAs. After that, a many-objective differential evolution with the new ranking method (MODER for handling many-objective optimization problems is designed. At last, the experiments are conducted and the proposed algorithm is compared with several well-known algorithms. The experimental results show that the proposed algorithm can guide the search to converge to the true PF and maintain the diversity of solutions for many-objective problems.

  2. 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.

  3. Go High or Go Low? Adaptive Evolution of High and Low Relatedness Societies in Social Hymenoptera

    Directory of Open Access Journals (Sweden)

    Peter Nonacs

    2017-08-01

    Full Text Available Cooperative groups can increase fitness either by helping kin or interacting with unlike individuals to produce social heterosis. They cannot, however, simultaneously maximize both benefits. This tradeoff between nepotism and diversity is modeled using Hamilton's rule (rb–c > 0, by allowing benefit and cost to be dynamic functions of relatedness (i.e., social heterosis predicts b and c depend on r. Simulations show that evolutionary outcomes tend to maximize either nepotism (with high genetic relatedness, or social heterosis (with low relatedness rather than produce an intermediate outcome. Although genetic diversity can arise through multiple mating, a second possible mechanism—the exchanging of individuals across groups—is similarly effective. Such worker “drifting” is common in many species of social Hymenoptera and may be a form of indirect reciprocity. Drifting individuals increase an unrelated group's productivity by enhancing its genetic diversity, with this effect being reciprocated by other unrelated drifters entering their natal group. The benefits from social heterosis and indirect reciprocity are robust against cheating and show that it is possible to evolve stable cooperation between individuals that are genetically distant or unrelated. As drifting becomes more prevalent colony boundaries may become weakly discriminated, which may predispose toward the evolution of unicoloniality in some species.

  4. 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.

  5. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.

    Science.gov (United States)

    Huang, Jinlong; Zhao, Yiping; Shiraigol, Wunierfu; Li, Bei; Bai, Dongyi; Ye, Weixing; Daidiikhuu, Dorjsuren; Yang, Lihua; Jin, Burenqiqige; Zhao, Qinan; Gao, Yahan; Wu, Jing; Bao, Wuyundalai; Li, Anaer; Zhang, Yuhong; Han, Haige; Bai, Haitang; Bao, Yanqing; Zhao, Lele; Zhai, Zhengxiao; Zhao, Wenjing; Sun, Zikui; Zhang, Yan; Meng, He; Dugarjaviin, Manglai

    2014-05-14

    Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.

  6. Evolution of ITER tritium confinement strategy and adaptation to Cadrache site conditions and French regulatory requirements

    International Nuclear Information System (INIS)

    Murdoch, D.

    2007-01-01

    The ITER Nuclear Buildings include the Tokamak, Tritium and Diagnostic Buildings (Tokamak Complex) and the Hot Cell and Low Level Radioactive Waste Buildings. The Tritium Confinement Strategy of the Nuclear Buildings comprises key features of the Atmosphere and Vent Detritiation Systems (ADS/VDS) and the Heating, Ventilation and Air Conditioning (HVAC) Systems. The designs developed during the ITER EDA (Engineering Design Activities) for these systems need to be adapted to the specific conditions of the Cadarache site and modified to conform with the regulatory requirements applicable to Installations Nucleaires de Base (INB) - Basic Nuclear Installations - in France. The highest priority for such adaptation has been identified as the Tritium Confinement of the Tokamak Complex and the progress in development of a robust, coherent design concept compliant with French practice is described in the paper. The Tokamak Complex HVAC concept for generic conditions was developed for operational cost minimisation under more extreme climatic conditions (primarily temperature) than those valid for Cadarache, and incorporated recirculation of a large fraction of the air flow through the HVAC systems to achieve this objective. Due to the impracticality of precluding the spread of contamination from areas of higher activity to less contaminated areas, this concept has been abandoned in favour of a once-through configuration, which requires a complete redesign, with revised air change rates, module sizes, layout, redundancy provisions and other features. The ADS/VDS concept developed for the generic design of the ITER Tokamak Complex is undergoing a radical revision in which the system architecture, module sizing and basic process are being optimised for the Cadarache conditions. Investigation is being launched into the implementation of a wet stripper concept to replace the molecular sieve (MS) beds incorporated in the generic design, where concerns have been raised over low

  7. Development and evolution of the mammalian limb: adaptive diversification of nails, hooves, and claws.

    Science.gov (United States)

    Hamrick, M W

    2001-01-01

    Paleontological evidence indicates that the evolutionary diversification of mammals early in the Cenozoic era was characterized by an adaptive radiation of distal limb structures. Likewise, neontological data show that morphological variation in distal limb integumentary appendages (e.g., nails, hooves, and claws) can be observed not only among distantly related mammalian taxa but also among closely related species within the same clade. Comparative analysis of nail, claw, and hoof morphogenesis reveals relatively subtle differences in mesenchymal and epithelial patterning underlying these adult differences in distal limb appendage morphology. Furthermore, studies of regulatory gene expression during vertebrate claw development demonstrate that many of the signaling molecules involved in patterning ectodermal derivatives such as teeth, hair, and feathers are also involved in organizing mammalian distal limb appendages. For example, Bmp4 signaling plays an important role during the recruitment of mesenchymal cells into the condensations forming the terminal phalanges, whereas Msx2 affects the length of nails and claws by suppressing proliferation of germinal epidermal cells. Evolutionary changes in the form of distal integumentary appendages may therefore result from changes in gene expression during formation of mesenchymal condensations (Bmp4, posterior Hox genes), induction of the claw fold and germinal matrix (shh), and/or proliferation of epidermal cells in the claw matrix (Msx1, Msx2). The prevalence of convergences and parallelisms in nail and claw structure among mammals underscores the existence of multiple morphogenetic pathways for evolutionary change in distal limb appendages.

  8. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

    Science.gov (United States)

    Berg, Jeremy J.; Birchler, James A.; Grote, Mark N.; Lorant, Anne; Quezada, Juvenal

    2018-01-01

    While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes. PMID:29746459

  9. 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.

  10. 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.

  11. 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.

  12. Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader.

    Science.gov (United States)

    Bernardi, Giacomo; Azzurro, Ernesto; Golani, Daniel; Miller, Michael Ryan

    2016-07-01

    Biological invasions are increasingly creating ecological and economical problems both on land and in aquatic environments. For over a century, the Mediterranean Sea has steadily been invaded by Indian Ocean/Red Sea species (called Lessepsian invaders) via the Suez Canal, with a current estimate of ~450 species. The bluespotted cornetfish, Fistularia commersonii, considered a 'Lessepsian sprinter', entered the Mediterranean in 2000 and by 2007 had spread through the entire basin from Israel to Spain. The situation is unique and interesting both because of its unprecedented rapidity and by the fact that it took this species c. 130 years to immigrate into the Mediterranean. Using genome scans, with restriction site-associated DNA (RAD) sequencing, we evaluated neutral and selected genomic regions for Mediterranean vs. Red Sea cornetfish individuals. We found that few fixed neutral changes were detectable among populations. However, almost half of the genes associated with the 47 outlier loci (potentially under selection) were related to disease resistance and osmoregulation. Due to the short time elapsed from the beginning of the invasion to our sampling, we interpret these changes as signatures of rapid adaptation that may be explained by several mechanisms including preadaptation and strong local selection. Such genomic regions are therefore good candidates to further study their role in invasion success. © 2016 John Wiley & Sons Ltd.

  13. 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.

  14. Australia: Population.

    Science.gov (United States)

    The Australian Bureau of Census and Statistics reported on 27 August 1979 that Australia's total population was 14,376,400 at the end of the first quarter of 1979. Net immigration gain during the same period was 12,700. Natural increase was 32,100--births were 57,100 and deaths were 25,000. In January 1979, Australia introduced a new immigration scheme to improve methods of selecting immigrants. Points are awarded on the basis of personal qualities and employability; an applicant must score 60 out of 100. This scheme supersedes the earlier system under which immigrants were selected on the family reunion criterion and employability. Migrants from Britain and Ireland made up the bulk of the new comers, but their proportion has dropped from 50% in the mid-1960s to 30% in early 1979. In contrast, Asian immigrants have risen from 2% to 22% over the same period. Asian immigration began in the mid-1960s with the relaxation of the "White Australia" policy which barred non-European migrants, and increased when the ban was abolished by Prime Minister Gough Whitlam in 1973.

  15. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many.

    Science.gov (United States)

    Kovaliski, John; Sinclair, Ron; Mutze, Greg; Peacock, David; Strive, Tanja; Abrantes, Joana; Esteves, Pedro J; Holmes, Edward C

    2014-02-01

    Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16-year period (1995-2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V-351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long-term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia -4.0 (3.3-4.7) × 10(-3) nucleotide substitutions per site per year - was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation. © 2013 John Wiley & Sons Ltd.

  16. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus (RHDV) in Australia: when one became many

    Science.gov (United States)

    Kovaliski, John; Sinclair, Ron; Mutze, Greg; Peacock, David; Strive, Tanja; Abrantes, Joana; Esteves, Pedro J.; Holmes, Edward C.

    2015-01-01

    Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16 year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared to those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V-351 and RHDV351INOC). Strikingly, despite more than 3000 re-releases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long-term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia – 4.0 (3.3 – 4.7) × 10−3 nucleotide substitutions per site per year – was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation. PMID:24251353

  17. [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

  18. Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species

    Science.gov (United States)

    Allison, Andrew B.; Kohler, Dennis J.; Ortega, Alicia; Hoover, Elizabeth A.; Grove, Daniel M.; Holmes, Edward C.; Parrish, Colin R.

    2014-01-01

    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. PMID:25375184

  19. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

    Directory of Open Access Journals (Sweden)

    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.

  20. Australia`s uranium opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Alder, K.

    1996-12-31

    The book is a personal account by an insider who was deeply involved in the rise and fall of the Australian Atomic Energy Commission (AAEC), and in particular in its efforts to bring Australia into the nuclear age. It reveals the thinking behind the Commission`s research programmes and major projects, such as the centrifuge enrichment program and Jervis Bay Nuclear Power project. It shows how politics, politicians and sensational journalism had disastrous effects on the AAEC, its programmes and aspirations. ills.

  1. 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

  2. The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity.

    Directory of Open Access Journals (Sweden)

    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

  3. TH-A-BRF-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY) - Modeling Tumor Evolution for Adaptive Radiation Therapy

    International Nuclear Information System (INIS)

    Liu, Y; Lee, CG; Chan, TCY; Cho, YB; Islam, MK

    2014-01-01

    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

  4. 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

  5. Palaeozoic synorogenic sedimentation in central and northern Australia: a review of distribution and timing with implications for the evolution of intracontinental orogens

    International Nuclear Information System (INIS)

    Haines, P.W.; Hand, M.; Sandiford, M.

    2001-01-01

    The Palaeozoic Alice Springs Orogeny was a major intraplate tectonic event in central and northern Australia. The sedimentological, structural and isotopic effects of the Alice Springs Orogeny have been well documented in the northern Amadeus Basin and adjacent exhumed Arunta lnlier, although the full regional extent of the event, as well as lateral variations in timing and intensity are less well known. Because of the lack of regional isotopic data, we take a sedimentological approach towards constraining these parameters, compiling the location and age constraints of inferred synorogenic sedimentation across a number of central and northern Australian basins. Such deposits are recorded from the Amadeus, Ngalia, Georgina, Wiso, Eastern Officer and, possibly, Warburton Basins. Deposits are commonly located adjacent to areas of significant basement uplift related to north-south shortening. In addition, similar aged orogenic deposits occur in association with strike-slip tectonism in the Ord and southern Bonaparte Basins of northwest Australia. From a combination of sedimentological and isotopic evidence it appears that localised convergent deformation started in the Late Ordovician in the eastern Arunta lnlier and adjacent Amadeus Basin. Synorogenic style sedimentation becomes synchronously widespread in the late Early Devonian and in most areas the record terminates abruptly close to the end of the Devonian. A notable exception is the Ngalia Basin in which such sedimentation continued until the mid-Carboniferous. In the Ord and Bonaparte Basins there is evidence of two discrete pulses of transcurrent activity in the Late Devonian and Carboniferous. The sedimentological story contrasts with the isotopic record from the southern Arunta lnlier, which has generally been interpreted in terms of continuous convergent orogenic activity spanning most of the Devonian and Carboniferous, with a suggestion that rates of deformation increased in the mid-Carboniferous. Either

  6. The evolution of concepts of vestibular peripheral information processing: toward the dynamic, adaptive, parallel processing macular model

    Science.gov (United States)

    Ross, Muriel D.

    2003-01-01

    In a letter to Robert Hooke, written on 5 February, 1675, Isaac Newton wrote "If I have seen further than certain other men it is by standing upon the shoulders of giants." In his context, Newton was referring to the work of Galileo and Kepler, who preceded him. However, every field has its own giants, those men and women who went before us and, often with few tools at their disposal, uncovered the facts that enabled later researchers to advance knowledge in a particular area. This review traces the history of the evolution of views from early giants in the field of vestibular research to modern concepts of vestibular organ organization and function. Emphasis will be placed on the mammalian maculae as peripheral processors of linear accelerations acting on the head. This review shows that early, correct findings were sometimes unfortunately disregarded, impeding later investigations into the structure and function of the vestibular organs. The central themes are that the macular organs are highly complex, dynamic, adaptive, distributed parallel processors of information, and that historical references can help us to understand our own place in advancing knowledge about their complicated structure and functions.

  7. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yu; Chen, Xiao; Peng, Bingyin; Chen, Liyuan; Hou, Jin; Bao, Xiaoming [Shandong Univ., Jinan (China). State Key Lab. of Microbial Technology

    2012-11-15

    Factors related to ethanol production from xylose in engineered Saccharomyces cerevisiae that contain an exogenous initial metabolic pathway are still to be elucidated. In the present study, a strain that expresses the xylose isomerase gene of Piromyces sp. Pi-xylA and overexpresses XKS1, RPE1, RKI1, TAL1, and TKL1, with deleted GRE3 and COX4 genes was constructed. The xylose utilization capacity of the respiratory deficiency strain was poor but improved via adaptive evolution in xylose. The {mu}{sub max} of the evolved strain in 20 gl{sup -1} xylose is 0.11 {+-} 0.00 h{sup -1}, and the evolved strain consumed 17.83 gl{sup -1} xylose within 72 h, with an ethanol yield of 0.43 gg{sup -1} total consumed sugars during glucose-xylose cofermentation. Global transcriptional changes and effect of several specific genes were studied. The result revealed that the increased xylose isomerase activity, the upregulation of enzymes involved in glycolysis and glutamate synthesis, and the downregulation of trehalose and glycogen synthesis, may have contributed to the improved xylose utilization of the strain. Furthermore, the deletion of PHO13 decreased the xylose growth in the respiration deficiency strain although deleting PHO13 can improve the xylose metabolism in other strains. (orig.)

  8. Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation

    Directory of Open Access Journals (Sweden)

    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 oxidative stress.

  9. Genomic evidence of gene duplication and adaptive evolution of Toll like receptors (TLR2 and TLR4) in reptiles.

    Science.gov (United States)

    Shang, Shuai; Zhong, Huaming; Wu, Xiaoyang; Wei, Qinguo; Zhang, Huanxin; Chen, Jun; Chen, Yao; Tang, Xuexi; Zhang, Honghai

    2018-04-01

    Toll-like receptors (TLRs) encoded by the TLR multigene family play an important role in initial pathogen recognition in vertebrates. Among the TLRs, TLR2 and TLR4 may be of particular importance to reptiles. In order to study the evolutionary patterns and structural characteristics of TLRs, we explored the available genomes of several representative members of reptiles. 25 TLR2 genes and 19 TLR4 genes from reptiles were obtained in this study. Phylogenetic results showed that the TLR2 gene duplication occurred in several species. Evolutionary analysis by at least two methods identified 30 and 13 common positively selected codons in TLR2 and TLR4, respectively. Most positively selected sites of TLR2 and TLR4 were located in the Leucine-rich repeat (LRRs). Branch model analysis showed that TLR2 genes were under different evolutionary forces in reptiles, while the TLR4 genes showed no significant selection pressure. The different evolutionary adaptation of TLR2 and TLR4 among the reptiles might be due to their different function in recognizing bacteria. Overall, we explored the structure and evolution of TLR2 and TLR4 genes in reptiles for the first time. Our study revealed valuable information regarding TLR2 and TLR4 in reptiles, and provided novel insights into the conservation concern of natural populations. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Multi-objective trajectory optimization of Space Manoeuvre Vehicle using adaptive differential evolution and modified game theory

    Science.gov (United States)

    Chai, Runqi; Savvaris, Al; Tsourdos, Antonios; Chai, Senchun

    2017-07-01

    Highly constrained trajectory optimization for Space Manoeuvre Vehicles (SMV) is a challenging problem. In practice, this problem becomes more difficult when multiple mission requirements are taken into account. Because of the nonlinearity in the dynamic model and even the objectives, it is usually hard for designers to generate a compromised trajectory without violating strict path and box constraints. In this paper, a new multi-objective SMV optimal control model is formulated and parameterized using combined shooting-collocation technique. A modified game theory approach, coupled with an adaptive differential evolution algorithm, is designed in order to generate the pareto front of the multi-objective trajectory optimization problem. In addition, to improve the quality of obtained solutions, a control logic is embedded in the framework of the proposed approach. Several existing multi-objective evolutionary algorithms are studied and compared with the proposed method. Simulation results indicate that without driving the solution out of the feasible region, the proposed method can perform better in terms of convergence ability and convergence speed than its counterparts. Moreover, the quality of the pareto set generated using the proposed method is higher than other multi-objective evolutionary algorithms, which means the newly proposed algorithm is more attractive for solving multi-criteria SMV trajectory planning problem.

  11. pSum-SaDE: A Modified p-Median Problem and Self-Adaptive Differential Evolution Algorithm for Text Summarization

    Directory of Open Access Journals (Sweden)

    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.

  12. A place to call home: study protocol for a longitudinal, mixed methods evaluation of two housing first adaptations in Sydney, Australia.

    Science.gov (United States)

    Whittaker, Elizabeth; Swift, Wendy; Flatau, Paul; Dobbins, Timothy; Schollar-Root, Olivia; Burns, Lucinda

    2015-04-09

    This protocol describes a study evaluating two 'Housing First' programs, Platform 70 and Common Ground, presently being implemented in the inner-city region of Sydney, Australia. The Housing First approach prioritises housing individuals who are homeless in standard lease agreement tenancies as rapidly as possible to lock in the benefits from long-term accommodation, even where the person may not be seen as 'housing ready'. The longitudinal, mixed methods evaluation utilises both quantitative and qualitative data collected at baseline and 12-month follow-up time points. For the quantitative component, clients of each program were invited to complete client surveys that reported on several factors associated with chronic homelessness and were hypothesised to improve under stable housing, including physical and mental health status and treatment rates, quality of life, substance use patterns, and contact with the health and criminal justice systems. Semi-structured interviews with clients and stakeholders comprised the qualitative component and focused on individual experiences with, and perceptions of, the two programs. In addition, program data on housing stability, rental subsidies and support levels provided to clients by agencies was collected and will be used in conjunction with the client survey data to undertake an economic evaluation of the two programs. This study will systematically evaluate the efficacy of a scatter site model (Platform 70) and a congregated model (Common Ground) of the Housing First approach; an examination that has not yet been made either in Australia or internationally. A clear strength of the study is its timing. It was designed and implemented as the programs in question themselves were introduced. Moreover, the programs were introduced when the Australian Government, with State and Territory support, began a more focused, coordinated response to homelessness and funded rapid expansion of innovative homelessness programs across the

  13. Evolution in Australia's mesic biome under past and future climates: Insights from a phylogenetic study of the Australian Rock Orchids (Dendrobium speciosum complex, Orchidaceae).

    Science.gov (United States)

    Simpson, Lalita; Clements, Mark A; Crayn, Darren M; Nargar, Katharina

    2018-01-01

    The Australian mesic biome spans c. 33° of latitude along Australia's east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary diversification and to predict the impact of future climate change on the distribution of species and genetic diversity within this biome, we inferred phylogenetic relationships within the Dendrobium speciosum complex (Orchidaceae) across its distribution and undertook environmental niche modelling (ENM) under past, contemporary and projected future climates. Neighbor Joining tree inference, NeighborNet and Structure analyses of Amplified Fragment Length Polymorphism (AFLP) profiles for D. speciosum sampled from across its distribution showed that the complex consists of two highly supported main groups that are geographically separated by the St. Lawrence gap, an area of dry sclerophyll forest and woodland. The presence of several highly admixed individuals identified by the Structure analysis provided evidence of genetic exchange between the two groups across this gap. Whereas previous treatments have recognised between one to eleven species, the molecular results support the taxonomic treatment of the complex as a single species with two subspecies. The ENM analysis supported the hypothesis that lineage divergence within the complex was driven by past climatic changes. The St. Lawrence gap represented a stronger biogeographic barrier for the D. speciosum complex during the cool and dry glacial climatic conditions of the Pleistocene than under today's interglacial conditions. Shallow genetic divergence was found within the two lineages, which mainly corresponded to three other biogeographic barriers: the Black Mountain Corridor, Glass House Mountains and the Hunter Valley. Our ENM analyses provide further support for the hypothesis that biogeographic barriers along Australia's east coast were somewhat permeable to genetic exchange due to

  14. Last Glacial Maximum to Holocene climate evolution controlled by sea-level change, Leeuwin Current, and Australian Monsoon in the Northwestern Australia

    Science.gov (United States)

    Ishiwa, T.; Yokoyama, Y.; McHugh, C.; Reuning, L.; Gallagher, S. J.

    2017-12-01

    The transition from cold to warm conditions during the last deglaciation influenced climate variability in the Indian Ocean and Pacific as a result of submerge of continental shelf and variations in the Indonesian Throughflow and Australian Monsoon. The shallow continental shelf (Program Expedition 356 Indonesian Throughflow drilled in the northwestern Australian shallow continental shelf and recovered an interval from the Last Glacial Maximum to Holocene in Site U1461. Radiocarbon dating on macrofossils, foraminifera, and bulk organic matter provided a precise age-depth model, leading to high-resolved paleoclimate reconstruction. X-ray elemental analysis results are interpreted as an indicator of sedimentary environmental changes. The upper 20-m part of Site U1461 apparently records the climate transition from the LGM to Holocene in the northwestern Australia, which could be associated with sea-level change, Leeuwin Current activity, and the Australian Monsoon.

  15. Harvesting Australia's mineral wealth

    Energy Technology Data Exchange (ETDEWEB)

    1982-07-01

    Anderson Strathclyde plc is becoming increasingly involved in supplying equipment for the coal industry in Australia. It now has 2 subsidiary companies based in Australia: Anderson Strathclyde Australia and A B Rea.

  16. Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group.

    Directory of Open Access Journals (Sweden)

    Tiago R Simões

    Full Text Available Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes that radiated during the Late Cretaceous (95-66 million years ago. They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates. In this study, we present the first mosasauroid phylogenetic analysis performed under different analytical methods, including maximum likelihood, Bayesian inference, and implied weighting maximum parsimony. The results indicate a lack of congruence in the topological position of halisaurines and Dallasaurus. Additionally, the genus Prognathodon is paraphyletic under all hypotheses. Interestingly, a number of traditional mosasauroid clades become weakly supported, or unresolved, under Bayesian analyses. The reduced resolutions in some consensus trees create ambiguities concerning the evolution of fully aquatic pelvic/pedal conditions under many analyses. However, when enough resolution was obtained, reversals of the pelvic/pedal conditions were favoured by parsimony and likelihood ancestral state reconstructions instead of independent origins of aquatic features in mosasauroids. It is concluded that most of the observed discrepancies among the results can be associated with different analytical procedures, but also due to limited postcranial data on halisaurines, yaguarasaurines and Dallasaurus.

  17. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.

    Science.gov (United States)

    Ceapa, Corina; Davids, Mark; Ritari, Jarmo; Lambert, Jolanda; Wels, Michiel; Douillard, François P; Smokvina, Tamara; de Vos, Willem M; Knol, Jan; Kleerebezem, Michiel

    2016-07-02

    Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

    Directory of Open Access Journals (Sweden)

    David F Gruber

    Full Text Available We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs. Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp., two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II. We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein's fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

  19. Testing biological hypotheses with embodied robots: adaptations, accidents, and by-products in the evolution of vertebrates

    Directory of Open Access Journals (Sweden)

    Sonia F Roberts

    2014-11-01

    Full Text Available Evolutionary robotics allows biologists to test hypotheses about extinct animals. We modeled some of the first vertebrates, jawless fishes, in order to study the evolution of the trait after which vertebrates are named: vertebrae. We tested the hypothesis that vertebrae are an adaptation for enhanced feeding and fleeing performance. We created a population of autonomous embodied robots, Preyro, in which the number of vertebrae, N, were free to evolve. In addition, two other traits, the span of the caudal fin, b, and the predator detection threshold, ζ, a proxy for the lateral line sensory system, were also allowed to evolve. These three traits were chosen because they evolved early in vertebrates, are all potentially important in feeding and fleeing, and vary in form among species. Preyro took on individual identities in a given generation as defined by the population’s six diploid genotypes, Gi. Each Gi was a 3-tuple, with each element an integer specifying N, b, and, ζ. The small size of the population allowed for genetic drift to operate in concert with random mutation and mating; the presence of these mechanisms of chance provided an opportunity for N to evolve by accident. The presence of three evolvable traits provided an opportunity for direct selection on b and/or ζ to evolve N as a by-product linked trait correlation. In selection trials, different Gi embodied in Preyro attempted to feed at a light source and then flee to avoid a predator robot in pursuit. The fitness of each Gi was calculated from five different types of performance: speed, acceleration, distance to the light, distance to the predator, and the number of predator escapes initiated. In each generation, we measured the selection differential, the selection gradient, the strength of chance, and the indirect correlation selection gradient. These metrics allowed us to understand the relative contributions of the three mechanisms: direct selection, chance, and indirect

  20. Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group

    Science.gov (United States)

    Vernygora, Oksana; Paparella, Ilaria; Jimenez-Huidobro, Paulina; Caldwell, Michael W.

    2017-01-01

    Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes) that radiated during the Late Cretaceous (95–66 million years ago). They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted) maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates. In this study, we present the first mosasauroid phylogenetic analysis performed under different analytical methods, including maximum likelihood, Bayesian inference, and implied weighting maximum parsimony. The results indicate a lack of congruence in the topological position of halisaurines and Dallasaurus. Additionally, the genus Prognathodon is paraphyletic under all hypotheses. Interestingly, a number of traditional mosasauroid clades become weakly supported, or unresolved, under Bayesian analyses. The reduced resolutions in some consensus trees create ambiguities concerning the evolution of fully aquatic pelvic/pedal conditions under many analyses. However, when enough resolution was obtained, reversals of the pelvic/pedal conditions were favoured by parsimony and likelihood ancestral state reconstructions instead of independent origins of aquatic features in mosasauroids. It is concluded that most of the observed discrepancies among the results can be associated with different analytical procedures, but also due to limited postcranial data on halisaurines, yaguarasaurines and Dallasaurus. PMID:28467456

  1. Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

    KAUST Repository

    Auzinger, Winfried; Hofstä tter, Harald; Ketcheson, David I.; Koch, Othmar

    2016-01-01

    We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

  2. Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

    KAUST Repository

    Auzinger, Winfried

    2016-07-28

    We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

  3. The evolution of a Late Cretaceous-Cenozoic intraplate basin (Duaringa Basin), eastern Australia: evidence for the negative inversion of a pre-existing fold-thrust belt

    Science.gov (United States)

    Babaahmadi, Abbas; Sliwa, Renate; Esterle, Joan; Rosenbaum, Gideon

    2017-12-01

    The Duaringa Basin in eastern Australia is a Late Cretaceous?-early Cenozoic sedimentary basin that developed simultaneously with the opening of the Tasman and Coral Seas. The basin occurs on the top of an earlier (Permian-Triassic) fold-thrust belt, but the negative inversion of this fold-thrust belt, and its contribution to the development of the Duaringa Basin, are not well understood. Here, we present geophysical datasets, including recently surveyed 2D seismic reflection lines, aeromagnetic and Bouguer gravity data. These data provide new insights into the structural style in the Duaringa Basin, showing that the NNW-striking, NE-dipping, deep-seated Duaringa Fault is the main boundary fault that controlled sedimentation in the Duaringa Basin. The major activity of the Duaringa Fault is observed in the southern part of the basin, where it has undergone the highest amount of displacement, resulting in the deepest and oldest depocentre. The results reveal that the Duaringa Basin developed in response to the partial negative inversion of the pre-existing Permian-Triassic fold-thrust belt, which has similar orientation to the extensional faults. The Duaringa Fault is the negative inverted part of a single Triassic thrust, known as the Banana Thrust. Furthermore, small syn-depositional normal faults at the base of the basin likely developed due to the reactivation of pre-existing foliations, accommodation faults, and joints associated with Permian-Triassic folds. In contrast to equivalent offshore basins, the Duaringa Basin lacks a complex structural style and thick syn-rift sediments, possibly because of the weakening of extensional stresses away from the developing Tasman Sea.

  4. Oxygen isotopic composition of carbonate concretions from the lower Cretaceous of Victoria, Australia: Implications for the evolution of meteoric waters on the Australian continent in a paleopolar environment

    International Nuclear Information System (INIS)

    Gregory, R.T.

    1989-01-01

    Oxygen isotopic data from carbonate cements in concretions have been used to infer the isotopic composition of meteoric fluids present at the time of concretion growth in terrestrial sediments that were deposited within the early Cretaceous South Polar Circle at 75-80 0 S. Carbon and oxygen isotope compositions have been determined on over 135 samples of carbonate from 45 concretions taken from 24 localities (Aptian-Albian in age) in the terrestrial sedimentary basins associated with the Otway and Strzelecki groups, southeastern Australia. The carbonate cements include calcite having -26.4≤δ 13 C≤19.6 and 3.6≤δ 18 O≤29.6 or siderite having 17.6≤δ 18 O≤30.8. Calcite-cemented concretions are more abundant and are interpreted to represent early near-surface cementation events on the basis of textural evidence such as high (>30%) porosities at the time of cementation and mineralogical evidence such as the preferential preservation within concretions of labile detrital grains including plagioclase, pyroxene, and amphibole. The oxygen isotopic data indicate that meteoric fluids with very low δ 18 O, certainly less than -15per mille and probably on the order of -20per mille, were involved in the precipitation of the early calcites. The extremely low δ 18 O values of the fluids involved in the early diagenesis of both the Otway and Strzelecki groups suggest that the catchment area of the river system that carried sediments to these basins had a cold high-latitude climate (with mean annual temperatures less than 5 0 C and quite possibly below freezing). By analogy with the relationship between modern 18 O distribution of meteoric fluids and climate, these new data suggest that the early Cretaceous polar regions may not have been ice-free. (orig.)

  5. The emerging role of Australia in using adaptive management for developing built environment and sustainable architecture innovations as a contribution to stabilising the planet

    Energy Technology Data Exchange (ETDEWEB)

    Baverstock, Garry [Murdoch Univ., Western Australia (AU). RISE (Research Inst. for Sustainable Energy); Parker, Ian

    2008-07-01

    The built environment is severely affecting the Earth's ecology. If we continue to pursue our immediate comfort and interests, we will consign future generations to a world that we would not want to live in. CO{sub 2} levels are still rising. The last time CO{sub 2} reached current levels (Eocene), sea levels were 30-100m above present. Temperatures and sea levels are rising. Storms are increasing in frequency and intensity. To move forward effectively we must have a credible process that explores all options that reduce greenhouse emissions. A transparent systemic learning process, total accounting and adaptive model based scenario building are needed to guide reduction of built form impact on Global warming. (orig.)

  6. Optimal Decision Fusion for Urban Land-Use/Land-Cover Classification Based on Adaptive Differential Evolution Using Hyperspectral and LiDAR Data

    Directory of Open Access Journals (Sweden)

    Yanfei Zhong

    2017-08-01

    Full Text Available Hyperspectral images and light detection and ranging (LiDAR data have, respectively, the high spectral resolution and accurate elevation information required for urban land-use/land-cover (LULC classification. To combine the respective advantages of hyperspectral and LiDAR data, this paper proposes an optimal decision fusion method based on adaptive differential evolution, namely ODF-ADE, for urban LULC classification. In the ODF-ADE framework the normalized difference vegetation index (NDVI, gray-level co-occurrence matrix (GLCM and digital surface model (DSM are extracted to form the feature map. The three different classifiers of the maximum likelihood classifier (MLC, support vector machine (SVM and multinomial logistic regression (MLR are used to classify the extracted features. To find the optimal weights for the different classification maps, weighted voting is used to obtain the classification result and the weights of each classification map are optimized by the differential evolution algorithm which uses a self-adaptive strategy to obtain the parameter adaptively. The final classification map is obtained after post-processing based on conditional random fields (CRF. The experimental results confirm that the proposed algorithm is very effective in urban LULC classification.

  7. Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae).

    Science.gov (United States)

    Rix, Michael G; Cooper, Steven J B; Meusemann, Karen; Klopfstein, Seraina; Harrison, Sophie E; Harvey, Mark S; Austin, Andrew D

    2017-04-01

    The formation and spread of the Australian arid zone during the Neogene was a profoundly transformative event in the biogeographic history of Australia, resulting in extinction or range contraction in lineages adapted to mesic habitats, as well as diversification and range expansion in arid-adapted taxa (most of which evolved from mesic ancestors). However, the geographic origins of the arid zone biota are still relatively poorly understood, especially among highly diverse invertebrate lineages, many of which are themselves poorly documented at the species level. Spiny trapdoor spiders (Idiopidae: Arbanitinae) are one such lineage, having mesic 'on-the-continent' Gondwanan origins, while also having experienced major arid zone radiations in select clades. In this study, we present new orthologous nuclear markers for the phylogenetic inference of mygalomorph spiders, and use them to infer the phylogeny of Australasian Idiopidae with a 12-gene parallel tagged amplicon next-generation sequencing approach. We use these data to test the mode and timing of diversification of arid-adapted idiopid lineages across mainland Australia, and employ a continent-wide sampling of the fauna's phylogenetic and geographic diversity to facilitate ancestral area inference. We further explore the evolution of phenotypic and behavioural characters associated with both arid and mesic environments, and test an 'out of south-western Australia' hypothesis for the origin of arid zone clades. Three lineages of Idiopidae are shown to have diversified in the arid zone during the Miocene, one (genus Euoplos) exclusively in Western Australia. Arid zone Blakistonia likely had their origins in South Australia, whereas in the most widespread genus Aganippe, a more complex scenario is evident, with likely range expansion from southern Western Australia to southern South Australia, from where the bulk of the arid zone fauna then originated. In Aganippe, remarkable adaptations to phragmotic burrow

  8. Experimental Evolution of UV-C Radiation Tolerance: Emergence of Adaptive and Non-Adaptive Traits in Escherichia coli Under Differing Flux Regimes

    Science.gov (United States)

    Moffet, A.; Okansinski, A.; Sloan, C.; Grace, J. M.; Paulino-Lima, I. G.; Gentry, D.; Rothschild, L. J.; Camps, M.

    2014-12-01

    High-energy ultraviolet (UV-C) radiation is a significant challenge to life in environments such as high altitude areas, the early Earth, the Martian surface, and space. As UV-C exposure is both a selection pressure and a mutagen, adaptation dynamics in such environments include a high rate of change in both tolerance-related and non-tolerance-related genes, as well changes in linkages between the resulting traits. Determining the relationship between the intensity and duration of the UV-C exposure, mutation rate, and emergence of UV-C resistance will inform our understanding of both the emergence of radiation-related extremophily in natural environments and the optimal strategies for generating artificial extremophiles. In this study, we iteratively exposed an Escherichia colistrain to UV-C radiation of two different fluxes, 3.3 J/m^2/s for 6 seconds and 0.5 J/m^2/s for 40 seconds, with the same overall fluence of 20 J/m^2. After each iteration, cells from each exposure regime were assayed for increased UV-C tolerance as an adaptive trait. The exposed cells carried a plasmid bearing a TEM beta-lactamase gene, which in the absence of antibiotic treatment is a neutral reporter for mutagenesis. Sequencing of this gene allowed us to determine the baseline mutation frequency for each flux. As an additional readout for adaptation, the presence of extended-spectrum beta-lactamase mutations was tested by plating UV-exposed cultures in cefotaxime plates. We observed an increase of approximately one-million-fold in UV-C tolerance over seven iterations; no significant difference between the two fluxes was found. Future work will focus on identifying the genomic changes responsible for the change in UV-C tolerance; determining the mechanisms of the emerged UV-C tolerance; and performing competition experiments between the iteration strains to quantify fitness tradeoffs resulting from UV-C adaptation.

  9. Adaptive Laboratory Evolution Of Escherichia Coli Reveals Arduous Resistance Development To A Combination Of Three Novel Antimicrobial Compounds And To The Short Amp P9-4

    DEFF Research Database (Denmark)

    Citterio, Linda; Franzyk, Henrik; Gram, Lone

    2015-01-01

    Antimicrobial peptides (AMPs) were for long considered as promising new antimicrobials since resistance was not expected. However, adaptive evolution experiments have demonstrated that bacteria may indeed develop resistance also to AMPs. However, we and others hypothesize that the risk...... of resistance development decreases when two or more compounds are combined as compared to single-drug treatments. The purpose of this study was to determine if resistance could develop in Escherichia coli ATCC 25922 to the peptidomimetic HF-1002 2 and the AMPs novicidin and P9-4. The mentioned compounds were...... adaptation to 32 x MIC. This shows that resistance to novicidin and HF-1002 2, administered alone, developed more easily than it occurred in lineages exposed to the combination of three drugs. This result further supports combinatorial treatment as a way to circumvent resistance development. Surprisingly...

  10. Besshi-type mineral systems in the Palaeoproterozoic Bryah Rift-Basin, Capricorn Orogen, Western Australia: Implications for tectonic setting and geodynamic evolution

    Directory of Open Access Journals (Sweden)

    Franco Pirajno

    2016-05-01

    Full Text Available In this contribution we use VMS mineral systems in the Bryah rift-basin to constrain the tectonic setting of the widespread mafic and ultramafic magmatism that characterises the rift-basin in question. Two distinct, but temporally closely associated, lithostratigraphic sequences, Narracoota and Karalundi Formations, are discussed. The Karalundi Formation is the main host of VMS mineral systems in the region. The Karalundi Formation consists of turbiditic and immature clastic sediments, which are locally intercalated with basaltic hyaloclastites, dolerites and banded jaspilites. We propose that the basaltic hyaloclastites, dolerites and clastics and jaspilites rocks, form a distinct unit of the Karalundi Formation, named Noonyereena Member. The VMS mineral systems occur near the north-east trending Jenkin Fault and comprise the giant and world-class DeGrussa and the Red Bore deposits. The nature of these deposits and their intimate association with terrigenous clastic rocks and dominantly marine mafic volcanic and subvolcanic rocks, as well as the common development of peperitic margins, are considered indicative of a Besshi-type environment, similar to that of present-day Gulf of California. Our Re-Os age data from a primary pyrite yielded a mean model age of 2012 ± 48 Ma, which coincides (within error with recent published Re-Os data (Hawke et al., 2015 and confirms the timing of the proposed geodynamic evolution. We propose a geodynamic model that attempts to explain the presence of the Narracoota and Karalundi Formations as the result of mantle plume activity, which began with early uplift of continental crust with intraplate volcanism, followed by early stages of rifting with the deposition of the Karalundi Formation (and Noonyereena Member, which led to the formation of Besshi-type VMS deposits. With on-going mantle plume activity and early stages of continental separation, an oceanic plateau was formed and is now represented by mafic

  11. Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China

    Directory of Open Access Journals (Sweden)

    Yun Jia

    2017-07-01

    Full Text Available The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq to characterize the transcriptomes of the two species. In total, more than 130 million sequence reads, 81,446 and 63,153 unigenes with total lengths of 86,924,837 and 62,615,693 bp, were generated for the two herbal species, respectively. OrthoMCL analysis identified 6375 single-copy orthologous genes between N. incisum and N. franchetii. In total, 381 positively-selected candidate genes were identified for both plants by using estimations of the non-synonymous to synonymous substitution rate. At least 18 of these genes potentially participate in RNA splicing, DNA repair, glutathione metabolism and the plant–pathogen interaction pathway, which were further enriched in various functional gene categories possibly responsible for environment adaptation in high mountains. Meanwhile, we detected various transcription factors that regulated the material and energy metabolism in N. incisum and N. franchetii, which probably play vital roles in the tolerance to stress in surroundings. In addition, 60 primer pairs based on orthologous microsatellite-containing sequences between the both Notopterygium species were determined. Finally, 17 polymorphic microsatellite markers (SSR were successfully characterized for the two endangered species. Based on these candidate orthologous and SSR markers, we detected that the adaptive evolution and species divergence

  12. Uranium mining in Australia

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    The mining of uranium in Australia is criticised in relation to it's environmental impact, economics and effects on mine workers and Aborigines. A brief report is given on each of the operating and proposed uranium mines in Australia

  13. Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in 'Evolution Canyon', Israel.

    Science.gov (United States)

    Sikorski, Johannes; Pukall, Rüdiger; Stackebrandt, Erko

    2008-10-01

    The 'Evolution Canyons' I and II in Israel are model habitats to study adaptation and speciation of bacteria in the environment. These canyons represent similar ecological replicates, separated by 40 km, with a strongly sun-exposed and hot 'African' south-facing slope (SFS) vs. a cooler and mesic-lush 'European' north-facing slope (NFS). Previously, among 131 Bacillus simplex isolates, distinct genetic lineages (ecotypes), each specific for either SFS or NFS, were identified, suggesting a temperature-driven slope-specific adaptation. Here, we asked whether the ecological heterogeneity of SFS vs. NFS also affected carbon utilization abilities, as determined using the Biolog assay. Contrary to expectation, a correlation between substrate utilization patterns and the ecological origin of strains was not found. Rather, the patterns split according to the two major phylogenetic lineages each of which contain SFS and NFS ecotypes. We conclude that traits related to the general energy metabolism, as far as assessed here, are neither shaped by the major abiotic features of 'Evolution Canyon', namely solar radiation, temperature, and drought, nor by the soil characteristics. We further conclude that some traits diverge rather neutrally from each other, whereas other, more environmentally related traits are shaped by natural selection and show evolutionary convergence.

  14. What kind of memory has evolution wrought? Introductory article for the special issue of memory: adaptive memory: the emergence and nature of proximate mechanisms.

    Science.gov (United States)

    Otgaar, Henry; Howe, Mark L

    2014-01-01

    It is without question that our memory system evolved through a process of natural selection. However, basic research into the evolutionary foundations of memory has begun in earnest only recently. This is quite peculiar as the majority, perhaps even all, of memory research relates to whether memory is adaptive or not. In this Special Issue of Memory we have assembled a variety of papers that represent the cutting edge in research on the evolution of memory. These papers are centred on issues about the ultimate and proximate explanations of memory, the development of the adaptive functions of memory, as well as the positive consequences that arise from the current evolutionary form that our memory has taken. In this introductory article we briefly outline these different areas and indicate why they are vital for a more complete theory of memory. Further we argue that, by adopting a more applied stance in the area of the evolution of memory, one of the many future directions in this field could be a new branch of psychology that addresses questions in evolutionary legal psychology.

  15. The evolution and adaptation of clinical Pseudomonas aeruginosa isolates from early cystic fibrosis infections

    DEFF Research Database (Denmark)

    Lindegaard, Mikkel

    system (T3SS). This suggests that the current dogma of this regulatory system does not adequately explain the biological significance of this system, as the opposite mutation pattern would be expected if this dogma were true. Furthermore, we show that the residual evolution caused by other mutations also...

  16. Adaptive evolution during the establishment of European avian-like H1N1 influenza A virus in swine.

    Science.gov (United States)

    Joseph, Udayan; Vijaykrishna, Dhanasekaran; Smith, Gavin J D; Su, Yvonne C F

    2018-04-01

    An H1N1 subtype influenza A virus with all eight gene segments derived from wild birds (including mallards), ducks and chickens, caused severe disease outbreaks in swine populations in Europe beginning in 1979 and successfully adapted to form the European avian-like swine (EA-swine) influenza lineage. Genes of the EA-swine lineage that are clearly segregated from its closest avian relatives continue to circulate in swine populations globally and represent a unique opportunity to study the adaptive process of an avian-to-mammalian cross-species transmission. Here, we used a relaxed molecular clock model to test whether the EA-swine virus originated through the introduction of a single avian ancestor as an entire genome, followed by an analysis of host-specific selection pressures among different gene segments. Our data indicated independent introduction of gene segments via transmission of avian viruses into swine followed by reassortment events that occurred at least 1-4 years prior to the EA-swine outbreak. All EA-swine gene segments exhibit greater selection pressure than avian viruses, reflecting both adaptive pressures and relaxed selective constraints that are associated with host switching. Notably, we identified key amino acid mutations in the viral surface proteins (H1 and N1) that play a role in adaptation to new hosts. Following the establishment of EA-swine lineage, we observed an increased frequency of intrasubtype reassortment of segments compared to the earlier strains that has been associated with adaptive amino acid replacements, disease severity and vaccine escape. Taken together, our study provides key insights into the adaptive changes in viral genomes following the transmission of avian influenza viruses to swine and the early establishment of the EA-swine lineage.

  17. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    Directory of Open Access Journals (Sweden)

    Giuseppina Rea

    2011-01-01

    Full Text Available Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues

  18. When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations

    Science.gov (United States)

    For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human-mediated environmental changes. Yet large persistent populations of small bodied fish residing in some of the most contaminated estuaries of the US have provided some...

  19. Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

    Science.gov (United States)

    Andrew J. Eckert; Andrew D. Bower; Kathleen D. Jermstad; Jill L. Wegrzyn; Brian J. Knaus; John V. Syring; David B. Neale

    2013-01-01

    Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life history strategies as they influence the effective population size (Ne). Ample variation for these estimates, however, remains even when...

  20. Can a genetic correlation with seed mass constrain adaptive evolution of seedling desiccation tolerance in wild barley?

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Biere, A.; Nevo, E.; Van Damme, J.M.M.

    2004-01-01

    Very young seedlings of wild barley Hordeum spontaneum have the ability to survive extended periods of severe drought. This desiccation tolerance is considered an adaptation to the rain-limited and unpredictable habitats that the species occupies. Genetic variation has been observed for this trait,

  1. Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution ▿†

    OpenAIRE

    Fricke, W. Florian; Mammel, Mark K.; McDermott, Patrick F.; Tartera, Carmen; White, David G.; LeClerc, J. Eugene; Ravel, Jacques; Cebula, Thomas A.

    2011-01-01

    Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss pla...

  2. Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution ▿†

    Science.gov (United States)

    Fricke, W. Florian; Mammel, Mark K.; McDermott, Patrick F.; Tartera, Carmen; White, David G.; LeClerc, J. Eugene; Ravel, Jacques; Cebula, Thomas A.

    2011-01-01

    Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks. PMID:21602358

  3. Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.

    Science.gov (United States)

    Kishimoto, Toshihiko; Iijima, Leo; Tatsumi, Makoto; Ono, Naoaki; Oyake, Ayana; Hashimoto, Tomomi; Matsuo, Moe; Okubo, Masato; Suzuki, Shingo; Mori, Kotaro; Kashiwagi, Akiko; Furusawa, Chikara; Ying, Bei-Wen; Yomo, Tetsuya

    2010-10-21

    It remains to be determined experimentally whether increasing fitness is related to positive selection, while stationary fitness is related to neutral evolution. Long-term laboratory evolution in Escherichia coli was performed under conditions of thermal stress under defined laboratory conditions. The complete cell growth data showed common continuous fitness recovery to every 2°C or 4°C stepwise temperature upshift, finally resulting in an evolved E. coli strain with an improved upper temperature limit as high as 45.9°C after 523 days of serial transfer, equivalent to 7,560 generations, in minimal medium. Two-phase fitness dynamics, a rapid growth recovery phase followed by a gradual increasing growth phase, was clearly observed at diverse temperatures throughout the entire evolutionary process. Whole-genome sequence analysis revealed the transition from positive to neutral in mutation fixation, accompanied with a considerable escalation of spontaneous substitution rate in the late fitness recovery phase. It suggested that continually increasing fitness not always resulted in the reduction of genetic diversity due to the sequential takeovers by fit mutants, but caused the accumulation of a considerable number of mutations that facilitated the neutral evolution.

  4. The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

    2009-04-01

    Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have

  5. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

    OpenAIRE

    Sosa, Victoria; Ornelas, Juan Francisco; Ram?rez-Barahona, Santiago; G?ndara, Etelvina

    2016-01-01

    Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted...

  6. Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes.

    Science.gov (United States)

    Zhu, Lifeng; Wu, Qi; Deng, Cao; Zhang, Mengjie; Zhang, Chenglin; Chen, Hua; Lu, Guoqing; Wei, Fuwen

    2018-05-01

    Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g., Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g., badgers, bears and pandas). The relative proportions of genes encoding enzymes involved in uric acid degradation were higher in the gut microbiomes of meat-eating carnivorans than plant-eating species. Adaptive amino acid substitutions in two enzymes, carnitine O-palmitoyltransferase 1 (CPT1A) and lipase F (LIPF), which play a role in fat digestion, were identified in Felidae-Candidae species. Carnivorous carnivorans appear to endure diets high in purines and fats via gut microbiomic and genomic adaptations. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Depression in Aboriginal men in central Australia

    DEFF Research Database (Denmark)

    Brown, Alex D.H.; Mentha, Ricky; Rowley, Kevin G.

    2013-01-01

    groups comprising of members from primary Indigenous language groups in central Australia. First, focus group participants were asked to review and select a screening measure for adaptation. Bi-lingual experts then translated and back translated the language within the selected measure. Focus group...

  8. Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats

    Science.gov (United States)

    Zhang, Nan; Yang, Dongqing; Kendall, Joshua R. A.; Borriss, Rainer; Druzhinina, Irina S.; Kubicek, Christian P.; Shen, Qirong; Zhang, Ruifu

    2016-01-01

    Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens—B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production. PMID:28066362

  9. Myxomatosis in Australia and Europe: a model for emerging infectious diseases.

    Science.gov (United States)

    Kerr, Peter J

    2012-03-01

    Myxoma virus is a poxvirus naturally found in two American leporid (rabbit) species (Sylvilagus brasiliensis and Sylvilagus bachmani) in which it causes an innocuous localised cutaneous fibroma. However, in European rabbits (Oryctolagus cuniculus) the same virus causes the lethal disseminated disease myxomatosis. The introduction of myxoma virus into the European rabbit population in Australia in 1950 initiated the best known example of what happens when a novel pathogen jumps into a completely naïve new mammalian host species. The short generation time of the rabbit and their vast numbers in Australia meant evolution could be studied in real time. The carefully documented emergence of attenuated strains of virus that were more effectively transmitted by the mosquito vector and the subsequent selection of rabbits with genetic resistance to myxomatosis is the paradigm for pathogen virulence and host-pathogen coevolution. This natural experiment was repeated with the release of a separate strain of myxoma virus in France in 1952. The subsequent spread of the virus throughout Europe and its coevolution with the rabbit essentially paralleled what occurred in Australia. Detailed molecular studies on myxoma virus have dissected the role of virulence genes in the pathogenesis of myxomatosis and when combined with genomic data and reverse genetics should in future enable the understanding of the molecular evolution of the virus as it adapted to its new host. This review describes the natural history and evolution of myxoma virus together with the molecular biology and experimental pathogenesis studies that are informing our understanding of evolution of emerging diseases. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

  10. The Evolution of an Ecosystem Approach: the Diamond Schematic and an Adaptive Methodology for Ecosystem Sustainability and Health

    Directory of Open Access Journals (Sweden)

    David Waltner-Toews

    2005-06-01

    Full Text Available Over the past 15 yr, an international network of researchers has developed and tested a methodology for integrating complex systems theories into sustainable development projects. Drawing on our best theoretical understanding of complex systems and combining it with best practices of community engagement drawn from a wide variety of sources, we have developed a methodology that is theoretically sound and practically effective. AMESH, an Adaptive Methodology for Ecosystem Sustainability and Health, has emerged from, and been tested in, Nepal, Kenya, Canada, and Peru.

  11. Resilience through adaptation

    NARCIS (Netherlands)

    Broeke, ten Guus; Voorn, van George A.K.; Ligtenberg, Arend; Molenaar, Jaap

    2017-01-01

    Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations

  12. Toward a new task assignment and path evolution (TAPE) for missile defense system (MDS) using intelligent adaptive SOM with recurrent neural networks (RNNs).

    Science.gov (United States)

    Wang, Chi-Hsu; Chen, Chun-Yao; Hung, Kun-Neng

    2015-06-01

    In this paper, a new adaptive self-organizing map (SOM) with recurrent neural network (RNN) controller is proposed for task assignment and path evolution of missile defense system (MDS). We address the problem of N agents (defending missiles) and D targets (incoming missiles) in MDS. A new RNN controller is designed to force an agent (or defending missile) toward a target (or incoming missile), and a monitoring controller is also designed to reduce the error between RNN controller and ideal controller. A new SOM with RNN controller is then designed to dispatch agents to their corresponding targets by minimizing total damaging cost. This is actually an important application of the multiagent system. The SOM with RNN controller is the main controller. After task assignment, the weighting factors of our new SOM with RNN controller are activated to dispatch the agents toward their corresponding targets. Using the Lyapunov constraints, the weighting factors for the proposed SOM with RNN controller are updated to guarantee the stability of the path evolution (or planning) system. Excellent simulations are obtained using this new approach for MDS, which show that our RNN has the lowest average miss distance among the several techniques.

  13. Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains.

    Science.gov (United States)

    Zhang, Ming-Ying; Fritsch, Peter W; Ma, Peng-Fei; Wang, Hong; Lu, Lu; Li, De-Zhu

    2017-05-01

    Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is

  14. Perception Evolution Network Based on Cognition Deepening Model--Adapting to the Emergence of New Sensory Receptor.

    Science.gov (United States)

    Xing, Youlu; Shen, Furao; Zhao, Jinxi

    2016-03-01

    The proposed perception evolution network (PEN) is a biologically inspired neural network model for unsupervised learning and online incremental learning. It is able to automatically learn suitable prototypes from learning data in an incremental way, and it does not require the predefined prototype number or the predefined similarity threshold. Meanwhile, being more advanced than the existing unsupervised neural network model, PEN permits the emergence of a new dimension of perception in the perception field of the network. When a new dimension of perception is introduced, PEN is able to integrate the new dimensional sensory inputs with the learned prototypes, i.e., the prototypes are mapped to a high-dimensional space, which consists of both the original dimension and the new dimension of the sensory inputs. In the experiment, artificial data and real-world data are used to test the proposed PEN, and the results show that PEN can work effectively.

  15. Energy in Australia 2011

    International Nuclear Information System (INIS)

    Cuevas-Cubria, C.; Schultz, A.; Petchey, R.; Beaini, F.; New, R.

    2011-04-01

    Securing access to affordable, reliable and clean energy is one of the great challenges facing governments around the world. The Australian Government is committed to ensuring the security of Australia's domestic energy systems as a fundamental part of Australia's social and economic prosperity. Energy in Australia 2011 is a key reference for anyone with an interest in Australian energy issues. It provides a detailed overview of energy in Australia from production to consumption, and serves as a useful resource to inform industry, government and the community.

  16. Multi-objective differential evolution with adaptive Cauchy mutation for short-term multi-objective optimal hydro-thermal scheduling

    Energy Technology Data Exchange (ETDEWEB)

    Qin Hui [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Zhou Jianzhong, E-mail: jz.zhou@hust.edu.c [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Lu Youlin; Wang Ying; Zhang Yongchuan [College of Hydropower and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2010-04-15

    A new multi-objective optimization method based on differential evolution with adaptive Cauchy mutation (MODE-ACM) is presented to solve short-term multi-objective optimal hydro-thermal scheduling (MOOHS) problem. Besides fuel cost, the pollutant gas emission is also optimized as an objective. The water transport delay between connected reservoirs and the effect of valve-point loading of thermal units are also taken into account in the presented problem formulation. The proposed algorithm adopts an elitist archive to retain non-dominated solutions obtained during the evolutionary process. It modifies the DE's operators to make it suit for multi-objective optimization (MOO) problems and improve its performance. Furthermore, to avoid premature convergence, an adaptive Cauchy mutation is proposed to preserve the diversity of population. An effective constraints handling method is utilized to handle the complex equality and inequality constraints. The effectiveness of the proposed algorithm is tested on a hydro-thermal system consisting of four cascaded hydro plants and three thermal units. The results obtained by MODE-ACM are compared with several previous studies. It is found that the results obtained by MODE-ACM are superior in terms of fuel cost as well as emission output, consuming a shorter time. Thus it can be a viable alternative to generate optimal trade-offs for short-term MOOHS problem.

  17. Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species

    Science.gov (United States)

    Zhang, Yanjie; Sun, Jin; Chen, Chong; Watanabe, Hiromi K.; Feng, Dong; Zhang, Yu; Chiu, Jill M.Y.; Qian, Pei-Yuan; Qiu, Jian-Wen

    2017-01-01

    Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.). PMID:28397791

  18. Adaptive evolution of Escherichia coli to Ciprofloxacin in controlled stress environments: emergence of resistance in continuous and step-wise gradients

    Science.gov (United States)

    Deng, J.; Zhou, L.; Dong, Y.; Sanford, R. A.; Shechtman, L. A.; Alcalde, R.; Werth, C. J.; Fouke, B. W.

    2017-12-01

    Microorganisms in nature have evolved in response to a variety of environmental stresses, including gradients in pH, flow and chemistry. While environmental stresses are generally considered to be the driving force of adaptive evolution, the impact and extent of any specific stress needed to drive such changes has not been well characterized. In this study, a microfluidic diffusion chamber (MDC) and a batch culturing system were used to systematically study the effects of continuous versus step-wise stress increments on adaptation of E. coli to the antibiotic ciprofloxacin. In the MDC, a diffusion gradient of ciprofloxacin was established across a microfluidic well array to microscopically observe changes in Escherichia coli strain 307 replication and migration patterns that would indicate emergence of resistance due to genetic mutations. Cells recovered from the MDC only had resistance of 50-times the original minimum inhibition concentration (MICoriginal) of ciprofloxacin, although minimum exposure concentrations were over 80 × MICoriginal by the end of the experiment. In complementary batch experiments, E. coli 307 were exposed to step-wise daily increases of ciprofloxacin at rates equivalent to 0.1×, 0.2×, 0.4× or 0.8× times MICoriginal/day. Over a period of 18 days, E. coli cells were able to acquire resistance of up to 225 × MICoriginal, with exposure to ciprofloxacin concentration up to only 14.9 × MIC­original. The different levels of acquired resistance in the continuous MDC versus step-wise batch increment experiments suggests that the intrinsic rate of E. coli adaptation was exceeded in the MDC, while the step-wise experiments favor adaptation to the highest ciprofloxacin experiments. Genomic analyses of E. coli DNA extracted from the microfluidic cell and batch cultures indicated four single nucleotide polymorphism (SNP) mutations of amino acid 82, 83 and 87 in the gyrA gene. The progression of adaptation in the step-wise increments of

  19. Modified Covariance Matrix AdaptationEvolution Strategy algorithm for constrained optimization under uncertainty, application to rocket design

    Directory of Open Access Journals (Sweden)

    Chocat Rudy

    2015-01-01

    Full Text Available The design of complex systems often induces a constrained optimization problem under uncertainty. An adaptation of CMA-ES(λ, μ optimization algorithm is proposed in order to efficiently handle the constraints in the presence of noise. The update mechanisms of the parametrized distribution used to generate the candidate solutions are modified. The constraint handling method allows to reduce the semi-principal axes of the probable research ellipsoid in the directions violating the constraints. The proposed approach is compared to existing approaches on three analytic optimization problems to highlight the efficiency and the robustness of the algorithm. The proposed method is used to design a two stage solid propulsion launch vehicle.

  20. Robustness and Radiation Resistance of the Pale Grass Blue Butterfly from Radioactively Contaminated Areas: A Possible Case of Adaptive Evolution.

    Science.gov (United States)

    Nohara, Chiyo; Hiyama, Atsuki; Taira, Wataru; Otaki, Joji M

    2018-02-14

    The pale grass blue butterfly, Zizeeria maha, has been used to evaluate biological impacts of the Fukushima nuclear accident in March 2011. Here, we examined the possibility that butterflies have adapted to be robust in the contaminated environment. Larvae (n = 2432) were obtained from adult butterflies (n = 20) collected from 7 localities with various contamination levels in May 2012, corresponding to the 7th generation after the accident. When the larvae were reared on non-contaminated host plant leaves from Okinawa, the normality rates of natural exposure without artificial irradiation (as an indication of robustness) were high not only in the least contaminated locality but also in the most contaminated localities. The normality rates were similarly obtained when the larvae were reared on non-contaminated leaves with external irradiation or on contaminated leaves from Fukushima to deliver internal irradiation. The normality rate of natural exposure and that of external or internal exposure were correlated, suggesting that radiation resistance (or susceptibility) likely reflects general state of health. The normality rate of external or internal exposure was divided by the relative normality rate of natural exposure, being defined as the resistance value. The resistance value was the highest in the populations of heavily contaminated localities and was inversely correlated with the distance from the Fukushima Dai-ichi nuclear power plant. These results suggest that the butterfly population might have adapted to the contaminated environment within approximately 1 year after the accident. The present study may partly explain the decrease in mortality and abnormality rates later observed in the contaminated areas. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.

    Directory of Open Access Journals (Sweden)

    Sarah Green

    Full Text Available A recently emerging bleeding canker disease, caused by Pseudomonas syringae pathovar aesculi (Pae, is threatening European horse chestnut in northwest Europe. Very little is known about the origin and biology of this new disease. We used the nucleotide sequences of seven commonly used marker genes to investigate the phylogeny of three strains isolated recently from bleeding stem cankers on European horse chestnut in Britain (E-Pae. On the basis of these sequences alone, the E-Pae strains were identical to the Pae type-strain (I-Pae, isolated from leaf spots on Indian horse chestnut in India in 1969. The phylogenetic analyses also showed that Pae belongs to a distinct clade of P. syringae pathovars adapted to woody hosts. We generated genome-wide Illumina sequence data from the three E-Pae strains and one strain of I-Pae. Comparative genomic analyses revealed pathovar-specific genomic regions in Pae potentially implicated in virulence on a tree host, including genes for the catabolism of plant-derived aromatic compounds and enterobactin synthesis. Several gene clusters displayed intra-pathovar variation, including those encoding type IV secretion, a novel fatty acid biosynthesis pathway and a sucrose uptake pathway. Rates of single nucleotide polymorphisms in the four Pae genomes indicate that the three E-Pae strains diverged from each other much more recently than they diverged from I-Pae. The very low genetic diversity among the three geographically distinct E-Pae strains suggests that they originate from a single, recent introduction into Britain, thus highlighting the serious environmental risks posed by the spread of an exotic plant pathogenic bacterium to a new geographic location. The genomic regions in Pae that are absent from other P. syringae pathovars that infect herbaceous hosts may represent candidate genetic adaptations to infection of the woody parts of the tree.

  2. Archean crustal evolution of the Narryer Gneiss Terrane, Western Australia, as revealed by the U-Pb age and Hf-isotope compositions of zircon from the granitic gneisses

    Science.gov (United States)

    Sylvester, P.; Souders, K.; Crowley, J. L.; Myers, J.

    2011-12-01

    The Narryer Gneiss Terrane of the Yilgarn Craton, Western Australia, is an important area for studies of early crustal evolution because of the preservation of (1) detrital zircons of Hadean to Archean age in the Jack Hills and Mt. Narryer metasedimentary belts, and (2) several widespread units of granitic gneisses emplaced between ca. 3.7 and 2.6 Ga. We have analyzed the U-Pb geochronology and Hf-isotope geochemistry of magmatic zircons from 38 samples of the granitic gneisses using laser ablation - (multicollector) - ICPMS. The sample suite is dominated by the Meeberrie gneiss, a banded quartz-microcline-oligoclase-biotite gneiss of monzogranite to granodiorite composition, and the Dugel gneiss, a leucocratic, pegmatite-layered syenogranite gneiss, but gneisses of dioritic to tonalitic composition, as well as less deformed granite sheets, are also represented. Magmatic zircons were identified on the basis of the preservation of oscillatory zoning in BSE and CL images, igneous Th/U ratios (>0.2), and concordant U-Pb isotopic systematics with low common Pb contents. The results indicate many of the gneisses are composed of the products of multiple magmatic events, as has been reported previously for samples of the Meeberrie gneiss (Kinny & Nutman, 1996, Precambrian Res. 78, 165-178). Major ages of magmatism preserved in the gneisses occurred at ca. 3685-3665 Ma, 3620-3565 Ma, 3495-3440 Ma, 3375-3330 Ma, and 3300-3260 Ma. The late granite sheets crystallized at 2710-2645 Ma. Hf-isotope compositions of the zircons trend to less radiogenic values with decreasing age, with ɛHf values of ca. 0 to -5 for 3.7-3.4 Ga gneisses, ca. -1 to -9 for 3.4-3.2 Ga gneisses and ca. -5 to -20 for the late granite sheets. The array of the Hf isotopic compositions with time for the entire sample set are fit well by a regression indicating a source reservoir with a 176Lu/177Hf of 0.022 extracted from the depleted mantle at 3.9 Ga. This suggests that the Narryer gneisses and late granite

  3. 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; Pavinski Bitar, Paulina D.; Lefébure, Tristan; Schukken, Ynte H.; Zadoks, Ruth N.; Stanhope, Michael J.

    2011-01-01

    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: p 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 intomechanismsfacilitatingenvironmentaladaptationandacquisitionofpotential 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. PMID:21536150

  4. Evolution of the developmental plasticity and a coupling between left mechanosensory neuromasts and an adaptive foraging behavior.

    Science.gov (United States)

    Fernandes, Vânia Filipa Lima; Macaspac, Christian; Lu, Louise; Yoshizawa, Masato

    2018-05-18

    Many animal species exhibit laterality in sensation and behavioral responses, namely, the preference for using either the left or right side of the sensory system. For example, some fish use their left eye when observing social stimuli, whereas they use their right eye to observe novel objects. However, it is largely unknown whether such laterality in sensory-behavior coupling evolves during rapid adaptation processes. Here, in the Mexican tetra, Astyanax mexicanus, we investigate the laterality in the relationship between an evolved adaptive behavior, vibration attraction behavior (VAB), and its main sensors, mechanosensory neuromasts. A. mexicanus has a surface-dwelling form and cave-dwelling forms (cavefish), whereby a surface fish ancestor colonized the new environment of a cave, eventually evolving cave-type morphologies such as increased numbers of neuromasts at the cranium. These neuromasts are known to regulate VAB, and it is known that, in teleosts, the budding (increasing) process of neuromasts is accompanied with dermal bone formation. This bone formation is largely regulated by endothelin signaling. To assess the evolutionary relationship between bone formation, neuromast budding, and VAB, we treated 1-3 month old juvenile fish with endothelin receptor antagonists. This treatment significantly increased cranial neuromasts in both surface and cavefish, and the effect was significantly more pronounced in cavefish. Antagonist treatment also increased the size of dermal bones in cavefish, but neuromast enhancement was observed earlier than dermal bone formation, suggesting that endothelin signaling may independently regulate neuromast development and bone formation. In addition, although we did not detect a major change in VAB level under this antagonist treatment, cavefish did show a positive correlation of VAB with the number of neuromasts on their left side but not their right. This laterality in correlation was observed when VAB emerged during cavefish

  5. Community Music in Australia

    Science.gov (United States)

    Harrison, Gillian

    2010-01-01

    This paper presents a historical perspective to the development of community music in Australia. Finding political support in Australia's progressive arts policies of the late 1970s, community music is discussed as embracing the principles of access and equity and supporting the development of musical skills in the context of social change and…

  6. The 2014 Ebola virus outbreak in West Africa highlights no evidence of rapid evolution or adaptation to humans.

    Science.gov (United States)

    Li, Xingguang; Zai, Junjie; Liu, Haizhou; Feng, Yi; Li, Fan; Wei, Jing; Zou, Sen; Yuan, Zhiming; Shao, Yiming

    2016-10-21

    Following its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences of the EBOV full-length genome obtained from West Africa from the 2014 outbreak, combined with 30 from earlier outbreaks between 1976 and 2008 were used to investigate the genetic divergence, evolutionary history, population dynamics, and selection pressure of EBOV among distinct epidemic waves. Results from our dataset showed that no non-synonymous substitutions occurred on the GP gene coding sequences of EBOV that were likely to have affected protein structure or function in any way. Furthermore, the significantly different dN/dS ratios observed between the 2014 West African outbreak and earlier outbreaks were more likely due to the confounding presence of segregating polymorphisms. Our results highlight no robust evidence that the 2014 EBOV outbreak is fast-evolving and adapting to humans. Therefore, the unprecedented nature of the 2014 EBOV outbreak might be more likely related to non-virological elements, such as environmental and sociological factors.

  7. Evolution, epigenetics and cooperation

    Indian Academy of Sciences (India)

    Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the ...

  8. Is the Success of Plant Invasions the Result of Rapid Adaptive Evolution in Seed Traits? Evidence from a Latitudinal Rainfall Gradient

    Science.gov (United States)

    Molina-Montenegro, Marco A.; Acuña-Rodríguez, Ian S.; Flores, Tomás S. M.; Hereme, Rasme; Lafon, Alejandra; Atala, Cristian; Torres-Díaz, Cristian

    2018-01-01

    It has been widely suggested that invasion success along broad environmental gradients may be partially due to phenotypic plasticity, but rapid evolution could also be a relevant factor for invasions. Seed and fruit traits can be relevant for plant invasiveness since they are related to dispersal, germination, and fitness. Some seed traits vary along environmental gradients and can be heritable, with the potential to evolve by means of natural selection. Utilizing cross-latitude and reciprocal-transplant experiments, we evaluated the adaptive value of seed thickness as assessed by survival and biomass accumulation in Taraxacum officinale plants. In addition, thickness of a seed and Endosperm to Seed Coat Proportion (ESCP) in a second generation (F2) was measured to evaluate the heritability of this seed trait. On the other hand, we characterized the genetic variability of the sampled individuals with amplified fragment length polymorphism (AFLP) markers, analyzing its spatial distribution and population structure. Overall, thickness of seed coat (plus wall achene) decreases with latitude, indicating that individuals of T. officinale from northern populations have a thicker seed coat than those from southern populations. Germination increased with greater addition of water and seeds from southern localities germinated significantly more than those from the north. Additionally, reciprocal transplants showed significant differences in survival percentage and biomass accumulation among individuals from different localities and moreover, the high correlation between maternal plants and their offspring can be suggesting a high grade of heritability of this trait. Although genetic differentiation was found when was considered all populations, there was no significant differentiation when only was compared the northernmost populations which inhabit in the driest climate conditions. Our results suggest that climatic conditions could affect both, the ESCP and the genetic

  9. Is the Success of Plant Invasions the Result of Rapid Adaptive Evolution in Seed Traits? Evidence from a Latitudinal Rainfall Gradient

    Directory of Open Access Journals (Sweden)

    Marco A. Molina-Montenegro

    2018-02-01

    Full Text Available It has been widely suggested that invasion success along broad environmental gradients may be partially due to phenotypic plasticity, but rapid evolution could also be a relevant factor for invasions. Seed and fruit traits can be relevant for plant invasiveness since they are related to dispersal, germination, and fitness. Some seed traits vary along environmental gradients and can be heritable, with the potential to evolve by means of natural selection. Utilizing cross-latitude and reciprocal-transplant experiments, we evaluated the adaptive value of seed thickness as assessed by survival and biomass accumulation in Taraxacum officinale plants. In addition, thickness of a seed and Endosperm to Seed Coat Proportion (ESCP in a second generation (F2 was measured to evaluate the heritability of this seed trait. On the other hand, we characterized the genetic variability of the sampled individuals with amplified fragment length polymorphism (AFLP markers, analyzing its spatial distribution and population structure. Overall, thickness of seed coat (plus wall achene decreases with latitude, indicating that individuals of T. officinale from northern populations have a thicker seed coat than those from southern populations. Germination increased with greater addition of water and seeds from southern localities germinated significantly more than those from the north. Additionally, reciprocal transplants showed significant differences in survival percentage and biomass accumulation among individuals from different localities and moreover, the high correlation between maternal plants and their offspring can be suggesting a high grade of heritability of this trait. Although genetic differentiation was found when was considered all populations, there was no significant differentiation when only was compared the northernmost populations which inhabit in the driest climate conditions. Our results suggest that climatic conditions could affect both, the ESCP and

  10. Differential Adaptations of Methicillin-Resistant Staphylococcus aureus to Serial In Vitro Passage in Daptomycin: Evolution of Daptomycin Resistance and Role of Membrane Carotenoid Content and Fluidity

    Directory of Open Access Journals (Sweden)

    Nagendra N. Mishra

    2012-01-01

    Full Text Available Previous studies showed serial 20 d in vitro passage of MRSA strain MW2 in sublethal daptomycin (DAP resulted in diverse perturbations in both cell membrane (CM and cell wall (CW characteristics, including increased CM rigidity; increased CW thickness; “gain-in-function” single nucleotide polymorphisms (SNPs in the mprF locus (i.e., increased synthesis and translocation of lysyl-phosphatidylglycerol (L-PG; progressive accumulation of SNPs in yyc and rpo locus genes; reduced carotenoid production; cross-resistance to innate host defense peptides. The current study was designed to characterize the reproducibility of these phenotypic and genotypic modifications following in vitro serial passages of the same parental strain. After a second 20d serial in vitro passage of parental MW2, emergence of DAP-R was associated with evolution of several phenotypes closely mirroring previous passage outcomes. However, in contrast to the initial serial passage strain set, we observed (i only modest increase in L-PG synthesis and no increase in L-PG outer CM translocation; (ii significantly increased carotenoid synthesis (P<0.05; (iii a different order of SNP accumulations (mprF≫rpoB≫yycG; (iv a different cadre and locations of such SNPs. Thus, MRSA strains are not “pre-programmed” to phenotypically and/or genotypically adapt in an identical manner during induction of DAP resistance.

  11. Classification of breast masses in ultrasound images using self-adaptive differential evolution extreme learning machine and rough set feature selection.

    Science.gov (United States)

    Prabusankarlal, Kadayanallur Mahadevan; Thirumoorthy, Palanisamy; Manavalan, Radhakrishnan

    2017-04-01

    A method using rough set feature selection and extreme learning machine (ELM) whose learning strategy and hidden node parameters are optimized by self-adaptive differential evolution (SaDE) algorithm for classification of breast masses is investigated. A pathologically proven database of 140 breast ultrasound images, including 80 benign and 60 malignant, is used for this study. A fast nonlocal means algorithm is applied for speckle noise removal, and multiresolution analysis of undecimated discrete wavelet transform is used for accurate segmentation of breast lesions. A total of 34 features, including 29 textural and five morphological, are applied to a [Formula: see text]-fold cross-validation scheme, in which more relevant features are selected by quick-reduct algorithm, and the breast masses are discriminated into benign or malignant using SaDE-ELM classifier. The diagnosis accuracy of the system is assessed using parameters, such as accuracy (Ac), sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), Matthew's correlation coefficient (MCC), and area ([Formula: see text]) under receiver operating characteristics curve. The performance of the proposed system is also compared with other classifiers, such as support vector machine and ELM. The results indicated that the proposed SaDE algorithm has superior performance with [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] compared to other classifiers.

  12. Adaptive evolution of the lager brewing yeast Saccharomyces pastorianus for improved growth under hyperosmotic conditions and its influence on fermentation performance.

    Science.gov (United States)

    Ekberg, Jukka; Rautio, Jari; Mattinen, Laura; Vidgren, Virve; Londesborough, John; Gibson, Brian R

    2013-05-01

    An adaptive evolution method to obtain stable Saccharomyces pastorianus brewing yeast variants with improved fermentation capacity is described. The procedure involved selection for rapid growth resumption at high osmotic strength. It was applied to a lager strain and to a previously isolated ethanol-tolerant strain. Fermentation performance of strains was compared at 15 °P wort strength. A selected osmotolerant variant of the ethanol-tolerant strain showed significantly shorter fermentation time than the parent strain, producing 6.45% alcohol by volume beer in 4-5 days with mostly similar organoleptic properties to the original strain. Diacetyl and pentanedione contents were 50-75% and 3-methylbutyl acetate and 2-phenylethyl acetate 50% higher than with the original strain, leading to a small flavour change. The variant contained significantly less intracellular trehalose and glycogen than the parent. Transcriptional analysis of selected genes at 24 h revealed reduced transcription of hexose transport genes and increased transcription of the MALx1 and MALx2 genes, responsible for α-glucoside uptake and metabolism. It is suggested that an attenuated stress response contributes to the improved fermentation performance. Results show that sequential selection for both ethanol tolerance and rapid growth at high osmotic strength can provide strains with enhanced fermentation speed with acceptable product quality. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  13. Uranium mining in Australia

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    Known uranium deposits and the companies involved in uranium mining and exploration in Australia are listed. The status of the development of the deposits is outlined and reasons for delays to mining are given

  14. Uranium production in Australia

    International Nuclear Information System (INIS)

    Fisk, B.G.

    1984-01-01

    The history of uranium mining and milling in Australia is briefly outlined, particular attention being given to the development of Australia's only two operating mills, Nabarlek and Ranger, and its only operating mine, Ranger. The latter project is used to illustrate the prerequisites for development of the industry and the complex roles of the various parties involved in establishing a new mine: equity holders, customers, financiers, the securities industry, trade unions, and the public. The moves currently being taken to resolve the future of the industry in Australia, particularly the examination of issues relating to Australia's role in the nuclear fuel cycle being conducted by the Australian Science and Technology Council, preclude any firm conclusions being drawn, but the various options open to the government are reviewed and the record of Australian governments and unions and the attitude of the Australian public are described. (Author) (3 tabs., fig.)

  15. Uranium mining in Australia

    International Nuclear Information System (INIS)

    Mackay, G.A.

    1978-01-01

    Western world requirements for uranium based on increasing energy consumption and a changing energy mix, will warrant the development of Australia's resources. By 1985 Australian mines could be producing 9500 tonnes of uranium oxide yearly and by 1995 the export value from uranium could reach that from wool. In terms of benefit to the community the economic rewards are considerable but, in terms of providing energy to the world, Australias uranium is vital

  16. Has Human Evolution Stopped?

    Directory of Open Access Journals (Sweden)

    Alan R. Templeton

    2010-07-01

    Full Text Available It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.

  17. Developing a Shuffled Complex-Self Adaptive Hybrid Evolution (SC-SAHEL) Framework for Water Resources Management and Water-Energy System Optimization

    Science.gov (United States)

    Rahnamay Naeini, M.; Sadegh, M.; AghaKouchak, A.; Hsu, K. L.; Sorooshian, S.; Yang, T.

    2017-12-01

    Meta-Heuristic optimization algorithms have gained a great deal of attention in a wide variety of fields. Simplicity and flexibility of these algorithms, along with their robustness, make them attractive tools for solving optimization problems. Different optimization methods, however, hold algorithm-specific strengths and limitations. Performance of each individual algorithm obeys the "No-Free-Lunch" theorem, which means a single algorithm cannot consistently outperform all possible optimization problems over a variety of problems. From users' perspective, it is a tedious process to compare, validate, and select the best-performing algorithm for a specific problem or a set of test cases. In this study, we introduce a new hybrid optimization framework, entitled Shuffled Complex-Self Adaptive Hybrid EvoLution (SC-SAHEL), which combines the strengths of different evolutionary algorithms (EAs) in a parallel computing scheme, and allows users to select the most suitable algorithm tailored to the problem at hand. The concept of SC-SAHEL is to execute different EAs as separate parallel search cores, and let all participating EAs to compete during the course of the search. The newly developed SC-SAHEL algorithm is designed to automatically select, the best performing algorithm for the given optimization problem. This algorithm is rigorously effective in finding the global optimum for several strenuous benchmark test functions, and computationally efficient as compared to individual EAs. We benchmark the proposed SC-SAHEL algorithm over 29 conceptual test functions, and two real-world case studies - one hydropower reservoir model and one hydrological model (SAC-SMA). Results show that the proposed framework outperforms individual EAs in an absolute majority of the test problems, and can provide competitive results to the fittest EA algorithm with more comprehensive information during the search. The proposed framework is also flexible for merging additional EAs, boundary

  18. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution.

    Science.gov (United States)

    Modahl, Cassandra M; Mackessy, Stephen P

    2016-06-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  19. Nuclear issues in Australia

    International Nuclear Information System (INIS)

    Switkowski, Z.

    2007-01-01

    Full text: After a twenty year pause in discussion of nuclear power in Australia, the public debate has resumed in this past year - partly in search for clean, non fossil fuel energy alternatives, and partly from the different political strategies in the lead up to this year's federal election. Although there is evidence of a revival of interest in the nuclear power globally, countries considering installing their first nuclear reactor confront formidable obstacles including community concerns and long lead times. This presentation will describe the Climate Change context which shapes political and corporate strategies, possible nuclear scenarios for Australia, solutions to the still long list of reservations, and likely milestones ahead. It concludes that if we are to decarbonise our economy, and continue on a path of improving standards of living and prosperity, then any strategy for adding the required base-load electricity generation capacity must consider nuclear power for Australia

  20. Nudging Evolution?

    OpenAIRE

    Katharine N. Farrell; Andreas Thiel

    2013-01-01

    This Special Feature, "Nudging Evolution? Critical Exploration of the Potential and Limitations of the Concept of Institutional Fit for the Study and Adaptive Management of Social-Ecological Systems," aims to contribute toward the development of social theory and social research methods for the study of social-ecological system dynamics. Our objective is to help strengthen the academic discourse concerning if, and if so, how, to what extent, and in what concrete ways the concept of institut...

  1. Adaptive social learning strategies in temporally and spatially varying environments : how temporal vs. spatial variation, number of cultural traits, and costs of learning influence the evolution of conformist-biased transmission, payoff-biased transmission, and individual learning.

    Science.gov (United States)

    Nakahashi, Wataru; Wakano, Joe Yuichiro; Henrich, Joseph

    2012-12-01

    Long before the origins of agriculture human ancestors had expanded across the globe into an immense variety of environments, from Australian deserts to Siberian tundra. Survival in these environments did not principally depend on genetic adaptations, but instead on evolved learning strategies that permitted the assembly of locally adaptive behavioral repertoires. To develop hypotheses about these learning strategies, we have modeled the evolution of learning strategies to assess what conditions and constraints favor which kinds of strategies. To build on prior work, we focus on clarifying how spatial variability, temporal variability, and the number of cultural traits influence the evolution of four types of strategies: (1) individual learning, (2) unbiased social learning, (3) payoff-biased social learning, and (4) conformist transmission. Using a combination of analytic and simulation methods, we show that spatial-but not temporal-variation strongly favors the emergence of conformist transmission. This effect intensifies when migration rates are relatively high and individual learning is costly. We also show that increasing the number of cultural traits above two favors the evolution of conformist transmission, which suggests that the assumption of only two traits in many models has been conservative. We close by discussing how (1) spatial variability represents only one way of introducing the low-level, nonadaptive phenotypic trait variation that so favors conformist transmission, the other obvious way being learning errors, and (2) our findings apply to the evolution of conformist transmission in social interactions. Throughout we emphasize how our models generate empirical predictions suitable for laboratory testing.

  2. Uranium exploration in Australia

    International Nuclear Information System (INIS)

    Battey, G.C.; Hawkins, B.W.

    1977-01-01

    As a result of exploration which recommenced in 1966 Australia's uranium reserves increased from 6,200 tonnes in 1967 to 227,000 tonnes uranium by June 1976. Most discoveries in the early 1950's were made by prospectors. The increase in reserves during the past decade is the result of exploration by companies utilising improved technology in areas selected as geologically favourable. These reserves were established at relatively low cost. In the Alligator Rivers Uranium Province the ''vein'' type deposits at Jabiluka, Ranger, Koongarra and Nabarlek contain 17% of the world's reserves. Most of these discoveries resulted from the investigation of airborne radiometric anomalies but cover over the prospective host rocks will necessitate the future use of costlier and more indirect exploration techniques. There was exploration for sandstone type uranium deposits in most of Australia's sedimentary basins. The greatest success was achieved in the Lake Frome Basin in South Australia. Other deposits were found in the Ngalia and Amadeus Basins in Central Australia and in the Westmoreland area, N.W. Queensland. A major uranium deposit was found in an unusual environment at Yeelirrie, Western Australia where carnotite occurs in a caliche and clay host which fills a shallow, ancient drainage channel. Although caliche occurrences are relatively widespread on the Precambrian shield no other economic deposit has been found. Recent discoveries in the Georgetown area of Queensland indicate the presence of another uranium province but it is too early to assess its potential. The ore occurs in clastic sediments at the base of a volcanic sequence overlying a Precambrian basement. Several companies which have established large uranium reserves have a number of additional attractive prospects. Exploration activity in Australia in 1975 was at a lower level than in previous years, but the potential for discovering further deposits is considered to be high

  3. Economy Profile of Australia

    OpenAIRE

    World Bank Group

    2017-01-01

    Doing Business 2018 is the 15th in a series of annual reports investigating the regulations that enhance business activity and those that constrain it. This economy profile presents the Doing Business indicators for Australia. Doing Business presents quantitative indicators on business regulation and the protection of property rights that can be compared across 190 economies; for 2018 Aust...

  4. Australia's nuclear graveyard

    International Nuclear Information System (INIS)

    Milliken, R.

    1987-01-01

    Britain and Australia have become locked in a battle of wills and wits over a nuclear legacy that is now more than 30 years old. At stake is the issue of who will pay to clean up a stretch of the central Australian outback where at least 23 kilograms of plutonium are buried in nuclear graveyards or scattered in fine particles on the ground. The plutonium was left there after a series of British nuclear weapons tests in the 1950s and 1960s. The cost of cleaning it up today, and rendering the ground safe the the Aborigines who claim it as their tribal homeland, has been estimated at up to $158 million. Australia's minister for resources, Senator Gareth Evans, went to London in October 1986 to try to involve the British in the cleanup. But Britain is still taking the stand that it had discharged any obligations on this score long ago. This question is at the heart of controversy that began mounting in the late 1970s over the British nuclear tests. It was then that Aborigines and test veterans from Britain and Australia started alleging that they had been exposed to unduly high doses of radiation. Clearly, the nuclear tests, which began as a political exercise between Britain and Australia more than 30 years ago, seem destined to remain the source of much legal, diplomatic, and financial fallout between the two countries for a long time to come

  5. Mathematical Sciences in Australia

    Science.gov (United States)

    Thomas, Jan; Muchatuta, Michelle; Wood, Leigh

    2009-01-01

    This article investigates enrolment trends in mathematical sciences in Australian universities. Data has been difficult to extract and the coding for mathematical disciplines has made investigation challenging. We show that the number of mathematics major undergraduates in Australia is steadily declining though the number studying…

  6. Creating White Australia

    DEFF Research Database (Denmark)

    McLisky, Claire Louise; Carey, Jane

    Vedtagelsen af White Australien som regeringens politik i 1901 viser, at hvidheden var afgørende for den måde, hvorpå den nye nation i Australien blev konstitueret. Og alligevel har historikere i vid udstrækning overset hvidhed i deres studier af Australiens race fortid. 'Creating White Australia...

  7. Banknote Quality in Australia

    OpenAIRE

    Arianna Cowling; Monica Howlett

    2012-01-01

    The Reserve Bank aims to keep the quality of banknotes in circulation high to ensure that they meet the needs of the public and to make it more difficult for counterfeits to be passed or remain in circulation. This article discusses the quality of banknotes in Australia and Reserve Bank initiatives that have improved the quality of banknotes in recent years.

  8. Australia's nuclear headache

    International Nuclear Information System (INIS)

    Marinova, D.

    1997-01-01

    With the temporary storage of nuclear waste, constituted by HIFAR spent fuel, at Lucas Heights reaching full capacity by 1998, there is an urgent need for a technical, social and political solution. Some of the fundamental uncertainties in relation to nuclear waste disposal and hence the operation of a nuclear research reactor in Australia are presented

  9. Australia's uranium export potential

    International Nuclear Information System (INIS)

    Mosher, D.V.

    1981-01-01

    During the period 1954-71 in Australia approximately 9000 MT of U 3 O 8 was produced from five separate localities. Of this, 7000 MT was exported to the United Kingdom and United States and the balance stockpiled by the Australian Atomic Energy Commission (AAEC). Australia's uranium ore reserves occur in eight deposits in three states and the Northern Territory. However, 83% of Australia's reserves are contained in four deposits in lower Proterozoic rocks in the East Alligator River region of the Northern Territory. The AAEC has calculated Australia's recoverable uranium reserves by eliminating estimated losses during the mining and milling of the ores. AAEC has estimated reasonably assured resources of 289,000 MT of uranium at a recovery cost of less than US$80 per kilogram uranium. The companies have collectively announced a larger ore reserve than the Australian Atomic Energy Commission. This difference is a result of the companies adopting different ore reserve categories. On August 25, 1977, the federal government announced that Australia would develop its uranium resources subject to stringent environmental controls, recognition of Aboriginal Land Rights, and international safeguards. Australian uranium production should gradually increase from 1981 onward, growing to 10,000 to 15,000 MT by 1985-86. Further increases in capacity may emerge during the second half of the 1980s when expansion plans are implemented. Exploration for uranium has not been intensive due to delays in developing the existing deposits. It is likely that present reserves can be substantially upgraded if more exploration is carried out. 6 figures, 3 tables

  10. Climate Change. Solutions for Australia

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, T.; Hoegh-Guldberg, O.; Karoly, D.; Lowe, I.; McMichael, T.; Mitchell, C.; Pearman, G.; Scaife, P.; Reynolds, A. (eds.)

    2004-06-01

    The Australian Climate Group was convened in late 2003 by WWF Australia and the Insurance Australia Group (IAG) in response to the increasing need for action on climate change in Australia. This group proposes a set of solutions to lower the risk that climate change will reach a dangerous level.

  11. The Art of Being an English Teacher in Australia

    Science.gov (United States)

    Loyden, Grace

    2015-01-01

    The role of the English teacher in Australia is constantly being negotiated and with every ideological development teachers are positioned to question their professional values and practices. Much attention has been afforded to this discussion. The purpose of this paper is to (a) provide an analysis of the evolution of the art of being an English…

  12. WAVFH delegates' reports: Australia

    International Nuclear Information System (INIS)

    Scanlan, W.A.

    1986-01-01

    Radiation measuring and control before Chernobyl: Continuous measurements of fallout in different parts of Australia, including the food producing areas, have been made since the mid 1950s. Levels have decreased rapidly since the cessation of atmospheric nuclear tests in the Southern Hemisphere in 1974 and in the Northern Hemisphere in 1980. Measurements of concentrations of radionuclides arising from fallout were made for the major groups of foods affected by the radioactive contaminants, starting in the 1950s and continuing until concentrations were so low that further effort in measurement was not warranted, i.e., less than 0.1 Bq/kg or 0.1 Bq/l. Changes in the concentrations of radionuclides in foods follow the same trends as the fallout levels. Based on the low levels of fallout measured in Australia since the 1950s, and taking into account the extremely low levels during the past decade, the concentrations of radionuclides arising from fallout in foods grown and processed in Australia are extremely small. Results from the fall-out from Chernobyl. Since the Chernobyl accident, measurements of the concentrations of 137 Cs in a variety of foodstuffs grown in Australia have been made, mainly for export purposes. A summary of the results of these measurements is given in Table 111 of Attachment 2. No 134 Cs has been detected, nor is it likely to be. By taking into account these measurements, the earlier measurements of foodstuffs, predictive modelling values and the very low levels of fall-out in deposit and in air, it is concluded that the concentrations of 137 Cs in all foodstuffs grown in Australia are extremely small. Accordingly, their consumption would result in no significant risk to the health of a population. With world atmospheric conditions being as they are, it will probably be 12 to 18 months before any fallout reaches Australia. Even if some fall-out does occur, it will be minimal and should not significantly increase our very low natural levels

  13. Tissue banking in australia.

    Science.gov (United States)

    Ireland, Lynette; McKelvie, Helen

    2003-01-01

    The legal structure for the regulation of tissue banking has existed for many years. In Australia, the donation of human tissue is regulated by legislation in each of the eight States and Territories. These substantially uniform Acts were passed in the late 1970's and early 1980's, based on model legislation and underpinned by the concept of consensual giving. However, it was not until the early 1990's that tissue banking came under the notice of regulatory authorities. Since then the Australian Government has moved quickly to oversee the tissue banking sector in Australia. Banked human tissue has been deemed to be a therapeutic good under the Therapeutic Goods Act 1989, and tissue banks are required to be licensed by the Therapeutic Goods Administration and are audited for compliance with the Code of Good Manufacturing Practice- Human Blood and Tissues. In addition, tissue banks must comply with a myriad of other standards, guidelines and recommendations.

  14. Pleistocene Paleoart of Australia

    Directory of Open Access Journals (Sweden)

    Robert G. Bednarik

    2014-02-01

    Full Text Available Pleistocene rock art is abundant in Australia, but has so far received only limited attention. Instead there has been a trend, begun over a century ago, to search for presumed depictions of extinct megafauna and the tracks of such species. All these notions have been discredited, however, and the current evidence suggests that figurative depiction was introduced only during the Holocene, never reaching Tasmania. Nevertheless, some Australian rock art has been attributed to the Pleistocene by direct dating methods, and its nature implies that a significant portion of the surviving corpus of rock art may also be of such age. In particular much of Australian cave art is of the Ice Age, or appears to be so, and any heavily weathered or patinated petroglyphs on particularly hard rocks are good candidates for Pleistocene antiquity. On the other hand, there is very limited evidence of mobiliary paleoart of such age in Australia.

  15. Synchrotron radiation in Australia

    International Nuclear Information System (INIS)

    Garrett, R.F.

    2002-01-01

    Full text: Synchrotron radiation research in Australia is entering a new era with the commencement of the Australian synchrotron project, which will construct a 3 GeV third generation synchrotron facility at Monash University in Victoria. To date Australian scientists have used overseas facilities, primarily those managed by the Australian Synchrotron Research Program in Japan and the USA. A fast developing and maturing Australian synchrotron user program has developed around these overseas facilities. The field of synchrotron radiation and its importance to a wide range of research will be introduced and Australia's current involvement and facilities will be described. The current status and technical specifications of the Australian synchrotron will be presented. Copyright (2002) Australian X-ray Analytical Association Inc

  16. Mineral industry in Australia

    International Nuclear Information System (INIS)

    Parbo, S.A.

    1982-01-01

    The paper reviews the history and growth of the mineral industry in Australia and its significance to the nation's economic growth and overseas trade, particularly over the last twenty years during which time production of coal, iron ore, manganese and mineral sands has increased greatly and new discoveries of petroleum, bauxite and nickel have given rise to major new industries. Australia ranks fourteenths in the value of world trade and is among the world's largest exporters of alumina, iron ore, mineral sands, coal, lead, zinc and nickel. Some details of production, processing and exports of the major minerals are given. Comment is made on the policies and roles of the six State Governments and the Federal Government in respect of ownership and control of the mining, processing and exporting of both energy and non-energy minerals. (orig.) [de

  17. Casemix funding in Australia.

    Science.gov (United States)

    Braithwaite, J; Hindle, D; Phelan, P D; Hanson, R

    1998-06-01

    Casemix funding for hospitals with the use of diagnosis-related groups (DRGs), which organise patients' conditions into similar clinical categories with similar costs, was introduced in Australia five years ago. It has been applied in different ways and to a greater or lesser extent in different Australian States. Only Victoria and South Australia have implemented casemix funding across all healthcare services. Attempts have been made to formally evaluate its impact, but they have not met the required scientific standards in controlling for confounding factors. Casemix funding remains a much-discussed issue. In this Debate, Braithwaite and Hindle take a contrary position, largely to stimulate policy debate; Phelan defends the casemix concept and advocates retaining its best features; and Hanson adds a plea for consumer input.

  18. Mapping Homophobia in Australia

    OpenAIRE

    Flood, Michael Gaston; Flood, Michael; Flood, C.; Hamilton, Clive

    2008-01-01

    One-third of the Australian population believe that 'homosexuality is immoral', and this belief is spread in distinct ways across the nation. Using data from a survey of nearly 25,000 Australians, we can 'map' homophobia in Australia. Homophobic attitudes are worst in country areas of Queensland and Tasmania. Men are far more likely than women to feel that homosexuality does not have moral legitimacy, and this gender gap in attitudes persists across age, socioeconomic, educational, and region...

  19. Australia's atomic conspiracy theory

    International Nuclear Information System (INIS)

    Binnie, A.

    2001-01-01

    The author questions claims by the Newcastle University historian Wayne Reynolds in his book 'Australia's Bid for the Bomb', that the impetus behind the Snowy Mountains Scheme was to provide a secure source of power for the enrichment of uranium and production of heavy water so that Australia could produce its own atomic bombs. Reynolds also argued that the Australian Atomic Energy Commission (AAEC) was set up so that Australia had a trained scientific workforce to produce plutonium for the bomb. While the book is well researched, Reynolds does not seem to understand the principles of basic science and engineering. After the Second World War, a manufacturing and industrial base with a skilled and trained workforce was needed so it could be converted to war or defence manufacturing when the need arose. This new manufacturing community would require electrical power to sustain it. Hydroelectricity and atomic energy could help provide these needs. Even though war was still raging, Prime Minister John Curtin looked ahead and set up a Department of Post-War Reconstruction. It was through this department that the Snowy Mountains Scheme would be established. Curtin did not live to see this. He died in 1945 but his successor, Ben Chifley, continued the vision. The author believes, an understanding of the science behind these developments and an appreciation of how how humans interact with each others when it comes to getting something they want is likely to give a more balanced view of the past

  20. Australia's energy profile

    International Nuclear Information System (INIS)

    Dickson, A.

    1999-01-01

    Australian Bureau of Agricultural and Resource Economics (ABARE)'s biennial fuel and electricity survey provides a comprehensive database with which is possible to examine recent trends and developments in Australia's energy market. Some key development are outlined in this article. While energy consumption in Australia has been increasing steadily since 1973-74, substantial changes have occurred 'behind the scenes' in terms of the states and sectors in which energy is consumed and the overall fuel mix. Historically, the south-eastern states of New South Wales and Victoria have accounted for the largest shares of total energy consumption In recent years, however, the dominance of New South Wales and Victoria (and particularly New South Wales) has come under pressure from the states of Queensland. Western Australia, and to a lesser extent, the Northern Territory. Each of these states has experienced rapid growth in energy consumption, due mainly to a number of strongly growing energy intensive industries, particularly in the mining and minerals processing sectors. High economic and population growth over this period were also important factors. An increase in the share of natural gas- and a corresponding decline in the share of crude oil - is the most evident change to have occurred in the fuel mix since 1973-1974. However, since 1993, the trend has changed, the share of coal (and particularly brown coal) increased strongly, making it the primary fuel source for thermal electricity generation. This recent shift has been driven by developments in Queensland and Victoria

  1. Contemporary evolution strategies

    CERN Document Server

    Bäck, Thomas; Krause, Peter

    2013-01-01

    Evolution strategies have more than 50 years of history in the field of evolutionary computation. Since the early 1990s, many algorithmic variations of evolution strategies have been developed, characterized by the fact that they use the so-called derandomization concept for strategy parameter adaptation. Most importantly, the covariance matrix adaptation strategy (CMA-ES) and its successors are the key representatives of this group of contemporary evolution strategies. This book provides an overview of the key algorithm developments between 1990 and 2012, including brief descriptions of the a

  2. Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean.

    Science.gov (United States)

    Ledoux, Jean-Baptiste; Aurelle, Didier; Bensoussan, Nathaniel; Marschal, Christian; Féral, Jean-Pierre; Garrabou, Joaquim

    2015-03-01

    Studying population-by-environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.

  3. Climate change in Australia: technical report 2007

    International Nuclear Information System (INIS)

    2007-01-01

    The purpose of this report is to provide an up-to-date assessment of observed climate change over Australia, the likely causes, and projections of future changes to Australia's climate. It also provides information on how to apply the projections in impact studies and in risk assessments. The two main strategies for managing climate risk are mitigation (net reductions in greenhouse gas emissions) to slow climate change and adaptation to climate impacts that are unavoidable. A number of major advances have been made since the last report on climate change projections in Australia (CSIRO 2001) including: a much larger number of climate and ocean variables are projected (21 and 6 respectively); a much larger number (23) of climate models are used; the provision of probabilistic information on some of the projections, including the probability of exceeding the 10th, 50th and 90th percentiles; greater emphasis on projections from models that are better able to simulate observed Australian climate; a detailed assessment of observed changes in Australian climate and likely causes; and information on risk assessment, to provide guidance for using climate projections in impact studies

  4. Australia needs nuclear education

    International Nuclear Information System (INIS)

    Kemeny, L.G.

    1999-01-01

    A matter of increasing concern in Australian society is the absence of a Commonwealth Government policy on the peaceful use of nuclear energy. The lack of University level teaching facilities in nuclear energy engineering is also perceived to be an issue of national importance which must be addressed. More and more Australians deeply regret the lack of informed realism and scientific integrity which goes into endless debates on the technical, environmental and societal aspects of nuclear energy. Within the Australian community such important issues as uranium mining in Kakadu National Park, research reactor operation at Lucas Heights, the establishment of an international nuclear waste repository in Western Australia or the domestic use of nuclear electricity generation to minimise Australia's greenhouse emissions are still being debated at the intellectual level of radio talkback programs. Decision making in such areas deserves the disciplines of appropriate tertiary education. The Australian community has a right to know the relative risks and the environmental impacts of various fuel cycles as well as the technical limitations, true costs and energy audits of the 'alternative' energy technologies. Presently the Commonwealth of Australia is without a single School of Nuclear Engineering operating at a University level. Such a situation is believed to be unprecedented amongst the developed countries of the world. It is viewed with a measure of incredulity by the academic, diplomatic and political communities of the 'developing' countries of East Asia and the Pacific Basin. Many of these have a massive investment in the growth of peaceful nuclear energy and nuclear science and technology within their borders. Copyright (1999) Australian Institute of Energy News

  5. Australia's approach to monetary policy

    OpenAIRE

    Jane Sneddon Little

    2002-01-01

    According to Australia's Reserve Bank Act, the central bank's broad policy objectives include maintaining the stability of the currency, full employment, and the economic prosperity and welfare of the people of Australia. In 1993 the Reserve Bank of Australia adopted a specific, and thus transparent, inflation target as its operating objective; it aims to keep overall inflation between 2 percent and 3 percent on average over the business cycle.

  6. Lake Carnegie, Western Australia

    Science.gov (United States)

    2002-01-01

    Ephemeral Lake Carnegie, in Western Australia, fills with water only during periods of significant rainfall. In dry years, it is reduced to a muddy marsh. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on May 19, 1999. This is a false-color composite image made using shortwave infrared, infrared, and red wavelengths. The image has also been sharpened using the sensor's panchromatic band. Image provided by the USGS EROS Data Center Satellite Systems Branch. This image is part of the ongoing Landsat Earth as Art series.

  7. Australia's radiation protection standards

    International Nuclear Information System (INIS)

    1989-01-01

    In Australia, public exposure to ionizing radiation above background is considered to be negligible. Average occupational exposures are about 0.5 millisievert per year, although there are some specialized industries and professions where they are much higher. The National Health and Medical Research Council has therefore adopted a position similar to that of the International Commission on Radiological Protection. For the moment, no revision of exposure limits is recommended, but users are remined of their responsibility to ensure that exposures are kept low, particularly in those workplaces where significant exposures take place

  8. Evolution, epigenetics and cooperation.

    Science.gov (United States)

    Bateson, Patrick

    2014-04-01

    Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is givingway to adaptation at the level of the organism and higher-order assemblages of organisms. These ideas impact on the theories of how cooperation might have evolved. Two of the theories, i.e. that cooperating individuals are genetically related or that they cooperate for self-interested reasons, have been accepted for a long time. The idea that adaptation takes place at the level of groups is much more controversial. However, bringing together studies of development with those of evolution is taking away much of the heat in the debate about the evolution of group behaviour.

  9. Lingue e migrazione. Un caso di studio: l’Australia

    Directory of Open Access Journals (Sweden)

    Thomas Wulstan Christiansen

    2016-01-01

    Full Text Available Abstract – This chapter focuses upon two contrasting features of the linguistic situation in Australia. On the one hand, together with nationhood, the past hundred or so years have seen the evolution of a distinct national variety of English in Australia recognizable also outside Australia. On the other, Australia, though a young nation, has been continuously inhabited by the various Aborigine and Torre Strait Islander communities for thousands of years. These have traditionally spoken a wide variety of different languages, some of which of great interest to linguists due to their peculiarity. Increasingly, although the use of Aborigine languages has until very recently been in steady decline, since the 1950s in particular, diverse ethnic groups speaking a variety of languages, both European and Asian, have settled in Australia. The National Policy on Languages (1987 formally directed Australia towards multilingualism and the teaching of English as a first and second language is promoted together with that of Aborigine and community languages. Consequently, Australia has been one of the first nations to try to capitalise on its own linguistic diversity, both as a means of strengthening links with the outside world and as a way of promoting a multiethnic and multicultural society at home. Australia presents then an interesting case study for those working with discourse in immigration domains who are concerned with the way that language policy (or the lack of one may effect social harmony and serve not only as an indicator of the way that migrants are received and treated, but also a catalyst in itself for greater mutual respect.

  10. Coal mining in Australia

    Energy Technology Data Exchange (ETDEWEB)

    Mills, L J

    1981-12-01

    In 1959 black coal production in Australia totalled some 21.9 million tonnes per annum, 70% of this being produced from underground mines in the coalfields of New South Wales. By 1980 output levels had increased by nearly 350% to 75.4 million tonnes per annum (54% of which was exported) compared with 5% some 20 years earlier. Because it is blessed with large reserves of coal and other forms of energy, it is inevitable that the Australian coal mining industry will be required to play a major role in the development of the international coal market through to the end of the present century. Experts now predict a need for the black coal output in Australia to be developed from its present level to a minimum of 293 million tonnes per annum by the year 2000. This paper examines the present circumstances in the Australian coal industry and attempts to outline the development which has to be undertaken in order to meet the needs of an energy hungry world.

  11. Year book Australia 1985

    Energy Technology Data Exchange (ETDEWEB)

    Cameron, R J

    1985-01-01

    The Year Book is the principal reference work produced by the Central Office of the Australian Bureau of Statistics (ABS). It provides a comprehensive and detailed statistical review of all aspects of the economy and social conditions of Australia. In addition, it contains descriptive matter dealing with Australia's history, geography, physiography, climate and meteorology, government, defence and repatriation services and international relations. The first Official Year Book was published in 1908. This is the sixty-ninth Year Book issued under the authority of the Commonwealth Government and follows a similar pattern to previous editions. However, chapters have been revised and new material has been added. Most of the statistics contained in this volume relate to the years ended June or December 1983 or 1984. More detailed, and in many cases more recent, statistics are available in other ABS publications. The more significant of these publications are listed at the end of the relevant chapters of the Year book; the ABS Catalogue of Publications (1101.0) lists all current publications of the ABS.

  12. Ground for concern. Australia's uranium and human survival. [Australia

    Energy Technology Data Exchange (ETDEWEB)

    Elliot, M

    1977-01-01

    The book contains a number of articles which propose that Australia should not mine and export its uranium in order to influence the nuclear establishment against uncontrollable proliferation. Topics covered include: uranium mining in Australia, reactor safety, nuclear wastes, nuclear weapons proliferation, nuclear theft and the politics of the nuclear industry.

  13. Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua.

    Science.gov (United States)

    Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel

    2013-02-01

    The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)-from two Great Lakes and two crater lakes in Nicaragua-to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ(13)C and δ(15)N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

  14. The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

    Science.gov (United States)

    Chung, Oksung; Jin, Seondeok; Cho, Yun Sung; Lim, Jeongheui; Kim, Hyunho; Jho, Sungwoong; Kim, Hak-Min; Jun, JeHoon; Lee, HyeJin; Chon, Alvin; Ko, Junsu; Edwards, Jeremy; Weber, Jessica A; Han, Kyudong; O'Brien, Stephen J; Manica, Andrea; Bhak, Jong; Paek, Woon Kee

    2015-10-21

    The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene. We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.

  15. New research reactor for Australia

    International Nuclear Information System (INIS)

    Miller, R.

    1992-01-01

    HIFAR, Australia's major research reactor was commissioned in 1958 to test materials for an envisaged indigenous nuclear power industry. HIFAR is a Dido type reactor which is operated at 10 MW. With the decision in the early 1970's not to proceed to nuclear power, HIFAR was adapted to other uses and has served Australia well as a base for national nuclear competence; as a national facility for neutron scattering/beam research; as a source of radioisotopes for medical diagnosis and treatment; and as a source of export revenue from the neutron transmutation doping of silicon for the semiconductor industry. However, all of HIFAR's capabilities are becoming less than optimum by world and regional standards. Neutron beam facilities have been overtaken on the world scene by research reactors with increased neutron fluxes, cold sources, and improved beams and neutron guides. Radioisotope production capabilities, while adequate to meet Australia's needs, cannot be easily expanded to tap the growing world market in radiopharmaceuticals. Similarly, neutron transmutation doped silicon production, and export income from it, is limited at a time when the world market for this material is expanding. ANSTO has therefore embarked on a program to replace HIFAR with a new multi-purpose national facility for nuclear research and technology in the form of a reactor: a) for neutron beam research, - with a peak thermal flux of the order of three times higher than that from HIFAR, - with a cold neutron source, guides and beam hall, b) that has radioisotope production facilities that are as good as, or better than, those in HIFAR, c) that maximizes the potential for commercial irradiations to offset facility operating costs, d) that maximizes flexibility to accommodate variations in user requirements during the life of the facility. ANSTO's case for the new research reactor received significant support earlier this month with the tabling in Parliament of a report by the Australian Science

  16. 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.

  17. Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs

    DEFF Research Database (Denmark)

    Hickman, Rachel A.; Munck, Christian; Sommer, Morten Otto Alexander

    2017-01-01

    + CHL and CHL + CIP). We find that lineages evolved to antibiotic combinations exhibit different resistance allele dynamics compared with those of single-drug evolved lineages, especially for a drug pair with reciprocal collateral sensitivity. During adaptation, we observed interfering, superimposing...

  18. Australia's marine virtual laboratory

    Science.gov (United States)

    Proctor, Roger; Gillibrand, Philip; Oke, Peter; Rosebrock, Uwe

    2014-05-01

    In all modelling studies of realistic scenarios, a researcher has to go through a number of steps to set up a model in order to produce a model simulation of value. The steps are generally the same, independent of the modelling system chosen. These steps include determining the time and space scales and processes of the required simulation; obtaining data for the initial set up and for input during the simulation time; obtaining observation data for validation or data assimilation; implementing scripts to run the simulation(s); and running utilities or custom-built software to extract results. These steps are time consuming and resource hungry, and have to be done every time irrespective of the simulation - the more complex the processes, the more effort is required to set up the simulation. The Australian Marine Virtual Laboratory (MARVL) is a new development in modelling frameworks for researchers in Australia. MARVL uses the TRIKE framework, a java-based control system developed by CSIRO that allows a non-specialist user configure and run a model, to automate many of the modelling preparation steps needed to bring the researcher faster to the stage of simulation and analysis. The tool is seen as enhancing the efficiency of researchers and marine managers, and is being considered as an educational aid in teaching. In MARVL we are developing a web-based open source application which provides a number of model choices and provides search and recovery of relevant observations, allowing researchers to: a) efficiently configure a range of different community ocean and wave models for any region, for any historical time period, with model specifications of their choice, through a user-friendly web application, b) access data sets to force a model and nest a model into, c) discover and assemble ocean observations from the Australian Ocean Data Network (AODN, http://portal.aodn.org.au/webportal/) in a format that is suitable for model evaluation or data assimilation, and

  19. Indigenous actinorhizal plants of Australia

    Indian Academy of Sciences (India)

    Indigenous species of actinorhizal plants of Casuarinaceae, Elaeagnaceae and Rhamnaceae are found in specific regions of Australia. Most of these plants belong to Casuarinaceae, the dominant actinorhizal family in Australia. Many of them have significant environmental and economical value. The other two families with ...

  20. Building nuclear skills in Australia

    International Nuclear Information System (INIS)

    Cameron, R.

    2007-01-01

    Demand for nuclear skills in Australia has traditionally been met by recruitment but as the nuclear industry grows worldwide, such skills are in demand. This paper discusses he likely numbers of skilled people needed for a nuclear industry in Australia and what initiatives have been, or could be in, taken to address the needs

  1. Lexicography in Australia | Delbridge | Lexikos

    African Journals Online (AJOL)

    The emergence of Australian English as the national language is traced, and its relations with the Australian Aboriginal languages touched on. The greatest change in the language setting came with Australia's immigration policy in its post-World War II form. This resulted in the government's eventual recognition of Australia ...

  2. Recent developments: Japan and Australia

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    Recent developments in the nuclear industry in Japan and Australia are briefly reviewed. Topics discussed include: the world energy situation; and nuclear power generation trends and completion the nuclear fuel cycle in Japan. Recent events that suggest possible policy changes in Australia are briefly discussed

  3. Warragamba. Sydney, Australia

    Directory of Open Access Journals (Sweden)

    Seshadri, B.

    1959-02-01

    Full Text Available El pantano de Warragamba, cuyo objeto es el de producir energía hidroeléctrica en su primera fase de explotación y solamente agua potable cuando las necesidades de ésta así lo requieran, se haya situado en las proximidades de Sydney (Australia. Su extensa cuenca está constituida por una serie de ríos en cuyas cabeceras se han construido diques de retención, que no solamente almacenan grandes cantidades de agua, sino que sirven parcialmente para la regularización de caudales, función de gran interés en esta zona donde las avenidas, seguidas de extensas inundaciones, se hacen sentir con relativa frecuencia.

  4. South Australia, uranium enrichment

    International Nuclear Information System (INIS)

    1976-02-01

    The Report sets out the salient data relating to the establishment of a uranium processing centre at Redcliff in South Australia. It is conceived as a major development project for the Commonwealth, the South Australian Government and Australian Industry comprising the refining and enrichment of uranium produced from Australian mines. Using the data currently available in respect of markets, demand, technology and possible financial return from overseas sales, the project could be initiated immediately with hexafluoride production, followed rapidly in stages by enrichment production using the centrifuge process. A conceptual development plan is presented, involving a growth pattern that would be closely synchronised with the mining and production of yellowcake. The proposed development is presented in the form of an eight-and-half-year programme. Costs in this Report are based on 1975 values, unless otherwise stated. (Author)

  5. Astronomy in Australia

    Science.gov (United States)

    Watson, F.; Couch, W.

    2017-12-01

    Australians have watched the sky for tens of thousands of years. The nineteenth century saw the foundation of government observatories in capital cities such as Sydney and Melbourne. While early twentieth-century astronomy focused largely on solar physics, the advent of radio astronomy at the end of the Second World War enabled Australia to take a leading role in the new science, with particular emphasis on low-frequency studies. Today, the radio quietness of its outback interior provides an excellent location for the Australian core of the Square Kilometre Array. Australian optical astronomy has flourished since the 1960s, with the 3.9-metre Anglo-Australian Telescope becoming the principal national facility in 1974. Access to ESO’s facilities at the La Silla Paranal Observatory is warmly welcomed by all Australian astronomers.

  6. Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress.

    Science.gov (United States)

    Ma, Jianchao; Lu, Jing; Xu, Jianmei; Duan, Bingbing; He, Xiaodong; Liu, Jianquan

    2015-01-01

    WRKY transcription factors play important roles in plant development and responses to various stresses in plants. However, little is known about the evolution of the WRKY genes in the desert poplar species Populus euphratica, which is highly tolerant of salt stress. In this study, we identified 107 PeWRKY genes from the P. euphratica genome and examined their evolutionary relationships with the WRKY genes of the salt-sensitive congener Populus trichocarpa. Ten PeWRKY genes are specific to P. euphratica, and five of these showed altered expression under salt stress. Furthermore, we found that two pairs of orthologs between the two species showed evidence of positive evolution, with dN/dS ratios>1 (nonsynonymous/synonymous substitutions), and both of them altered their expression in response to salinity stress. These findings suggested that both the development of new genes and positive evolution in some orthologs of the WRKY gene family may have played an important role in the acquisition of high salt tolerance by P. euphratica.

  7. Thermodynamical interpretation of an adaptive walk on a Mt. Fuji-type fitness landscape: Einstein relation-like formula holds in a stochastic evolution.

    Science.gov (United States)

    Aita, Takuyo; Husimi, Yuzuru

    2003-11-21

    We have theoretically studied the statistical properties of adaptive walks (or hill-climbing) on a Mt. Fuji-type fitness landscape in the multi-dimensional sequence space through mathematical analysis and computer simulation. The adaptive walk is characterized by the "mutation distance" d as the step-width of the walker and the "population size" N as the number of randomly generated d-fold point mutants to be screened. In addition to the fitness W, we introduced the following quantities analogous to thermodynamical concepts: "free fitness" G(W) is identical with W+T x S(W), where T is the "evolutionary temperature" T infinity square root of d/lnN and S(W) is the entropy as a function of W, and the "evolutionary force" X is identical with d(G(W)/T)/dW, that is caused by the mutation and selection pressure. It is known that a single adaptive walker rapidly climbs on the fitness landscape up to the stationary state where a "mutation-selection-random drift balance" is kept. In our interpretation, the walker tends to the maximal free fitness state, driven by the evolutionary force X. Our major findings are as follows: First, near the stationary point W*, the "climbing rate" J as the expected fitness change per generation is described by J approximately L x X with L approximately V/2, where V is the variance of fitness distribution on a local landscape. This simple relationship is analogous to the well-known Einstein relation in Brownian motion. Second, the "biological information gain" (DeltaG/T) through adaptive walk can be described by combining the Shannon's information gain (DeltaS) and the "fitness information gain" (DeltaW/T).

  8. Australia's Uranium and thorium resources and their global significance

    International Nuclear Information System (INIS)

    Lambert, I.B.; McKay, A.; Miezitis, Y.

    2006-01-01

    Full text: Full text: Australia's world-leading uranium endowment appears to result from the emplacement of uranium enriched felsic igneous rocks in three major periods during the geological evolution of the continent. Australia has over 27% of the world's total reasonably assured uranium resources (RAR) recoverable at < US$80/kgU (which approximates recent uranium spot prices). Olympic Dam is the largest known uranium deposit, containing approximately 19% of global RAR (and over 40% of global inferred resources) recoverable at < US$80/kg U; the uranium is present at low concentrations and the viability of its recovery is underpinned by co-production of copper and gold. Most of Australia's other identified resources are within Ranger, Jabiluka, Koongarra, Kintyre and Yeelirrie, the last four of which are not currently accessible for mining. In 2004, Australia's three operating uranium mines - Ranger, Olympic Dam, and Beverley -produced 22% of global production. Canada was the only country to produce more uranium (29%) and Kazakhstan (9%) ranked third. Considerably increased uranium production has been recently foreshadowed from Australia (through developing a large open pit at Olympic Dam), Canada (mainly through opening of the Cigar Lake mine), and Kazakhstan (developing several new in situ leach mines). These increases should go a long way towards satisfying demand from about 2010. Olympic Dam has sufficient resources to sustain such increased production over many decades. Thorium is expected to be used in some future generations of nuclear reactors. Australia also has major (but incompletely quantified) resources of this commodity, mainly in heavy mineral sands deposits and associated with alkaline igneous rocks. It is inevitable that the international community will be looking increasingly to Australia to sustain its vital role in providing fuels for future nuclear power generation, given its world-leading identified resources, considerable potential for new

  9. Animal evolution and atmospheric pO2: is there a link between gradual animal adaptation to terrain elevation due to Ural orogeny and survival of subsequent hypoxic periods?

    Science.gov (United States)

    Kurbel, Sven

    2014-10-22

    Considering evolution of terrestrial animals as something happening only on flat continental plains seems wrong. Many mountains have arisen and disappeared over the geologic time scale, so in all periods some areas of high altitude existed, with reduced oxygen pressure (pO2) and increased aridity. During orogeny, animal species of the raising terrain can slowly adapt to reduced oxygen levels.This review proposes that animal evolution was often driven by atmospheric oxygen availability. Transitions of insect ancestors and amphibians out of water are here interpreted as events forced by the lack of oxygen in shallow and warm water during Devonian. Hyperoxia during early Carboniferous allowed giant insects to be predators of lowlands, forcing small amphibians to move to higher terrains, unsuitable to large insects due to reduced pO2. In arid mountainous habitats, ascended animals evolved in early reptiles with more efficient lungs and improved circulation. Animals with alveolar lungs became the mammalian ancestors, while those with respiratory duct lungs developed in archosaurs. In this interpretation, limb precursors of wings and pneumatised bones might have been adaptations for moving on steep slopes.Ural mountains have risen to an estimated height of 3000 m between 318 and 251 Mya. The earliest archosaurs have been found on the European Ural side, estimated 275 Myr old. It is proposed that Ural orogeny slowly elevated several highland habitats within the modern Ural region to heights above 2500 m. Since this process took near 60 Myr, animals in these habitats fully to adapted to hypoxia.The protracted P-Tr hypoxic extinction event killed many aquatic and terrestrial animals. Devastated lowland areas were repopulated by mammaliaformes that came down from mountainous areas. Archosaurs were better adapted to very low pO2, so they were forced to descend to the sea level later when the lack of oxygen became severe. During the Triassic period, when the relative content

  10. Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles

    DEFF Research Database (Denmark)

    Greenwold, Matthew J.; Bao, Weier; Jarvis, Erich D.

    2014-01-01

    BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes...... of 48 phylogenetically diverse birds and their expression in the scales and feathers of the chicken. RESULTS: We found that the total number of α-keratins is lower in birds than mammals and non-avian reptiles, yet two α-keratin genes (KRT42 and KRT75) have expanded in birds. The β-keratins, however...

  11. Asian student migration to Australia.

    Science.gov (United States)

    Shu, J; Hawthorne, L

    1996-01-01

    "This paper presents an overview of Asian student migration to Australia, together with an analysis of political and educational aspects of the overseas student programme. It focuses on some significant consequences of this flow for Australia. The characteristics of key student groups are contrasted to provide some perspective of the diversity of historical and cultural backgrounds, with the source countries of Malaysia, Indonesia and PRC [China] selected as case studies. Since the issue of PRC students in Australia has attracted considerable public attention and policy consideration, particular focus is placed on their experience." (SUMMARY IN FRE AND SPA) excerpt

  12. Adaptive Management of Environmental Flows

    Science.gov (United States)

    Webb, J. Angus; Watts, Robyn J.; Allan, Catherine; Conallin, John C.

    2018-03-01

    Adaptive management enables managers to work with complexity and uncertainty, and to respond to changing biophysical and social conditions. Amid considerable uncertainty over the benefits of environmental flows, governments are embracing adaptive management as a means to inform decision making. This Special Issue of Environmental Management presents examples of adaptive management of environmental flows and addresses claims that there are few examples of its successful implementation. It arose from a session at the 11th International Symposium on Ecohydraulics held in Australia, and is consequently dominated by papers from Australia. We classified the papers according to the involvement of researchers, managers and the local community in adaptive management. Five papers report on approaches developed by researchers, and one paper on a community-led program; these case studies currently have little impact on decision making. Six papers provide examples involving water managers and researchers, and two papers provide examples involving water managers and the local community. There are no papers where researchers, managers and local communities all contribute equally to adaptive management. Successful adaptive management of environmental flows occurs more often than is perceived. The final paper explores why successes are rarely reported, suggesting a lack of emphasis on reflection on management practices. One major challenge is to increase the documentation of successful adaptive management, so that benefits of learning extend beyond the project where it takes place. Finally, moving towards greater involvement of all stakeholders is critical if we are to realize the benefits of adaptive management for improving outcomes from environmental flows.

  13. Resilience through adaptation.

    Directory of Open Access Journals (Sweden)

    Guus A Ten Broeke

    Full Text Available Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS. Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

  14. Resilience through adaptation.

    Science.gov (United States)

    Ten Broeke, Guus A; van Voorn, George A K; Ligtenberg, Arend; Molenaar, Jaap

    2017-01-01

    Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

  15. Algae Reefs in Shark Bay, Western Australia, Australia

    Science.gov (United States)

    1990-01-01

    Numerous algae reefs are seen in Shark Bay, Western Australia, Australia (26.0S, 113.5E) especially in the southern portions of the bay. The south end is more saline because tidal flow in and out of the bay is restricted by sediment deposited at the north and central end of the bay opposite the mouth of the Wooramel River. This extremely arid region produces little sediment runoff so that the waters are very clear, saline and rich in algae.

  16. Neutron scattering in Australia

    International Nuclear Information System (INIS)

    Knott, R.B.

    1994-01-01

    Neutron scattering techniques have been part of the Australian scientific research community for the past three decades. The High Flux Australian Reactor (HIFAR) is a multi-use facility of modest performance that provides the only neutron source in the country suitable for neutron scattering. The limitations of HIFAR have been recognized and recently a Government initiated inquiry sought to evaluate the future needs of a neutron source. In essence, the inquiry suggested that a delay of several years would enable a number of key issues to be resolved, and therefore a more appropriate decision made. In the meantime, use of the present source is being optimized, and where necessary research is being undertaken at major overseas neutron facilities either on a formal or informal basis. Australia has, at present, a formal agreement with the Rutherford Appleton Laboratory (UK) for access to the spallation source ISIS. Various aspects of neutron scattering have been implemented on HIFAR, including investigations of the structure of biological relevant molecules. One aspect of these investigations will be presented. Preliminary results from a study of the interaction of the immunosuppressant drug, cyclosporin-A, with reconstituted membranes suggest that the hydrophobic drug interdigitated with lipid chains

  17. Neutron scattering in Australia

    Energy Technology Data Exchange (ETDEWEB)

    Knott, R.B. [Australian Nuclear Science and Technology Organisation, Menai (Australia)

    1994-12-31

    Neutron scattering techniques have been part of the Australian scientific research community for the past three decades. The High Flux Australian Reactor (HIFAR) is a multi-use facility of modest performance that provides the only neutron source in the country suitable for neutron scattering. The limitations of HIFAR have been recognized and recently a Government initiated inquiry sought to evaluate the future needs of a neutron source. In essence, the inquiry suggested that a delay of several years would enable a number of key issues to be resolved, and therefore a more appropriate decision made. In the meantime, use of the present source is being optimized, and where necessary research is being undertaken at major overseas neutron facilities either on a formal or informal basis. Australia has, at present, a formal agreement with the Rutherford Appleton Laboratory (UK) for access to the spallation source ISIS. Various aspects of neutron scattering have been implemented on HIFAR, including investigations of the structure of biological relevant molecules. One aspect of these investigations will be presented. Preliminary results from a study of the interaction of the immunosuppressant drug, cyclosporin-A, with reconstituted membranes suggest that the hydrophobic drug interdigitated with lipid chains.

  18. Australia's unresolved nuclear problems

    International Nuclear Information System (INIS)

    Kemeny, L.G.

    1987-01-01

    This paper examines three acts of monumental incompetence which have all but destroyed Australia's once great potential to play a leading role in nuclear technology in South East Asia. Political chicanery and monumental technological and economic foresight, professional weakness and vacillation in the engineering community and the vicious pseudo scientific propaganda of most branches of the media, the teaching profession and sadly, even the politicisation of our churches, has all but destroyed a potential Australian ''sunrise industry''. Over the next forty years the population of planet Earth will approximately double. Unless Australians realise that their children and grand-children, and future generations of our neighbouring third world countries will require nuclear technology for an equitable and acceptable shared life-style, they will continue to allow taxpayers' money to be wasted on costly, technically unacceptable and environmentally undesirable attempts to develop ''alternative'' or ''renewable'' energy sources. These are neither alternative nor renewable but politically trendy. The tragedy of such projects is that their limited applicability and suitability for small scale energy production by wealthy users in limited geographical locations will only increase the need for base load energy supplies of the conventional type. Unless this is nuclear, planet Earth faces environmental despolation of monumental proportions. (J.P.N.)

  19. Environmental radioactivity in Australia

    Energy Technology Data Exchange (ETDEWEB)

    Twining, John [Environmental Science Division, ANSTO, Menai (Australia)

    2002-06-01

    Environmental research mainly carried out at Australian Nuclear Science and Technology Organization (ANSTO) related to nuclear activities in Australia such as uranium mining, transfer factor studies related to U- and Th-series radionuclides, dose assessment modelling, radiation monitoring, and nuclear waste repository, is outlined. Many aspects of radioecology, marine and freshwater geochemistry and radiochemical dating techniques; bioaccumulation including archival monitoring and kinetics, ground water studies, atmospheric issues including climate change and geomorphology are being studied with the help of a high neutron flux reactor, a cyclotron and a tandem accelerator as well as modern analytical equipment. Only a very small number of examples of radioactivity applications are presented: Microbiotic crusts covering up to 50% of the soil surface at Maralinga nuclear test site where more than 80% of the residual Am-241 was found to retain within the top 5 mm after 30 years. SIMS analysis of crocodile bones indicating that the only metal affected by U mining in Kakadu region was lead (Pb). In mineral sands such as zircon, U(VI) is more stable than U(IV) as evidenced by ion beam and SEM imaging and XANES analysis. Use of radioisotopes in atmospheric and climate studies, terrestrial studies particularly in dating techniques, and aquatic-continental and aquatic-ocean waters, and in biological studies such as biokinetics of copper metabolism in rainbow fishes living downstream of a mine are presented. (S. Ohno)

  20. Heron Island, Australia

    Science.gov (United States)

    2002-01-01

    Heron Island is located at the sourthern end of Australia's 2,050 km-long Great Barrier Reef. Surrounded by coral reef and home to over 1000 species of fish, scuba divers and scientists alike are drawn to the island's resort and research station. The true-color image above was taken by Space Imaging's Ikonos satellite with a resolution of 4 meters per pixel-high enough to see individual boats tied up at the small marina. The narrow channel leading from the marina to the ocean was blasted and dredged decades ago, before the island became a national park. Since then the Australian government has implemented conservation measures, such as limiting the number of tourists and removing or recycling, instead of incinerating, all trash. One of the applications of remote sensing data from Ikonos is environmental monitoring, including studies of coral reef health. For more information about the island, read Heron Island. Image by Robert Simmon, based on data copyright Space Imaging

  1. Climate change and viticulture in Mediterranean climates: the complex response of socio-ecosystems. A comparative case study from France and Australia (1955-2040)

    Science.gov (United States)

    Lereboullet, A.-L.; Beltrando, G.; Bardsley, D. K.

    2012-04-01

    The wine industry is very sensitive to extreme weather events, especially to temperatures above 35°C and drought. In a context of global climate change, Mediterranean climate regions are predicted to experience higher variability in rainfall and temperatures and an increased occurrence of extreme weather events. Some viticultural systems could be particularly at risk in those regions, considering their marginal position in the growth climatic range of Vitis vinifera, the long commercial lifespan of a vineyard, the high added-value of wine and the volatile nature of global markets. The wine industry, like other agricultural systems, is inserted in complex networks of climatic and non-climatic (other physical, economical, social and legislative) components, with constant feedbacks. We use a socio-ecosystem approach to analyse the adaptation of two Mediterranean viticultural systems to recent and future increase of extreme weather events. The present analysis focuses on two wine regions with a hot-summer Mediterranean climate (CSb type in the Köppen classification): Côtes-du-Roussillon in southern France and McLaren Vale in southern Australia. Using climate data from two synoptic weather stations, Perpignan (France) and Adelaide (Australia), with time series running from 1955 to 2010, we highlight changes in rainfall patterns and an increase in the number of days with Tx >35°c since the last three decades in both regions. Climate models (DRIAS project data for France and CSIRO Mk3.5 for Australia) project similar trends in the future. To date, very few projects have focused on an international comparison of the adaptive capacity of viticultural systems to climate change with a holistic approach. Here, the analysis of climate data was complemented by twenty in-depth semi-structured interviews with key actors of the two regional wine industries, in order to analyse adaptation strategies put in place regarding recent climate evolution. This mixed-methods approach

  2. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus (RHDV) in Australia: when one became many

    OpenAIRE

    Kovaliski, John; Sinclair, Ron; Mutze, Greg; Peacock, David; Strive, Tanja; Abrantes, Joana; Esteves, Pedro J.; Holmes, Edward C.

    2013-01-01

    Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16 year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared to those sampled globally, revealed that they form a monophyletic group with t...

  3. Expectations of vulnerability in Australia

    Directory of Open Access Journals (Sweden)

    Alice M Neikirk

    2017-02-01

    Full Text Available The ability of refugees to gain admission to Australia is increasingly based on perceptions of helplessness, suffering and ‘deservingness’. One consequence is that men in particular are marginalised following resettlement.

  4. Migration from India to Australia.

    Science.gov (United States)

    Awasthi, S P; Chandra, A

    1994-01-01

    "The article examines the contemporary trends and future prospects of migration from India to Australia. The focus is on Indian Settlers and Temporary Entrants admitted to Australia for employment and Indian students admitted to Australia for higher studies. The volume of emigration for permanent residence during the early 1990s has made India one of the leading source countries of migration to Australia. A majority of Indians admitted as Settlers every year join the labor force. Recent data indicate that, among Indian Settlers, there is a preponderance of unsponsored Independent Skilled Migrants. Given the anticipated growth in the number of Indian students, the coming years are likely to witness a spurt in Skilled Temporary Workers from India." excerpt

  5. Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

    Science.gov (United States)

    Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

    2015-08-07

    We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary 'arms race' between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.

  6. Rethinking "Commercial" Surrogacy in Australia.

    Science.gov (United States)

    Millbank, Jenni

    2015-09-01

    This article proposes reconsideration of laws prohibiting paid surrogacy in Australia in light of increasing transnational commercial surrogacy. The social science evidence base concerning domestic surrogacy in developed economies demonstrates that payment alone cannot be used to differentiate "good" surrogacy arrangements from "bad" ones. Compensated domestic surrogacy and the introduction of professional intermediaries and mechanisms such as advertising are proposed as a feasible harm-minimisation approach. I contend that Australia can learn from commercial surrogacy practices elsewhere, without replicating them.

  7. Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: evidence from genome-wide analyses.

    Science.gov (United States)

    Crosley, E J; Elliot, M G; Christians, J K; Crespi, B J

    2013-02-01

    Recent evidence from chimpanzees and gorillas has raised doubts that preeclampsia is a uniquely human disease. The deep extravillous trophoblast (EVT) invasion and spiral artery remodeling that characterizes our placenta (and is abnormal in preeclampsia) is shared within great apes, setting Homininae apart from Hylobatidae and Old World Monkeys, which show much shallower trophoblast invasion and limited spiral artery remodeling. We hypothesize that the evolution of a more invasive placenta in the lineage ancestral to the great apes involved positive selection on genes crucial to EVT invasion and spiral artery remodeling. Furthermore, identification of placentally-expressed genes under selection in this lineage may identify novel genes involved in placental development. We tested for positive selection in approximately 18,000 genes using the ratio of non-synonymous to synonymous amino acid substitution for protein-coding DNA. DAVID Bioinformatics Resources identified biological processes enriched in positively selected genes, including processes related to EVT invasion and spiral artery remodeling. Analyses revealed 295 and 264 genes under significant positive selection on the branches ancestral to Hominidae (Human, Chimp, Gorilla, Orangutan) and Homininae (Human, Chimp, Gorilla), respectively. Gene ontology analysis of these gene sets demonstrated significant enrichments for several functional gene clusters relevant to preeclampsia risk, and sets of placentally-expressed genes that have been linked with preeclampsia and/or trophoblast invasion in other studies. Our study represents a novel approach to the identification of candidate genes and amino acid residues involved in placental pathologies by implicating them in the evolution of highly-invasive placenta. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Australia: uranium and nuclear policy

    International Nuclear Information System (INIS)

    Crick, R.

    1991-01-01

    Australia's uranium and nuclear policies have gone through several stages of development since the commercialisation of the industry. The early stages laid the foundations and built the superstructure of Australia's uranium development, export and safeguards policies. The uranium industry and other governments have understood the nature and operation of these policies. An important aim of this paper will be to explain the design and current construction stage of policies. This needs to be done against the background of broader industry developments. Within the past twelve months (1989/90) there have been dramatic changes, both within Australia and internationally, which have affected the uranium market. Internationally, we have seen the spot price indicators for uranium fall to an all time low. Within Australia, we have seen the removal of the fixed floor price requirement for the sale of Australia uranium. This was replaced by a requirement that contract prices reflect the market. This change in policy allowed the outcome of several major long-term contract renegotiations to be approved. It also allowed Australian producers to secure several new long-term contracts, despite the overall depressed state of the market. The 'three mines' policy remains in place although only two, Ranger in Northern Territory and Olympic Dare in Southern Australia are currently operating. The biggest unknown is the extent of future uranium demand. (author)

  9. Evolution and ecology meet molecular genetics: adaptive phenotypic plasticity in two isolated Negev desert populations of Acacia raddiana at either end of a rainfall gradient

    Science.gov (United States)

    Ward, David; Shrestha, Madan K.; Golan-Goldhirsh, Avi

    2012-01-01

    Background and Aims The ecological, evolutionary and genetic bases of population differentiation in a variable environment are often related to the selection pressures that plants experience. We compared differences in several growth- and defence-related traits in two isolated populations of Acacia raddiana trees from sites at either end of an extreme environmental gradient in the Negev desert. Methods We used random amplified polymorphic DNA (RAPD) to determine the molecular differences between populations. We grew plants under two levels of water, three levels of nutrients and three levels of herbivory to test for phenotypic plasticity and adaptive phenotypic plasticity. Key Results The RAPD analyses showed that these populations are highly genetically differentiated. Phenotypic plasticity in various morphological traits in A. raddiana was related to patterns of population genetic differentiation between the two study sites. Although we did not test for maternal effects in these long-lived trees, significant genotype × environment (G × E) interactions in some of these traits indicated that such plasticity may be adaptive. Conclusions The main selection pressure in this desert environment, perhaps unsurprisingly, is water. Increased water availability resulted in greater growth in the southern population, which normally receives far less rain than the northern population. Even under the conditions that we defined as low water and/or nutrients, the performance of the seedlings from the southern population was significantly better, perhaps reflecting selection for these traits. Consistent with previous studies of this genus, there was no evidence of trade-offs between physical and chemical defences and plant growth parameters in this study. Rather, there appeared to be positive correlations between plant size and defence parameters. The great variation in several traits in both populations may result in a diverse potential for responding to selection pressures in

  10. Adaptation of an L-proline adenylation domain to use 4-propyl-L-proline in the evolution of lincosamide biosynthesis.

    Directory of Open Access Journals (Sweden)

    Stanislav Kadlčík

    Full Text Available Clinically used lincosamide antibiotic lincomycin incorporates in its structure 4-propyl-L-proline (PPL, an unusual amino acid, while celesticetin, a less efficient related compound, makes use of proteinogenic L-proline. Biochemical characterization, as well as phylogenetic analysis and homology modelling combined with the molecular dynamics simulation were employed for complex comparative analysis of the orthologous protein pair LmbC and CcbC from the biosynthesis of lincomycin and celesticetin, respectively. The analysis proved the compared proteins to be the stand-alone adenylation domains strictly preferring their own natural substrate, PPL or L-proline. The LmbC substrate binding pocket is adapted to accommodate a rare PPL precursor. When compared with L-proline specific ones, several large amino acid residues were replaced by smaller ones opening a channel which allowed the alkyl side chain of PPL to be accommodated. One of the most important differences, that of the residue corresponding to V306 in CcbC changing to G308 in LmbC, was investigated in vitro and in silico. Moreover, the substrate binding pocket rearrangement also allowed LmbC to effectively adenylate 4-butyl-L-proline and 4-pentyl-L-proline, substrates with even longer alkyl side chains, producing more potent lincosamides. A shift of LmbC substrate specificity appears to be an integral part of biosynthetic pathway adaptation to the PPL acquisition. A set of genes presumably coding for the PPL biosynthesis is present in the lincomycin--but not in the celesticetin cluster; their homologs are found in biosynthetic clusters of some pyrrolobenzodiazepines (PBD and hormaomycin. Whereas in the PBD and hormaomycin pathways the arising precursors are condensed to another amino acid moiety, the LmbC protein is the first functionally proved part of a unique condensation enzyme connecting PPL to the specialized amino sugar building unit.

  11. Determinate primary root growth as an adaptation to aridity in Cactaceae: towards an understanding of the evolution and genetic control of the trait.

    Science.gov (United States)

    Shishkova, Svetlana; Las Peñas, María Laura; Napsucialy-Mendivil, Selene; Matvienko, Marta; Kozik, Alex; Montiel, Jesús; Patiño, Anallely; Dubrovsky, Joseph G

    2013-07-01

    Species of Cactaceae are well adapted to arid habitats. Determinate growth of the primary root, which involves early and complete root apical meristem (RAM) exhaustion and differentiation of cells at the root tip, has been reported for some Cactoideae species as a root adaptation to aridity. In this study, the primary root growth patterns of Cactaceae taxa from diverse habitats are classified as being determinate or indeterminate, and the molecular mechanisms underlying RAM maintenance in Cactaceae are explored. Genes that were induced in the primary root of Stenocereus gummosus before RAM exhaustion are identified. Primary root growth was analysed in Cactaceae seedlings cultivated in vertically oriented Petri dishes. Differentially expressed transcripts were identified after reverse northern blots of clones from a suppression subtractive hybridization cDNA library. All species analysed from six tribes of the Cactoideae subfamily that inhabit arid and semi-arid regions exhibited determinate primary root growth. However, species from the Hylocereeae tribe, which inhabit mesic regions, exhibited mostly indeterminate primary root growth. Preliminary results suggest that seedlings of members of the Opuntioideae subfamily have mostly determinate primary root growth, whereas those of the Maihuenioideae and Pereskioideae subfamilies have mostly indeterminate primary root growth. Seven selected transcripts encoding homologues of heat stress transcription factor B4, histone deacetylase, fibrillarin, phosphoethanolamine methyltransferase, cytochrome P450 and gibberellin-regulated protein were upregulated in S. gummosus root tips during the initial growth phase. Primary root growth in Cactoideae species matches their environment. The data imply that determinate growth of the primary root became fixed after separation of the Cactiodeae/Opuntioideae and Maihuenioideae/Pereskioideae lineages, and that the genetic regulation of RAM maintenance and its loss in Cactaceae is

  12. Dual phase evolution

    CERN Document Server

    Green, David G; Abbass, Hussein A

    2014-01-01

    This book expl