Key issues review: evolution on rugged adaptive landscapes

NASA Astrophysics Data System (ADS)

Obolski, Uri; Ram, Yoav; Hadany, Lilach

2018-01-01

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

Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments.

PubMed

Hong, Jungeui; Gresham, David

2014-01-01

One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that

Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry.

PubMed

Duthie, A B; Bocedi, G; Germain, R R; Reid, J M

2018-01-01

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. 'degeneracy') potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post

Phenotypic convergence in bacterial adaptive evolution to ethanol stress.

PubMed

Horinouchi, Takaaki; Suzuki, Shingo; Hirasawa, Takashi; Ono, Naoaki; Yomo, Tetsuya; Shimizu, Hiroshi; Furusawa, Chikara

2015-09-03

Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. During adaptive evolution, phenotype and genotype dynamically changes; however, the relationship between these changes and associated constraints is yet to be fully elucidated. In this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and were similar among independently evolved ethanol tolerant populations, which indicate the existence of evolutionary constraints in the dynamics of adaptive evolution. Furthermore, the contribution of identified mutations in one of the tolerant strains was evaluated using site-directed mutagenesis. The result demonstrated that the introduction of all identified mutations cannot fully explain the observed tolerance in the tolerant strain. The results demonstrated that the convergence of adaptive phenotypic changes and diverse genotypic changes, which suggested that the phenotype-genotype mapping is complex. The integration of transcriptome and genome data provides a quantitative understanding of evolutionary constraints.

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

PubMed

Siepielski, Adam M; Beaulieu, Jeremy M

2017-04-01

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

The functional basis of adaptive evolution in chemostats.

PubMed

Gresham, David; Hong, Jungeui

2015-01-01

Two of the central problems in biology are determining the molecular basis of adaptive evolution and understanding how cells regulate their growth. The chemostat is a device for culturing cells that provides great utility in tackling both of these problems: it enables precise control of the selective pressure under which organisms evolve and it facilitates experimental control of cell growth rate. The aim of this review is to synthesize results from studies of the functional basis of adaptive evolution in long-term chemostat selections using Escherichia coli and Saccharomyces cerevisiae. We describe the principle of the chemostat, provide a summary of studies of experimental evolution in chemostats, and use these studies to assess our current understanding of selection in the chemostat. Functional studies of adaptive evolution in chemostats provide a unique means of interrogating the genetic networks that control cell growth, which complements functional genomic approaches and quantitative trait loci (QTL) mapping in natural populations. An integrated approach to the study of adaptive evolution that accounts for both molecular function and evolutionary processes is critical to advancing our understanding of evolution. By renewing efforts to integrate these two research programs, experimental evolution in chemostats is ideally suited to extending the functional synthesis to the study of genetic networks. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Adaptive laboratory evolution – principles and applications for biotechnology

PubMed Central

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

Expressing Adaptation Strategies Using Adaptation Patterns

ERIC Educational Resources Information Center

Zemirline, N.; Bourda, Y.; Reynaud, C.

2012-01-01

Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

Adaptation, plant evolution, and the fossil record

NASA Technical Reports Server (NTRS)

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

Adaptation, plant evolution, and the fossil record.

PubMed

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

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

PubMed

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.

Emergent Neutrality in Adaptive Asexual Evolution

PubMed Central

Schiffels, Stephan; Szöllősi, Gergely J.; Mustonen, Ville; Lässig, Michael

2011-01-01

In nonrecombining genomes, genetic linkage can be an important evolutionary force. Linkage generates interference interactions, by which simultaneously occurring mutations affect each other’s chance of fixation. Here, we develop a comprehensive model of adaptive evolution in linked genomes, which integrates interference interactions between multiple beneficial and deleterious mutations into a unified framework. By an approximate analytical solution, we predict the fixation rates of these mutations, as well as the probabilities of beneficial and deleterious alleles at fixed genomic sites. We find that interference interactions generate a regime of emergent neutrality: all genomic sites with selection coefficients smaller in magnitude than a characteristic threshold have nearly random fixed alleles, and both beneficial and deleterious mutations at these sites have nearly neutral fixation rates. We show that this dynamic limits not only the speed of adaptation, but also a population’s degree of adaptation in its current environment. We apply the model to different scenarios: stationary adaptation in a time-dependent environment and approach to equilibrium in a fixed environment. In both cases, the analytical predictions are in good agreement with numerical simulations. Our results suggest that interference can severely compromise biological functions in an adapting population, which sets viability limits on adaptive evolution under linkage. PMID:21926305

Adapting clinical paradigms to the challenges of cancer clonal evolution.

PubMed

Murugaesu, Nirupa; Chew, Su Kit; Swanton, Charles

2013-06-01

Emerging evidence suggests that cancer branched evolution may affect biomarker validation, clinical outcome, and emergence of drug resistance. The changing spatial and temporal nature of cancer subclonal architecture during the disease course suggests the need for longitudinal prospective studies of cancer evolution and robust and clinically implementable pathologic definitions of intratumor heterogeneity, genetic diversity, and chromosomal instability. Furthermore, subclonal heterogeneous events in tumors may evade detection through conventional biomarker strategies and influence clinical outcome. Minimally invasive methods for the study of cancer evolution and new approaches to clinical study design, incorporating understanding of the dynamics of tumor clonal architectures through treatment and during acquisition of drug resistance, have been suggested as important areas for development. Coordinated efforts will be required by the scientific and clinical trial communities to adapt to the challenges of detecting infrequently occurring somatic events that may influence clinical outcome and to understand the dynamics of cancer evolution and the waxing and waning of tumor subclones over time in advanced metastatic epithelial malignancies. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Comparing the refuge strategy for managing the evolution of insect resistance under different reproductive strategies.

PubMed

Crowder, David W; Carrière, Yves

2009-12-07

Genetically modified (GM) crops are used extensively worldwide to control diploid agricultural insect pests that reproduce sexually. However, future GM crops will likely soon target haplodiploid and parthenogenetic insects. As rapid pest adaptation could compromise these novel crops, strategies to manage resistance in haplodiploid and parthenogenetic pests are urgently needed. Here, we developed models to characterize factors that could delay or prevent the evolution of resistance to GM crops in diploid, haplodiploid, and parthenogenetic insect pests. The standard strategy for managing resistance in diploid pests relies on refuges of non-GM host plants and GM crops that produce high toxin concentrations. Although the tenets of the standard refuge strategy apply to all pests, this strategy does not greatly delay the evolution of resistance in haplodiploid or parthenogenetic pests. Two additional factors are needed to effectively delay or prevent the evolution of resistance in such pests, large recessive or smaller non-recessive fitness costs must reduce the fitness of resistance individuals in refuges (and ideally also on GM crops), and resistant individuals must have lower fitness on GM compared to non-GM crops (incomplete resistance). Recent research indicates that the magnitude and dominance of fitness costs could be increased by using specific host-plants, natural enemies, or pathogens. Furthermore, incomplete resistance could be enhanced by engineering desirable traits into novel GM crops. Thus, the sustainability of GM crops that target haplodiploid or parthenogenetic pests will require careful consideration of the effects of reproductive mode, fitness costs, and incomplete resistance.

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.

PubMed

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.

Effective Strategies for Teaching Evolution: The Primary Evolution Project

ERIC Educational Resources Information Center

Hatcher, Chris

2015-01-01

When Chris Hatcher joined the Primary Evolution Project team at the University of Reading, his goal was to find effective strategies to teach evolution in a way that keeps children engaged and enthused. Hatcher has collaborated with colleagues at the University's Institute of Education to break the evolution unit down into distinct topics and…

Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks.

PubMed

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-15

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.

Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks

NASA Astrophysics Data System (ADS)

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-01

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.

The rule of declining adaptability in microbial evolution experiments

PubMed Central

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

Adaptive Molecular Evolution for 13,000 Phage Generations

PubMed Central

Wichman, Holly A.; Millstein, Jack; Bull, J. J.

2005-01-01

Bacteriophage φX174 was evolved on a continuous supply of sensitive hosts for 180 days (∼13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell. PMID:15687276

A novel composite adaptive flap controller design by a high-efficient modified differential evolution identification approach.

PubMed

Li, Nailu; Mu, Anle; Yang, Xiyun; Magar, Kaman T; Liu, Chao

2018-05-01

The optimal tuning of adaptive flap controller can improve adaptive flap control performance on uncertain operating environments, but the optimization process is usually time-consuming and it is difficult to design proper optimal tuning strategy for the flap control system (FCS). To solve this problem, a novel adaptive flap controller is designed based on a high-efficient differential evolution (DE) identification technique and composite adaptive internal model control (CAIMC) strategy. The optimal tuning can be easily obtained by DE identified inverse of the FCS via CAIMC structure. To achieve fast tuning, a high-efficient modified adaptive DE algorithm is proposed with new mutant operator and varying range adaptive mechanism for the FCS identification. A tradeoff between optimized adaptive flap control and low computation cost is successfully achieved by proposed controller. Simulation results show the robustness of proposed method and its superiority to conventional adaptive IMC (AIMC) flap controller and the CAIMC flap controllers using other DE algorithms on various uncertain operating conditions. The high computation efficiency of proposed controller is also verified based on the computation time on those operating cases. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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.

Efficient community-based control strategies in adaptive networks

NASA Astrophysics Data System (ADS)

Yang, Hui; Tang, Ming; Zhang, Hai-Feng

2012-12-01

Most studies on adaptive networks concentrate on the properties of steady state, but neglect transient dynamics. In this study, we pay attention to the emergence of community structure in the transient process and the effects of community-based control strategies on epidemic spreading. First, by normalizing the modularity, we investigate the evolution of community structure during the transient process, and find that a strong community structure is induced by the rewiring mechanism in the early stage of epidemic dynamics, which, remarkably, delays the outbreak of disease. We then study the effects of control strategies started at different stages on the prevalence. Both immunization and quarantine strategies indicate that it is not ‘the earlier, the better’ for the implementation of control measures. And the optimal control effect is obtained if control measures can be efficiently implemented in the period of a strong community structure. For the immunization strategy, immunizing the susceptible nodes on susceptible-infected links and immunizing susceptible nodes randomly have similar control effects. However, for the quarantine strategy, quarantining the infected nodes on susceptible-infected links can yield a far better result than quarantining infected nodes randomly. More significantly, the community-based quarantine strategy performs better than the community-based immunization strategy. This study may shed new light on the forecast and the prevention of epidemics among humans.

The adaptive evolution of the mammalian mitochondrial genome

PubMed Central

da Fonseca, Rute R; Johnson, Warren E; O'Brien, Stephen J; Ramos, Maria João; Antunes, Agostinho

2008-01-01

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. PMID:18318906

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

PubMed

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.

Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila.

PubMed

Castellano, David; Coronado-Zamora, Marta; Campos, Jose L; Barbadilla, Antonio; Eyre-Walker, Adam

2016-02-01

Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

PubMed

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.

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

USGS Publications Warehouse

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

The genomic basis of adaptive evolution in threespine sticklebacks

PubMed Central

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Lander, Eric S; Di Palma, Federica

2012-01-01

Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature. PMID:22481358

The genomic basis of adaptive evolution in threespine sticklebacks.

PubMed

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Baldwin, Jen; Bloom, Toby; Jaffe, David B; Nicol, Robert; Wilkinson, Jane; Lander, Eric S; Di Palma, Federica; Lindblad-Toh, Kerstin; Kingsley, David M

2012-04-04

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

Exploring equivalence domain in nonlinear inverse problems using Covariance Matrix Adaption Evolution Strategy (CMAES) and random sampling

NASA Astrophysics Data System (ADS)

Grayver, Alexander V.; Kuvshinov, Alexey V.

2016-05-01

This paper presents a methodology to sample equivalence domain (ED) in nonlinear partial differential equation (PDE)-constrained inverse problems. For this purpose, we first applied state-of-the-art stochastic optimization algorithm called Covariance Matrix Adaptation Evolution Strategy (CMAES) to identify low-misfit regions of the model space. These regions were then randomly sampled to create an ensemble of equivalent models and quantify uncertainty. CMAES is aimed at exploring model space globally and is robust on very ill-conditioned problems. We show that the number of iterations required to converge grows at a moderate rate with respect to number of unknowns and the algorithm is embarrassingly parallel. We formulated the problem by using the generalized Gaussian distribution. This enabled us to seamlessly use arbitrary norms for residual and regularization terms. We show that various regularization norms facilitate studying different classes of equivalent solutions. We further show how performance of the standard Metropolis-Hastings Markov chain Monte Carlo algorithm can be substantially improved by using information CMAES provides. This methodology was tested by using individual and joint inversions of magneotelluric, controlled-source electromagnetic (EM) and global EM induction data.

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

PubMed

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

Adaptive evolution of the STRA6 genes in mammalian.

PubMed

Wu, Jianghong; Xiang, Hui; Qi, Yunxia; Yang, Ding; Wang, Xiaojuan; Sun, Hailian; Wang, Feng; Liu, Bin

2014-01-01

Stimulated by retinoic acid 6 (STRA6) is the receptor for retinol binding protein and is relevant for the transport of retinol to specific sites such as the eye. The adaptive evolution mechanism that vertebrates have occupied nearly every habitat available on earth and adopted various lifestyles associated with different light conditions and visual challenges, as well as their role in development and adaptation is thus far unknown. In this work, we have investigated different aspects of vertebrate STRA6 evolution and used molecular evolutionary analyses to detect evidence of vertebrate adaptation to the lightless habitat. Free-ratio model revealed significant rate shifts immediately after the species divergence. The amino acid sites detected to be under positive selection are within the extracellular loops of STRA6 protein. Branch-site model A test revealed that STRA6 has undergone positive selection in the different phyla of mammalian except for the branch of rodent. The results suggest that interactions between different light environments and host may be driving adaptive change in STRA6 by competition between species. In support of this, we found that altered functional constraints may take place at some amino acid residues after speciation. We suggest that STRA6 has undergone adaptive evolution in different branch of vertebrate relation to habitat environment.

Adaptive Evolution Is Substantially Impeded by Hill–Robertson Interference in Drosophila

PubMed Central

Castellano, David; Coronado-Zamora, Marta; Campos, Jose L.; Barbadilla, Antonio; Eyre-Walker, Adam

2016-01-01

Hill–Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald–Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect. PMID:26494843

Dynamic Convergent Evolution Drives the Passage Adaptation across 48 Years' History of H3N2 Influenza Evolution.

PubMed

Chen, Hui; Deng, Qiang; Ng, Sock Hoon; Lee, Raphael Tze Chuen; Maurer-Stroh, Sebastian; Zhai, Weiwei

2016-12-01

Influenza viruses are often propagated in a diverse set of culturing media and additional substitutions known as passage adaptation can cause extra evolution in the target strain, leading to ineffective vaccines. Using 25,482 H3N2 HA1 sequences curated from Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information databases, we found that passage adaptation is a very dynamic process that changes over time and evolves in a seesaw like pattern. After crossing the species boundary from bird to human in 1968, the influenza H3N2 virus evolves to be better adapted to the human environment and passaging them in embryonated eggs (i.e., an avian environment) leads to increasingly stronger positive selection. On the contrary, passage adaptation to the mammalian cell lines changes from positive selection to negative selection. Using two statistical tests, we identified 19 codon positions around the receptor binding domain strongly contributing to passage adaptation in the embryonated egg. These sites show strong convergent evolution and overlap extensively with positively selected sites identified in humans, suggesting that passage adaptation can confound many of the earlier studies on influenza evolution. Interestingly, passage adaptation in recent years seems to target a few codon positions in antigenic surface epitopes, which makes it difficult to produce antigenically unaltered vaccines using embryonic eggs. Our study outlines another interesting scenario whereby both convergent and adaptive evolution are working in synchrony driving viral adaptation. Future studies from sequence analysis to vaccine production need to take careful consideration of passage adaptation. © The Author 2016. 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.

Evolution of complex density-dependent dispersal strategies.

PubMed

Parvinen, Kalle; Seppänen, Anne; Nagy, John D

2012-11-01

The question of how dispersal behavior is adaptive and how it responds to changes in selection pressure is more relevant than ever, as anthropogenic habitat alteration and climate change accelerate around the world. In metapopulation models where local populations are large, and thus local population size is measured in densities, density-dependent dispersal is expected to evolve to a single-threshold strategy, in which individuals stay in patches with local population density smaller than a threshold value and move immediately away from patches with local population density larger than the threshold. Fragmentation tends to convert continuous populations into metapopulations and also to decrease local population sizes. Therefore we analyze a metapopulation model, where each patch can support only a relatively small local population and thus experience demographic stochasticity. We investigated the evolution of density-dependent dispersal, emigration and immigration, in two scenarios: adult and natal dispersal. We show that density-dependent emigration can also evolve to a nonmonotone, "triple-threshold" strategy. This interesting phenomenon results from an interplay between the direct and indirect benefits of dispersal and the costs of dispersal. We also found that, compared to juveniles, dispersing adults may benefit more from density-dependent vs. density-independent dispersal strategies.

Evolution and stability of altruist strategies in microbial games

NASA Astrophysics Data System (ADS)

Adami, Christoph; Schossau, Jory; Hintze, Arend

2012-01-01

When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory (EGT). We study the predictions of EGT for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

Inertia in strategy switching transforms the strategy evolution.

PubMed

Zhang, Yanling; Fu, Feng; Wu, Te; Xie, Guangming; Wang, Long

2011-12-01

A recent experimental study [Traulsen et al., Proc. Natl. Acad. Sci. 107, 2962 (2010)] shows that human strategy updating involves both direct payoff comparison and the cost of switching strategy, which is equivalent to inertia. However, it remains largely unclear how such a predisposed inertia affects 2 × 2 games in a well-mixed population of finite size. To address this issue, the "inertia bonus" (strategy switching cost) is added to the learner payoff in the Fermi process. We find how inertia quantitatively shapes the stationary distribution and that stochastic stability under inertia exhibits three regimes, with each covering seven regions in the plane spanned by two inertia parameters. We also obtain the extended "1/3" rule with inertia and the speed criterion with inertia; these two findings hold for a population above two. We illustrate the above results in the framework of the Prisoner's Dilemma game. As inertia varies, two intriguing stationary distributions emerge: the probability of coexistence state is maximized, or those of two full states are simultaneously peaked. Our results may provide useful insights into how the inertia of changing status quo acts on the strategy evolution and, in particular, the evolution of cooperation.

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

PubMed

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.

Evolution of speech-specific cognitive adaptations.

PubMed

de Boer, Bart

2015-01-01

This paper argues that an evolutionary perspective is natural when investigating cognitive adaptations related to language. This is because there appears to be correspondence between traits that linguists consider interesting and traits that have undergone selective pressure related to language. The paper briefly reviews theoretical results that shed light on what kind of adaptations we can expect to have evolved and then reviews concrete work related to the evolution of adaptations for combinatorial speech. It turns out that there is as yet no strong direct evidence for cognitive traits that have undergone selection related to speech, but there is indirect evidence that indicates selection. However, the traits that may have undergone selection are expected to be continuously variable ones, rather than the discrete ones that linguists have focused on traditionally.

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

PubMed

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.

Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.

PubMed

Hua, Qiang; Joyce, Andrew R; Fong, Stephen S; Palsson, Bernhard Ø

2006-12-05

Experimental evolution is now frequently applied to many biological systems to achieve desired objectives. To obtain optimized performance for metabolite production, a successful strategy has been recently developed that couples metabolic engineering techniques with laboratory evolution of microorganisms. Previously, we reported the growth characteristics of three lactate-producing, adaptively evolved Escherichia coli mutant strains designed by the OptKnock computational algorithm. Here, we describe the use of (13)C-labeled experiments and mass distribution measurements to study the evolutionary effects on the fluxome of these differently designed strains. Metabolic flux ratios and intracellular flux distributions as well as physiological data were used to elucidate metabolic responses over the course of adaptive evolution and metabolic differences among strains. The study of 3 unevolved and 12 evolved engineered strains as well as a wild-type strain suggests that evolution resulted in remarkable improvements in both substrate utilization rate and the proportion of glycolytic flux to total glucose utilization flux. Among three strain designs, the most significant increases in the fraction of glucose catabolized through glycolysis (>50%) and the glycolytic fluxes (>twofold) were observed in phosphotransacetylase and phosphofructokinase 1 (PFK1) double deletion (pta- pfkA) strains, which were likely attributed to the dramatic evolutionary increase in gene expression and catalytic activity of the minor PFK encoded by pfkB. These fluxomic studies also revealed the important role of acetate synthetic pathway in anaerobic lactate production. Moreover, flux analysis suggested that independent of genetic background, optimal relative flux distributions in cells could be achieved faster than physiological parameters such as nutrient utilization rate. (c) 2006 Wiley Periodicals, Inc.

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

PubMed

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.

Improved robustness of an ethanologenic yeast strain through adaptive evolution in acetic acid is associated with its enzymatic antioxidant ability.

PubMed

Gurdo, N; Novelli Poisson, G F; Juárez, Á B; Ríos de Molina, M C; Galvagno, M A

2018-05-16

To investigate multiple tolerance of Saccharomyces cerevisiae obtained through a laboratory strategy of adaptive evolution in acetic acid, its relation with enzymatic ROS detoxification and bioethanol 2G production. After adaptive evolution in acetic acid, a clone (Y8A) was selected for its tolerance to high acetic acid concentrations (13 g l -1 ) in batch cultures. Y8A was resistant to multiple stresses: osmotic, thermic, oxidative, saline, ethanol, organic acid, phenolic compounds and slow freeze-thawing cycles. Also, Y8A was able to maintain redox homeostasis under oxidative stress, whereas the isogenic parental strain (Y8) could not, indicating higher basal activity levels of antioxidative enzyme Catalase (CAT) and Gluthatione-S-Transferase (GST) in Y8A. Y8A reached higher bioethanol levels in a fermentation medium containing up to 8 g l -1 of acetic acid when compared to parental strain Y8. A multiple-stress-tolerant clone was obtained using adaptive evolution in acetic acid. Stress cross-tolerance could be explained by its enzymatic antioxidative capacity, namely CAT and GST. We demonstrate that adaptive evolution used in S. cerevisiae was a useful strategy to obtain a yeast clone tolerant to multiple stresses. At the same time, our findings support the idea that tolerance to oxidative stress is the common basis for stress co-tolerance, which is related to an increase in the specific enzymes CAT and GST but not in Superoxide dismutase (SOD), emphasizing the fact that detoxification of H 2 O 2 and not O 2 . is a key condition for multiple stress tolerance in S. cerevisiae. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat.

PubMed

Jeong, Haeyoung; Lee, Sang J; Kim, Pil

2016-09-20

Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) refers to the experimental situation in which evolution is observed using living organisms under controlled conditions and stressors; organisms are thereby artificially forced to make evolutionary changes. Microorganisms are subject to a variety of stressors in the environment and are capable of regulating certain stress-inducible proteins to increase their chances of survival. Naturally occurring spontaneous mutations bring about changes in a microorganism's genome that affect its chances of survival. Long-term exposure to chemostat culture provokes an accumulation of spontaneous mutations and renders the most adaptable strain dominant. Compared to the colony transfer and serial transfer methods, chemostat culture entails the highest number of cell divisions and, therefore, the highest number of diverse populations. Although chemostat culture for ALE requires more complicated culture devices, it is less labor intensive once the operation begins. Comparative genomic and transcriptome analyses of the adapted strain provide evolutionary clues as to how the stressors contribute to mutations that overcome the stress. The goal of the current paper is to bring about accelerated evolution of microorganisms under controlled laboratory conditions.

Covariance Matrix Adaptation Evolutionary Strategy for Drift Correction of Electronic Nose Data

NASA Astrophysics Data System (ADS)

Di Carlo, S.; Falasconi, M.; Sanchez, E.; Sberveglieri, G.; Scionti, A.; Squillero, G.; Tonda, A.

2011-09-01

Electronic Noses (ENs) might represent a simple, fast, high sample throughput and economic alternative to conventional analytical instruments [1]. However, gas sensors drift still limits the EN adoption in real industrial setups due to high recalibration effort and cost [2]. In fact, pattern recognition (PaRC) models built in the training phase become useless after a period of time, in some cases a few weeks. Although algorithms to mitigate the drift date back to the early 90 this is still a challenging issue for the chemical sensor community [3]. Among other approaches, adaptive drift correction methods adjust the PaRC model in parallel with data acquisition without need of periodic calibration. Self-Organizing Maps (SOMs) [4] and Adaptive Resonance Theory (ART) networks [5] have been already tested in the past with fair success. This paper presents and discusses an original methodology based on a Covariance Matrix Adaptation Evolution Strategy (CMA-ES) [6], suited for stochastic optimization of complex problems.

Evolutionary transitions in controls reconcile adaptation with continuity of evolution.

PubMed

Badyaev, Alexander V

2018-05-19

Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits. The key concept that captures such traversing is network controllability - the ability to move a network from one state into another while maintaining its functionality (reflecting evolvability) and to efficiently propagate information or products through the network within a phenotypic state (maintaining its robustness). Here I suggest that transitions in network controllability - specifically in the topology of controls - help to explain how robustness and evolvability are balanced during evolution. I will focus on evolutionary transitions in degeneracy of metabolic networks - a ubiquitous property of phenotypic robustness where distinct pathways achieve the same end product - to suggest that associated changes in network controls is a common rule underlying phenomena as distinct as phenotypic plasticity, organismal accommodation of novelties, genetic assimilation, and macroevolutionary diversification. Capitalizing on well understood principles by which network structure translates into function of control nodes, I show that accumulating redundancy in one type of network controls inevitably leads to the emergence of another type of controls, forming evolutionary cycles of network controllability that, ultimately, reconcile local adaptation with continuity of evolution

Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution

PubMed Central

Gong, Lizhi Ian; Bloom, Jesse D.

2014-01-01

Most experimental studies of epistasis in evolution have focused on adaptive changes—but adaptation accounts for only a portion of total evolutionary change. Are the patterns of epistasis during adaptation representative of evolution more broadly? We address this question by examining a pair of protein homologs, of which only one is subject to a well-defined pressure for adaptive change. Specifically, we compare the nucleoproteins from human and swine influenza. Human influenza is under continual selection to evade recognition by acquired immune memory, while swine influenza experiences less such selection due to the fact that pigs are less likely to be infected with influenza repeatedly in a lifetime. Mutations in some types of immune epitopes are therefore much more strongly adaptive to human than swine influenza—here we focus on epitopes targeted by human cytotoxic T lymphocytes. The nucleoproteins of human and swine influenza possess nearly identical numbers of such epitopes. However, mutations in these epitopes are fixed significantly more frequently in human than in swine influenza, presumably because these epitope mutations are adaptive only to human influenza. Experimentally, we find that epistatically constrained mutations are fixed only in the adaptively evolving human influenza lineage, where they occur at sites that are enriched in epitopes. Overall, our results demonstrate that epistatically interacting substitutions are enriched during adaptation, suggesting that the prevalence of epistasis is dependent on the underlying evolutionary forces at play. PMID:24811236

Comparative Evolution of an Archetypal Adaptive Radiation: Innovation and Opportunity in Anolis Lizards.

PubMed

Poe, Steven; de Oca, Adrián Nieto-Montes; Torres-Carvajal, Omar; de Queiroz, Kevin; Velasco, Julián A; Truett, Brad; Gray, Levi N; Ryan, Mason J; Köhler, Gunther; Ayala-Varela, Fernando; Latella, Ian

2018-06-01

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is a known source of bias in many comparative analyses, yet classic adaptive radiations have not been studied comparatively with comprehensively sampled phylogenies. In this study, we use unprecedented comprehensive phylogenetic sampling of Anolis lizard species to examine comparative evolution in this well-studied adaptive radiation. We compare adaptive radiation models within Anolis and in the Anolis clade and a potential sister lineage, the Corytophanidae. We find evidence for island (i.e., opportunity) effects and no evidence for trait (i.e., key innovation) effects causing accelerated body size evolution within Anolis. However, island effects are scale dependent: when Anolis and Corytophanidae are analyzed together, no island effect is evident. We find no evidence for an island effect on speciation rate and tenuous evidence for greater speciation rate due to trait effects. These results suggest the need for precision in treatments of classic adaptive radiations such as Anolis and further refinement of the concept of adaptive radiation.

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

PubMed

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.

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

PubMed Central

Bullaughey, Kevin

2016-01-01

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

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

PubMed

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

2012-12-07

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

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

PubMed Central

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

2012-01-01

Pollination by sexual deception is arguably one of the most unusual liaisons linking plants and insects, and perhaps the most illustrative example of extreme floral specialization in angiosperms. While considerable progress has been made in understanding the floral traits involved in sexual deception, less is known about how this remarkable mimicry system might have arisen, the role of pre-adaptations in promoting its evolution and its extent as a pollination mechanism outside the few groups of plants (primarily orchids) where it has been described to date. In the Euro-Mediterranean region, pollination by sexual deception is traditionally considered to be the hallmark of the orchid genus Ophrys. Here, we introduce two new cases outside of Ophrys, in plant groups dominated by generalized, shelter-mimicking species. On the basis of phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants, and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry. These findings, along with comparative analyses of floral traits (colours and scents), shed light on particular phenotypic changes that might have fuelled the parallel evolution of these extraordinary pollination strategies. Collectively, our results provide the first substantive insights into how pollination sexual deception might have evolved in the Euro-Mediterranean region, and demonstrate that even the most extreme cases of pollinator specialization can reverse to more generalized interactions, breaking ‘Cope's rule of specialization’. PMID:23055065

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

PubMed

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.

Molecular evolution and thermal adaptation

NASA Astrophysics Data System (ADS)

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

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

PubMed

Dey, Snigdhadip; Proulx, Stephen R; Teotónio, Henrique

2016-02-01

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 adaptation than

Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects

PubMed Central

Dey, Snigdhadip; Proulx, Stephen R.; Teotónio, Henrique

2016-01-01

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 adaptation than

Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum.

PubMed

Mahr, Regina; Gätgens, Cornelia; Gätgens, Jochem; Polen, Tino; Kalinowski, Jörn; Frunzke, Julia

2015-11-01

Adaptive laboratory evolution has proven a valuable strategy for metabolic engineering. Here, we established an experimental evolution approach for improving microbial metabolite production by imposing an artificial selective pressure on the fluorescent output of a biosensor using fluorescence-activated cell sorting. Cells showing the highest fluorescent output were iteratively isolated and (re-)cultivated. The L-valine producer Corynebacterium glutamicum ΔaceE was equipped with an L-valine-responsive sensor based on the transcriptional regulator Lrp of C. glutamicum. Evolved strains featured a significantly higher growth rate, increased L-valine titers (~25%) and a 3-4-fold reduction of by-product formation. Genome sequencing resulted in the identification of a loss-of-function mutation (UreD-E188*) in the gene ureD (urease accessory protein), which was shown to increase L-valine production by up to 100%. Furthermore, decreased L-alanine formation was attributed to a mutation in the global regulator GlxR. These results emphasize biosensor-driven evolution as a straightforward approach to improve growth and productivity of microbial production strains. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Origins of altruism diversity II: Runaway co-evolution of altruistic strategies via “reciprocal niche construction”

PubMed Central

Van Dyken, J. David; Wade, Michael J.

2012-01-01

Understanding the evolution of altruism requires knowledge of both its constraints and its drivers. Here we show that, paradoxically, ecological constraints on altruism may ultimately be its strongest driver. We construct a two-trait, co-evolutionary adaptive dynamics model of social evolution in a genetically structured population with local resource competition. The intensity of local resource competition, which influences the direction and strength of social selection and which is typically treated as a static parameter, is here allowed to be an evolvable trait. Evolution of survival/fecundity altruism, which requires weak local competition, increases local competition as it evolves, creating negative environmental feedback that ultimately inhibits its further evolutionary advance. Alternatively, evolution of resource-based altruism, which requires strong local competition, weakens local competition as it evolves, also ultimately causing its own evolution to stall. When evolving independently, these altruistic strategies are intrinsically self-limiting. However, the co-existence of these two altruism types transforms the negative eco-evolutionary feedback generated by each strategy on itself into positive feedback on the other, allowing the presence of one trait to drive the evolution of the other. We call this feedback conversion “reciprocal niche construction”. In the absence of constraints, this process leads to runaway co-evolution of altruism types. We discuss applications to the origins and evolution of eusociality, division of labor, the inordinate ecological success of eusocial species, and the interaction between technology and demography in human evolution. Our theory suggests that the evolution of extreme sociality may often be an autocatalytic process. PMID:22834748

Relevance of phenotypic noise to adaptation and evolution.

PubMed

Kaneko, K; Furusawa, C

2008-09-01

Biological processes are inherently noisy, as highlighted in recent measurements of stochasticity in gene expression. Here, the authors show that such phenotypic noise is essential to the adaptation of organisms to a variety of environments and also to the evolution of robustness against mutations. First, the authors show that for any growing cell showing stochastic gene expression, the adaptive cellular state is inevitably selected by noise, without the use of a specific signal transduction network. In general, changes in any protein concentration in a cell are products of its synthesis minus dilution and degradation, both of which are proportional to the rate of cell growth. In an adaptive state, both the synthesis and dilution terms of proteins are large, and so the adaptive state is less affected by stochasticity in gene expression, whereas for a non-adaptive state, both terms are smaller, and so cells are easily knocked out of their original state by noise. This leads to a novel, generic mechanism for the selection of adaptive states. The authors have confirmed this selection by model simulations. Secondly, the authors consider the evolution of gene networks to acquire robustness of the phenotype against noise and mutation. Through simulations using a simple stochastic gene expression network that undergoes mutation and selection, the authors show that a threshold level of noise in gene expression is required for the network to acquire both types of robustness. The results reveal how the noise that cells encounter during growth and development shapes any network's robustness, not only to noise but also to mutations. The authors also establish a relationship between developmental and mutational robustness.

Affect-Aware Adaptive Tutoring Based on Human-Automation Etiquette Strategies.

PubMed

Yang, Euijung; Dorneich, Michael C

2018-06-01

We investigated adapting the interaction style of intelligent tutoring system (ITS) feedback based on human-automation etiquette strategies. Most ITSs adapt the content difficulty level, adapt the feedback timing, or provide extra content when they detect cognitive or affective decrements. Our previous work demonstrated that changing the interaction style via different feedback etiquette strategies has differential effects on students' motivation, confidence, satisfaction, and performance. The best etiquette strategy was also determined by user frustration. Based on these findings, a rule set was developed that systemically selected the proper etiquette strategy to address one of four learning factors (motivation, confidence, satisfaction, and performance) under two different levels of user frustration. We explored whether etiquette strategy selection based on this rule set (systematic) or random changes in etiquette strategy for a given level of frustration affected the four learning factors. Participants solved mathematics problems under different frustration conditions with feedback that adapted dynamic changes in etiquette strategies either systematically or randomly. The results demonstrated that feedback with etiquette strategies chosen systematically via the rule set could selectively target and improve motivation, confidence, satisfaction, and performance more than changing etiquette strategies randomly. The systematic adaptation was effective no matter the level of frustration for the participant. If computer tutors can vary the interaction style to effectively mitigate negative emotions, then ITS designers would have one more mechanism in which to design affect-aware adaptations that provide the proper responses in situations where human emotions affect the ability to learn.

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

PubMed

Luján, Adela M; Maciá, María D; Yang, Liang; Molin, Søren; Oliver, Antonio; Smania, Andrea M

2011-01-01

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.

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

PubMed Central

Yang, Liang; Molin, Søren; Oliver, Antonio; Smania, Andrea M.

2011-01-01

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. PMID:22114708

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

PubMed

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

2013-09-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence (P < 0.05). Genome-wide heterogeneity in substitution rates was also observed, reflecting divergent genome evolution processes within these grasses. Our results provide evidence for a link between adaptation to cold habitats and adaptive evolution of LTI stress responses in early Pooideae evolution and shed light on a poorly understood chapter in the evolutionary history of some of the world's most important temperate crops. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution.

PubMed

Slater, Graham J

2015-04-21

A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein-Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.

Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution

NASA Astrophysics Data System (ADS)

Slater, Graham J.

2015-04-01

A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein-Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

PubMed Central

Palmer, William H.; Hadfield, Jarrod D.; Obbard, Darren J.

2018-01-01

Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races. PMID:29437826

An evolution strategy for lunar nuclear surface power

NASA Technical Reports Server (NTRS)

Mason, Lee S.

1992-01-01

The production and transmission of electric power for a permanently inhabited lunar base poses a significant challenge which can best be met through an evolution strategy. Nuclear systems offer the best opportunity for evolution in terms of both life and performance. Applicable nuclear power technology options include isotope systems (either radioisotope thermoelectric generators or dynamic isotope power systems) and reactor systems with either static (thermoelectric or thermionic) or dynamic (Brayton, Stirling, Rankine) conversion. A power system integration approach that takes evolution into account would benefit by reduced development and operations cost, progressive flight experience, and simplified logistics, and would permit unrestrained base expansion. For the purposes of defining a nuclear power system evolution strategy, the lunar base development shall consist of four phases: precursor, emplacement, consolidation, and operations.

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

PubMed

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

2017-02-01

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

Efficient receiver tuning using differential evolution strategies

NASA Astrophysics Data System (ADS)

Wheeler, Caleb H.; Toland, Trevor G.

2016-08-01

Differential evolution (DE) is a powerful and computationally inexpensive optimization strategy that can be used to search an entire parameter space or to converge quickly on a solution. The Kilopixel Array Pathfinder Project (KAPPa) is a heterodyne receiver system delivering 5 GHz of instantaneous bandwidth in the tuning range of 645-695 GHz. The fully automated KAPPa receiver test system finds optimal receiver tuning using performance feedback and DE. We present an adaptation of DE for use in rapid receiver characterization. The KAPPa DE algorithm is written in Python 2.7 and is fully integrated with the KAPPa instrument control, data processing, and visualization code. KAPPa develops the technologies needed to realize heterodyne focal plane arrays containing 1000 pixels. Finding optimal receiver tuning by investigating large parameter spaces is one of many challenges facing the characterization phase of KAPPa. This is a difficult task via by-hand techniques. Characterizing or tuning in an automated fashion without need for human intervention is desirable for future large scale arrays. While many optimization strategies exist, DE is ideal for time and performance constraints because it can be set to converge to a solution rapidly with minimal computational overhead. We discuss how DE is utilized in the KAPPa system and discuss its performance and look toward the future of 1000 pixel array receivers and consider how the KAPPa DE system might be applied.

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

NASA Astrophysics Data System (ADS)

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.

WAKES: Wavelet Adaptive Kinetic Evolution Solvers

NASA Astrophysics Data System (ADS)

Mardirian, Marine; Afeyan, Bedros; Larson, David

2016-10-01

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

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

NASA Astrophysics Data System (ADS)

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.

A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax.

PubMed

Ogbunugafor, C Brandon; Hartl, Daniel

2016-01-25

adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.

Reversible adapting layer produces robust single-crystal electrocatalyst for oxygen evolution.

PubMed

Tung, Ching-Wei; Hsu, Ying-Ya; Shen, Yen-Ping; Zheng, Yixin; Chan, Ting-Shan; Sheu, Hwo-Shuenn; Cheng, Yuan-Chung; Chen, Hao Ming

2015-08-28

Electrochemically converting water into oxygen/hydrogen gas is ideal for high-density renewable energy storage in which robust electrocatalysts for efficient oxygen evolution play crucial roles. To date, however, electrocatalysts with long-term stability have remained elusive. Here we report that single-crystal Co3O4 nanocube underlay with a thin CoO layer results in a high-performance and high-stability electrocatalyst in oxygen evolution reaction. An in situ X-ray diffraction method is developed to observe a strong correlation between the initialization of the oxygen evolution and the formation of active metal oxyhydroxide phase. The lattice of skin layer adapts to the structure of the active phase, which enables a reversible facile structural change that facilitates the chemical reactions without breaking the scaffold of the electrocatalysts. The single-crystal nanocube electrode exhibits stable, continuous oxygen evolution for >1,000 h. This robust stability is attributed to the complementary nature of defect-free single-crystal electrocatalyst and the reversible adapting layer.

Stepping strategies for regulating gait adaptability and stability.

PubMed

Hak, Laura; Houdijk, Han; Steenbrink, Frans; Mert, Agali; van der Wurff, Peter; Beek, Peter J; van Dieën, Jaap H

2013-03-15

Besides a stable gait pattern, gait in daily life requires the capability to adapt this pattern in response to environmental conditions. The purpose of this study was to elucidate the anticipatory strategies used by able-bodied people to attain an adaptive gait pattern, and how these strategies interact with strategies used to maintain gait stability. Ten healthy subjects walked in a Computer Assisted Rehabilitation ENvironment (CAREN). To provoke an adaptive gait pattern, subjects had to hit virtual targets, with markers guided by their knees, while walking on a self-paced treadmill. The effects of walking with and without this task on walking speed, step length, step frequency, step width and the margins of stability (MoS) were assessed. Furthermore, these trials were performed with and without additional continuous ML platform translations. When an adaptive gait pattern was required, subjects decreased step length (p<0.01), tended to increase step width (p=0.074), and decreased walking speed while maintaining similar step frequency compared to unconstrained walking. These adaptations resulted in the preservation of equal MoS between trials, despite the disturbing influence of the gait adaptability task. When the gait adaptability task was combined with the balance perturbation subjects further decreased step length, as evidenced by a significant interaction between both manipulations (p=0.012). In conclusion, able-bodied people reduce step length and increase step width during walking conditions requiring a high level of both stability and adaptability. Although an increase in step frequency has previously been found to enhance stability, a faster movement, which would coincide with a higher step frequency, hampers accuracy and may consequently limit gait adaptability. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

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

PubMed

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

2013-08-20

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.

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

PubMed

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.

Adaptive Multiscale Modeling of Geochemical Impacts on Fracture Evolution

NASA Astrophysics Data System (ADS)

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

Sensor Web Dynamic Measurement Techniques and Adaptive Observing Strategies

NASA Technical Reports Server (NTRS)

Talabac, Stephen J.

2004-01-01

Sensor Web observing systems may have the potential to significantly improve our ability to monitor, understand, and predict the evolution of rapidly evolving, transient, or variable environmental features and events. This improvement will come about by integrating novel data collection techniques, new or improved instruments, emerging communications technologies and protocols, sensor mark-up languages, and interoperable planning and scheduling systems. In contrast to today's observing systems, "event-driven" sensor webs will synthesize real- or near-real time measurements and information from other platforms and then react by reconfiguring the platforms and instruments to invoke new measurement modes and adaptive observation strategies. Similarly, "model-driven" sensor webs will utilize environmental prediction models to initiate targeted sensor measurements or to use a new observing strategy. The sensor web concept contrasts with today's data collection techniques and observing system operations concepts where independent measurements are made by remote sensing and in situ platforms that do not share, and therefore cannot act upon, potentially useful complementary sensor measurement data and platform state information. This presentation describes NASA's view of event-driven and model-driven Sensor Webs and highlights several research and development activities at the Goddard Space Flight Center.

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

PubMed

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.

Adapting Digital Libraries to Continual Evolution

NASA Technical Reports Server (NTRS)

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.

Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals

PubMed Central

2014-01-01

Background Genes associated with the neurodevelopmental disorder microcephaly display a strong signature of adaptive evolution in primates. Comparative data suggest a link between selection on some of these loci and the evolution of primate brain size. Whether or not either positive selection or this phenotypic association are unique to primates is unclear, but recent studies in cetaceans suggest at least two microcephaly genes evolved adaptively in other large brained mammalian clades. Results Here we analyse the evolution of seven microcephaly loci, including three recently identified loci, across 33 eutherian mammals. We find extensive evidence for positive selection having acted on the majority of these loci not just in primates but also across non-primate mammals. Furthermore, the patterns of selection in major mammalian clades are not significantly different. Using phylogenetically corrected comparative analyses, we find that the evolution of two microcephaly loci, ASPM and CDK5RAP2, are correlated with neonatal brain size in Glires and Euungulata, the two most densely sampled non-primate clades. Conclusions Together with previous results, this suggests that ASPM and CDK5RAP2 may have had a consistent role in the evolution of brain size in mammals. Nevertheless, several limitations of currently available data and gene-phenotype tests are discussed, including sparse sampling across large evolutionary distances, averaging gene-wide rates of evolution, potential phenotypic variation and evolutionary reversals. We discuss the implications of our results for studies of the genetic basis of brain evolution, and explicit tests of gene-phenotype hypotheses. PMID:24898820

Evolution of cooperative strategies from first principles.

PubMed

Burtsev, Mikhail; Turchin, Peter

2006-04-20

One of the greatest challenges in the modern biological and social sciences is to understand the evolution of cooperative behaviour. General outlines of the answer to this puzzle are currently emerging as a result of developments in the theories of kin selection, reciprocity, multilevel selection and cultural group selection. The main conceptual tool used in probing the logical coherence of proposed explanations has been game theory, including both analytical models and agent-based simulations. The game-theoretic approach yields clear-cut results but assumes, as a rule, a simple structure of payoffs and a small set of possible strategies. Here we propose a more stringent test of the theory by developing a computer model with a considerably extended spectrum of possible strategies. In our model, agents are endowed with a limited set of receptors, a set of elementary actions and a neural net in between. Behavioural strategies are not predetermined; instead, the process of evolution constructs and reconstructs them from elementary actions. Two new strategies of cooperative attack and defence emerge in simulations, as well as the well-known dove, hawk and bourgeois strategies. Our results indicate that cooperative strategies can evolve even under such minimalist assumptions, provided that agents are capable of perceiving heritable external markers of other agents.

Pollinator adaptation and the evolution of floral nectar sugar composition.

PubMed

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.

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

PubMed

Kuntner, Matjaž; Agnarsson, Ingi; Li, Daiqin

2015-02-01

emasculation, as well as lesser genital damage and sexual cannibalism, to be significantly associated with SSD. These behavioural and morphological traits thus likely co-evolve in spiders. Emasculation can be seen as an extreme form of genital mutilation, or even a terminal investment strategy linked to the evolution of monogyny. However, as different emasculation cases in araneoid spiders are neither homologous nor biologically identical, and may or may not serve as paternity protection, the direct link to monogyny is not clear cut. Understanding better the phylogenetic patterns of emasculation and its constituent morphologies and behaviours, a clearer picture of the intricate interplay of natural and sexual selection may arise. With the here improved evolutionary resolution of spider eunuch behaviour, we can more specifically tie the evidence from adaptive hypotheses to independent cases, and propose promising avenues for further research of spider eunuchs, and of the evolution of monogyny. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Nutritional strategies to influence adaptations to training.

PubMed

Spriet, Lawrence L; Gibala, Martin J

2004-01-01

This article highlights new nutritional concerns or practices that may influence the adaptation to training. The discussion is based on the assumption that the adaptation to repeated bouts of training occurs during recovery periods and that if one can train harder, the adaptation will be greater. The goal is to maximize with nutrition the recovery/adaptation that occurs in all rest periods, such that recovery before the next training session is complete. Four issues have been identified where recent scientific information will force sports nutritionists to embrace new issues and reassess old issues and, ultimately, alter the nutritional recommendations they give to athletes. These are: (1) caffeine ingestion; (2) creatine ingestion; (3) the use of intramuscular triacylglycerol (IMTG) as a fuel during exercise and the nutritional effects on IMTG repletion following exercise; and (4) the role nutrition may play in regulating the expression of genes during and after exercise training sessions. Recent findings suggest that low doses of caffeine exert significant ergogenic effects by directly affecting the central nervous system during exercise. Caffeine can cross the blood-brain barrier and antagonize the effects of adenosine, resulting in higher concentrations of stimulatory neurotransmitters. These new data strengthen the case for using low doses of caffeine during training. On the other hand, the data on the role that supplemental creatine ingestion plays in augmenting the increase in skeletal muscle mass and strength during resistance training remain equivocal. Some studies are able to demonstrate increases in muscle fibre size with creatine ingestion and some are not. The final two nutritional topics are new and have not progressed to the point that we can specifically identify strategies to enhance the adaptation to training. However, it is likely that nutritional strategies will be needed to replenish the IMTG that is used during endurance exercise. It is not

TU-H-CAMPUS-JeP3-01: Towards Robust Adaptive Radiation Therapy Strategies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boeck, M; KTH Royal Institute of Technology, Stockholm; Eriksson, K

Purpose: To set up a framework combining robust treatment planning with adaptive reoptimization in order to maintain high treatment quality, to respond to interfractional variations and to identify those patients who will benefit the most from an adaptive fractionation schedule. Methods: We propose adaptive strategies based on stochastic minimax optimization for a series of simulated treatments on a one-dimensional patient phantom. The plan should be able to handle anticipated systematic and random errors and is applied during the first fractions. Information on the individual geometric variations is gathered at each fraction. At scheduled fractions, the impact of the measured errorsmore » on the delivered dose distribution is evaluated. For a patient that receives a dose that does not satisfy specified plan quality criteria, the plan is reoptimized based on these individual measurements using one of three different adaptive strategies. The reoptimized plan is then applied during future fractions until a new scheduled adaptation becomes necessary. In the first adaptive strategy the measured systematic and random error scenarios and their assigned probabilities are updated to guide the robust reoptimization. The focus of the second strategy lies on variation of the fraction of the worst scenarios taken into account during robust reoptimization. In the third strategy the uncertainty margins around the target are recalculated with the measured errors. Results: By studying the effect of the three adaptive strategies combined with various adaptation schedules on the same patient population, the group which benefits from adaptation is identified together with the most suitable strategy and schedule. Preliminary computational results indicate when and how best to adapt for the three different strategies. Conclusion: A workflow is presented that provides robust adaptation of the treatment plan throughout the course of treatment and useful measures to identify patients in

Towards the identification of the loci of adaptive evolution

PubMed Central

Pardo-Diaz, Carolina; Salazar, Camilo; Jiggins, Chris D

2015-01-01

1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature. PMID:25937885

Multigrid solution strategies for adaptive meshing problems

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.

1995-01-01

This paper discusses the issues which arise when combining multigrid strategies with adaptive meshing techniques for solving steady-state problems on unstructured meshes. A basic strategy is described, and demonstrated by solving several inviscid and viscous flow cases. Potential inefficiencies in this basic strategy are exposed, and various alternate approaches are discussed, some of which are demonstrated with an example. Although each particular approach exhibits certain advantages, all methods have particular drawbacks, and the formulation of a completely optimal strategy is considered to be an open problem.

Evolution of Cooperation in Adaptive Social Networks

NASA Astrophysics Data System (ADS)

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.

Physics and evolution of thermophilic adaptation.

PubMed

Berezovsky, Igor N; Shakhnovich, Eugene I

2005-09-06

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.

Camelid genomes reveal evolution and adaptation to desert environments.

PubMed

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.

Local adaptation of plant viruses: lessons from experimental evolution.

PubMed

Elena, Santiago F

2017-04-01

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

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

PubMed

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

2012-03-24

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

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

PubMed Central

2012-01-01

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

[Coping strategies in adaptation of higher education students].

PubMed

das Neves Mira Freitas, Helena Cristina

2007-01-01

The adjustment to higher education can be understood as a multidimensional process, which requires by the student a development of adaptive skills to a new and dynamic context in itself. To meet these challenges students have to develop effective coping strategies, enabling them to be adapted to the context. The school has a key role in the help it can give to these young people, in order to adapt effectively.

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

PubMed

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

2011-12-01

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

Mechanisms of adaptive evolution. Darwinism and Lamarckism restated.

PubMed

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.

Dosimetric advantages of a clinical daily adaptive plan selection strategy compared with a non-adaptive strategy in cervical cancer radiation therapy.

PubMed

van de Schoot, Agustinus J A J; de Boer, Peter; Visser, Jorrit; Stalpers, Lukas J A; Rasch, Coen R N; Bel, Arjan

2017-05-01

Radiation therapy (RT) using a daily plan selection adaptive strategy can be applied to account for interfraction organ motion while limiting organ at risk dose. The aim of this study was to quantify the dosimetric consequences of daily plan selection compared with non-adaptive RT in cervical cancer. Ten consecutive patients who received pelvic irradiation, planning CTs (full and empty bladder), weekly post-fraction CTs and pre-fraction CBCTs were included. Non-adaptive plans were generated based on the PTV defined using the full bladder planning CT. For the adaptive strategy, multiple PTVs were created based on both planning CTs by ITVs of the primary CTVs (i.e., GTV, cervix, corpus-uterus and upper part of the vagina) and corresponding library plans were generated. Daily CBCTs were rigidly aligned to the full bladder planning CT for plan selection. For daily plan recalculation, selected CTs based on initial similarity were deformably registered to CBCTs. Differences in daily target coverage (D 98%  > 95%) and in V 0.5Gy , V 1.5Gy , V 2Gy , D 50% and D 2% for rectum, bladder and bowel were assessed. Non-adaptive RT showed inadequate primary CTV coverage in 17% of the daily fractions. Plan selection compensated for anatomical changes and improved primary CTV coverage significantly (p < 0.01) to 98%. Compared with non-adaptive RT, plan selection decreased the fraction dose to rectum and bowel indicated by significant (p < 0.01) improvements for daily V 0.5Gy , V 1.5Gy , V 2Gy , D 50% and D 2% . However, daily plan selection significantly increased the bladder V 1.5Gy , V 2Gy , D 50% and D 2% . In cervical cancer RT, a non-adaptive strategy led to inadequate target coverage for individual patients. Daily plan selection corrected for day-to-day anatomical variations and resulted in adequate target coverage in all fractions. The dose to bowel and rectum was decreased significantly when applying adaptive RT.

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

NASA Astrophysics Data System (ADS)

Nourmohammad, Armita

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

The locus of evolution: evo devo and the genetics of adaptation.

PubMed

Hoekstra, Hopi E; Coyne, Jerry A

2007-05-01

An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of

Competition and time-dependent behavior in spatial iterated prisoner’s dilemma incorporating adaptive zero-determinant strategies

NASA Astrophysics Data System (ADS)

Li, Yong; Xu, Chen; Liu, Jie; Hui, Pak Ming

2016-10-01

We propose and study the competitiveness of a class of adaptive zero-determinant strategies (ZDSs) in a population with spatial structure against four classic strategies in iterated prisoner’s dilemma. Besides strategy updating via a probabilistic mechanism by imitating the strategy of a better performing opponent, players using the ZDSs can also adapt their strategies to take advantage of their local competing environment with another probability. The adapted ZDSs could be extortionate-like to avoid being continually cheated by defectors or to take advantage of unconditional cooperators. The adapted ZDSs could also be a compliance strategy so as to cooperate with the conditionally cooperative players. This flexibility makes adaptive ZDSs more competitive than nonadaptive ZDSs. Results show that adaptive ZDSs can either dominate over other strategies or at least coexist with them when the ZDSs are allowed to adapt more readily than to imitate other strategies. The effectiveness of the adaptive ZDSs relies on how fast they can adapt to the competing environment before they are replaced by other strategies. The adaptive ZDSs generally work well as they could adapt gradually and make use of other strategies for suppressing their enemies. When adaptation happens more readily than imitation for the ZDSs, they outperform other strategies over a wide range of cost-to-benefit ratios.

Growing assisted migration: Synthesis of a climate change adaptation strategy

Treesearch

Mary I. Williams; R. Kasten Dumroese

2013-01-01

Assisted migration may be necessary as a climate change adaptation strategy for native plant species that are less adaptive or mobile. Moving plants has been practiced a long time in human history, but movement of species in response to climate change is a new context. First proposed in 1985, assisted migration has gained attention since 2007 as a strategy to prevent...

Adaptation to larval crowding in Drosophila ananassae leads to the evolution of population stability.

PubMed

Dey, Snigdhadip; Bose, Joy; Joshi, Amitabh

2012-05-01

Density-dependent selection is expected to lead to population stability, especially if r and K tradeoff. Yet, there is no empirical evidence of adaptation to crowding leading to the evolution of stability. We show that populations of Drosophila ananassae selected for adaptation to larval crowding have higher K and lower r, and evolve greater stability than controls. We also show that increased population growth rates at high density can enhance stability, even in the absence of a decrease in r, by ensuring that the crowding adapted populations do not fall to very low sizes. We discuss our results in the context of traits known to have diverged between the selected and control populations, and compare our results with previous work on the evolution of stability in D. melanogaster. Overall, our results suggest that density-dependent selection may be an important factor promoting the evolution of relatively stable dynamics in natural populations.

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

PubMed

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

2016-01-01

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

Adaptive Control Strategies for Flexible Robotic Arm

NASA Technical Reports Server (NTRS)

Bialasiewicz, Jan T.

1996-01-01

The control problem of a flexible robotic arm has been investigated. The control strategies that have been developed have a wide application in approaching the general control problem of flexible space structures. The following control strategies have been developed and evaluated: neural self-tuning control algorithm, neural-network-based fuzzy logic control algorithm, and adaptive pole assignment algorithm. All of the above algorithms have been tested through computer simulation. In addition, the hardware implementation of a computer control system that controls the tip position of a flexible arm clamped on a rigid hub mounted directly on the vertical shaft of a dc motor, has been developed. An adaptive pole assignment algorithm has been applied to suppress vibrations of the described physical model of flexible robotic arm and has been successfully tested using this testbed.

Linking Federal, State, and Local Adaptation Strategies in New York (Invited)

NASA Astrophysics Data System (ADS)

Rosenzweig, C.

2010-12-01

New York City and New York State are leaders in adaptation in the U.S. In 2008 Mayor Bloomberg convened the NYC Climate Change Adaptation Task Force and the New York City Panel on Climate Change (NPCC). Also in 2008, the New York State Energy Research and Development Authority (NYSERDA) initiated the Integrated Assessment for Effective Climate Change Adaptation Strategies (ClimAID), to provide New York State decision-makers with cutting-edge information on its vulnerability to climate change and to facilitate the development of adaptation strategies informed by both local experience and scientific knowledge. The two efforts are working together to develop effective adaptation strategies across multiple jurisdictions. The New York Task Force consists of approximate 40 city, state, and federal agencies, regional public authorities, and private companies that operate, maintain, or regulate critical infrastructure in the region. The NPCC consisted of climate change and impacts scientists, and legal, insurance, and risk-management experts and served as the technical advisory body for the Mayor and the Task Force on issues related to climate change, impacts, and adaptation. In its 2010 report, the NPCC recommended adoption of a risk-based approach to climate change; creation of a monitoring program to track and analyze key climate change factors, impacts, and adaptation indicators; review of relevant standards and codes; inclusion of multiple layers of government and a wide range of public and private stakeholder experts to build buy-in; and formation of crucial partnerships for development of coordinated adaptation strategies. The task now is for these partnerships to create pilot programs that move adaptation from the planning phase to implementation; urban areas can provide critical ‘test-beds’ for such efforts.

Experimental Evolution as a High-Throughput Screen for Genetic Adaptations.

PubMed

Cooper, Vaughn S

2018-06-27

Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates. Importantly, any mutant rising rapidly to high frequency in large populations must have acquired adaptive traits in the selective environment. Sequencing the genomes of these mutants can identify genes or pathways that contribute to an adaptation. I review the logic and simple mathematics why this evolve-and-resequence approach is a powerful way to find the mutations or mutation combinations that best increase fitness in any new environment. Copyright © 2018 Cooper.

Assessment of the effectiveness of flood adaptation strategies for HCMC

NASA Astrophysics Data System (ADS)

Lasage, R.; Veldkamp, T. I. E.; de Moel, H.; Van, T. C.; Phi, H. L.; Vellinga, P.; Aerts, J. C. J. H.

2014-06-01

Coastal cities are vulnerable to flooding, and flood risk to coastal cities will increase due to sea-level rise. Moreover, Asian cities in particular are subject to considerable population growth and associated urban developments, increasing this risk even more. Empirical data on vulnerability and the cost and benefits of flood risk reduction measures are therefore paramount for sustainable development of these cities. This paper presents an approach to explore the impacts of sea-level rise and socio-economic developments on flood risk for the flood-prone District 4 in Ho Chi Minh City, Vietnam, and to develop and evaluate the effects of different adaptation strategies (new levees, dry- and wet proofing of buildings and elevating roads and buildings). A flood damage model was developed to simulate current and future flood risk using the results from a household survey to establish stage-damage curves for residential buildings. The model has been used to assess the effects of several participatory developed adaptation strategies to reduce flood risk, expressed in expected annual damage (EAD). Adaptation strategies were evaluated assuming combinations of both sea-level scenarios and land-use scenarios. Together with information on costs of these strategies, we calculated the benefit-cost ratio and net present value for the adaptation strategies until 2100, taking into account depreciation rates of 2.5% and 5%. The results of this modelling study indicate that the current flood risk in District 4 is USD 0.31 million per year, increasing up to USD 0.78 million per year in 2100. The net present value and benefit-cost ratios using a discount rate of 5 % range from USD -107 to -1.5 million, and from 0.086 to 0.796 for the different strategies. Using a discount rate of 2.5% leads to an increase in both net present value and benefit-cost ratio. The adaptation strategies wet-proofing and dry-proofing generate the best results using these economic indicators. The information

Strategies to intervene on causal systems are adaptively selected.

PubMed

Coenen, Anna; Rehder, Bob; Gureckis, Todd M

2015-06-01

How do people choose interventions to learn about causal systems? Here, we considered two possibilities. First, we test an information sampling model, information gain, which values interventions that can discriminate between a learner's hypotheses (i.e. possible causal structures). We compare this discriminatory model to a positive testing strategy that instead aims to confirm individual hypotheses. Experiment 1 shows that individual behavior is described best by a mixture of these two alternatives. In Experiment 2 we find that people are able to adaptively alter their behavior and adopt the discriminatory model more often after experiencing that the confirmatory strategy leads to a subjective performance decrement. In Experiment 3, time pressure leads to the opposite effect of inducing a change towards the simpler positive testing strategy. These findings suggest that there is no single strategy that describes how intervention decisions are made. Instead, people select strategies in an adaptive fashion that trades off their expected performance and cognitive effort. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed

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.

Reduction of Ethanol Yield and Improvement of Glycerol Formation by Adaptive Evolution of the Wine Yeast Saccharomyces cerevisiae under Hyperosmotic Conditions

PubMed Central

Tilloy, Valentin; Ortiz-Julien, Anne

2014-01-01

There is a strong demand from the wine industry for methodologies to reduce the alcohol content of wine without compromising wine's sensory characteristics. We assessed the potential of adaptive laboratory evolution strategies under hyperosmotic stress for generation of Saccharomyces cerevisiae wine yeast strains with enhanced glycerol and reduced ethanol yields. Experimental evolution on KCl resulted, after 200 generations, in strains that had higher glycerol and lower ethanol production than the ancestral strain. This major metabolic shift was accompanied by reduced fermentative capacities, suggesting a trade-off between high glycerol production and fermentation rate. Several evolved strains retaining good fermentation performance were selected. These strains produced more succinate and 2,3-butanediol than the ancestral strain and did not accumulate undesirable organoleptic compounds, such as acetate, acetaldehyde, or acetoin. They survived better under osmotic stress and glucose starvation conditions than the ancestral strain, suggesting that the forces that drove the redirection of carbon fluxes involved a combination of osmotic and salt stresses and carbon limitation. To further decrease the ethanol yield, a breeding strategy was used, generating intrastrain hybrids that produced more glycerol than the evolved strain. Pilot-scale fermentation on Syrah using evolved and hybrid strains produced wine with 0.6% (vol/vol) and 1.3% (vol/vol) less ethanol, more glycerol and 2,3-butanediol, and less acetate than the ancestral strain. This work demonstrates that the combination of adaptive evolution and breeding is a valuable alternative to rational design for remodeling the yeast metabolic network. PMID:24532067

Contemporary evolution of plant reproductive strategies under global change is revealed by stored seeds.

PubMed

Thomann, M; Imbert, E; Engstrand, R C; Cheptou, P-O

2015-04-01

Global change is expected to impose new selection pressures on natural populations. Phenotypic responses, such as earlier phenology in response to climate warming, have been repeatedly observed in the field. The recent pollinator decline is also expected to change selection on reproductive traits in flowering plants. However, it remains unclear whether short-term adaptation of plant reproductive strategies occurs in response to global change. In this study, we report the evolution of some important reproductive traits of the annual self-incompatible weed Centaurea cyanus. In a common garden experiment, we germinated stored seeds, sampled 18 years apart from the same location, in a region where warmer springs and indices of pollinator decline have been reported. Compared to the ancestral population (1992), our results showed that plants of the descendant population (2010) flowered earlier and also produced larger capitula with longer receptivity and a larger floral display. QST -FST comparisons indicated that natural selection has likely contributed to the evolution of some of the traits investigated. Lower FST within temporal samples than among spatial samples further suggests a limited role of gene flow from neighbouring populations. We therefore propose that trait shifts could partly be due to adaptation to global change. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Trichinella spiralis: the evolution of adaptation and parasitism

USDA-ARS?s Scientific Manuscript database

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

Optimized satellite image compression and reconstruction via evolution strategies

NASA Astrophysics Data System (ADS)

Babb, Brendan; Moore, Frank; Peterson, Michael

2009-05-01

This paper describes the automatic discovery, via an Evolution Strategy with Covariance Matrix Adaptation (CMA-ES), of vectors of real-valued coefficients representing matched forward and inverse transforms that outperform the 9/7 Cohen-Daubechies-Feauveau (CDF) discrete wavelet transform (DWT) for satellite image compression and reconstruction under conditions subject to quantization error. The best transform evolved during this study reduces the mean squared error (MSE) present in reconstructed satellite images by an average of 33.78% (1.79 dB), while maintaining the average information entropy (IE) of compressed images at 99.57% in comparison to the wavelet. In addition, this evolved transform achieves 49.88% (3.00 dB) average MSE reduction when tested on 80 images from the FBI fingerprint test set, and 42.35% (2.39 dB) average MSE reduction when tested on a set of 18 digital photographs, while achieving average IE of 104.36% and 100.08%, respectively. These results indicate that our evolved transform greatly improves the quality of reconstructed images without substantial loss of compression capability over a broad range of image classes.

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

PubMed

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.

An adaptable navigation strategy for Virtual Microscopy from mobile platforms.

PubMed

Corredor, Germán; Romero, Eduardo; Iregui, Marcela

2015-04-01

Real integration of Virtual Microscopy with the pathologist service workflow requires the design of adaptable strategies for any hospital service to interact with a set of Whole Slide Images. Nowadays, mobile devices have the actual potential of supporting an online pervasive network of specialists working together. However, such devices are still very limited. This article introduces a novel highly adaptable strategy for streaming and visualizing WSI from mobile devices. The presented approach effectively exploits and extends the granularity of the JPEG2000 standard and integrates it with different strategies to achieve a lossless, loosely-coupled, decoder and platform independent implementation, adaptable to any interaction model. The performance was evaluated by two expert pathologists interacting with a set of 20 virtual slides. The method efficiently uses the available device resources: the memory usage did not exceed a 7% of the device capacity while the decoding times were smaller than the 200 ms per Region of Interest, i.e., a window of 256×256 pixels. This model is easily adaptable to other medical imaging scenarios. Copyright © 2015 Elsevier Inc. All rights reserved.

Employee stress management: An examination of adaptive and maladaptive coping strategies on employee health.

PubMed

Holton, M Kim; Barry, Adam E; Chaney, J Don

2015-01-01

Employees commonly report feeling stressed at work. Examine how employees cope with work and personal stress, whether their coping strategies are adaptive (protective to health) or maladaptive (detrimental to health), and if the manner in which employees cope with stress influences perceived stress management. In this cross-sectional study, a random sample of 2,500 full-time university non-student employees (i.e. faculty, salaried professionals, and hourly non-professionals) were surveyed on health related behaviors including stress and coping. Approximately 1,277 completed the survey (51% ). Hierarchical logistic regression was used to assess the ability of adaptive and maladaptive coping strategies to predict self-reported stress management, while controlling for multiple demographic variables. Over half of employees surveyed reported effective stress management. Most frequently used adaptive coping strategies were communication with friend/family member and exercise, while most frequently used maladaptive coping strategies were drinking alcohol and eating more than usual. Both adaptive and maladaptive coping strategies made significant (p < 0.05) contributions to predicting employee's perceived stress management. Only adaptive coping strategies (B = 0.265) predicted whether someone would self-identify as effectively managing stress. Use of maladaptive coping strategies decreased likelihood of self-reporting effective stress management. Actual coping strategies employed may influence employees' perceived stress management. Adaptive coping strategies may be more influential than maladaptive coping strategies on perceived stress management. Results illustrate themes for effective workplace stress management programs. Stress management programs focused on increasing use of adaptive coping may have a greater impact on employee stress management than those focused on decreasing use of maladaptive coping. Coping is not only a reaction to stressful experiences but also

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

Co-evolution of payoff strategy and interaction strategy in prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Zhang, Kangjie; Cheng, Hongyan

2016-11-01

Co-evolutionary dynamical models, providing a realistic paradigm for investigating complex system, have been extensively studied. In this paper, the co-evolution of payoff strategy and interaction strategy is studied. Starting with an initial Gaussian distribution of payoff strategy r with the mean u and the variance q, we focus on the final distribution of the payoff strategy. We find that final distribution of the payoff strategy may display different structures depending on parameters. In the ranges u < - 1 and u > 3, the distribution displays a single-peak structure which is symmetric about r = u. The distribution manifests itself as a double-peak structure in the range - 1 < u < 3 although a fake three-peak structure shows up in range 1 < u < 2. The explanations on the formation of different types of payoff strategy distributions are presented.

[Diversity of parasitic protozoan mitochondria and adaptive evolution].

PubMed

Tian, Hai-Feng; Wen, Jian-Fan

2010-02-01

Eukaryotic mitochondrion generally possess a definite and canonical structure and function. However, in the unicellular parasitic protozoa, various atypical mitochondria with respect to the number, structure, and function, have been discovered consecutively, revealing the variability, plasticity and rich diversity of mitochondrion. Here, we review the mitochondrial diversity in diverse parasitic protozoa, and the underlying reason for such diversity--the adaptive evolution of mitochondrion to the micro-oxygen or anaero parasitic environment of these parasites is also analyzed and discussed.

Biodiversity, evolution and adaptation of cultivated crops.

PubMed

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.

Long-term dynamics of adaptive evolution in a globally important phytoplankton species to ocean acidification

PubMed Central

Schlüter, Lothar; Lohbeck, Kai T.; Gröger, Joachim P.; Riebesell, Ulf; Reusch, Thorsten B. H.

2016-01-01

Marine phytoplankton may adapt to ocean change, such as acidification or warming, because of their large population sizes and short generation times. Long-term adaptation to novel environments is a dynamic process, and phenotypic change can take place thousands of generations after exposure to novel conditions. We conducted a long-term evolution experiment (4 years = 2100 generations), starting with a single clone of the abundant and widespread coccolithophore Emiliania huxleyi exposed to three different CO2 levels simulating ocean acidification (OA). Growth rates as a proxy for Darwinian fitness increased only moderately under both levels of OA [+3.4% and +4.8%, respectively, at 1100 and 2200 μatm partial pressure of CO2 (Pco2)] relative to control treatments (ambient CO2, 400 μatm). Long-term adaptation to OA was complex, and initial phenotypic responses of ecologically important traits were later reverted. The biogeochemically important trait of calcification, in particular, that had initially been restored within the first year of evolution was later reduced to levels lower than the performance of nonadapted populations under OA. Calcification was not constitutively lost but returned to control treatment levels when high CO2–adapted isolates were transferred back to present-day control CO2 conditions. Selection under elevated CO2 exacerbated a general decrease of cell sizes under long-term laboratory evolution. Our results show that phytoplankton may evolve complex phenotypic plasticity that can affect biogeochemically important traits, such as calcification. Adaptive evolution may play out over longer time scales (>1 year) in an unforeseen way under future ocean conditions that cannot be predicted from initial adaptation responses. PMID:27419227

[Adaptation strategies faced with chronic pain].

PubMed

Bioy, Antoine

2017-05-01

Chronic pain constitutes a challenge for patients. It makes them uneasy with regard to their personality, their corporality and their life balance, and leaves long-lasting effects on their experience as a patient. The development of adaptation strategies and resources to deal with chronic pain is therefore essential. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Exposure to stressful environments - Strategy of adaptive responses

NASA Technical Reports Server (NTRS)

Farhi, Leon E.

1991-01-01

Stresses such as hypoxia, water lack, and heat exposure can produce strains in more than a single organ system, in turn stimulating the body to adapt in multiple ways. Nevertheless, a general strategy of the various adaptive responses emerges when the challenges are divided into three groups: (1) conditions that affect the supply of essential molecules, (2) stresses that prevent the body from regulating properly the output of waste products such as CO2 and heat, and (3) environments that disrupt body transport systems. Problems may arise when there is a conflict between two stresses requiring conflicting adaptive changes. An alternative to adaptation, creation of microenvironment, is often favored by the animal.

A Self Adaptive Differential Evolution Algorithm for Global Optimization

NASA Astrophysics Data System (ADS)

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.

Harnessing recombination to speed adaptive evolution in Escherichia coli.

PubMed

Winkler, James; Kao, Katy C

2012-09-01

Evolutionary engineering typically involves asexual propagation of a strain to improve a desired phenotype. However, asexual populations suffer from extensive clonal interference, a phenomenon where distinct lineages of beneficial clones compete and are often lost from the population given sufficient time. Improved adaptive mutants can likely be generated by genetic exchange between lineages, thereby reducing clonal interference. We present a system that allows continuous in situ recombination by using an Esherichia coli F-based conjugation system lacking surface exclusion. Evolution experiments revealed that Hfr-mediated recombination significantly speeds adaptation in certain circumstances. These results show that our system is stable, effective, and suitable for use in evolutionary engineering applications. Copyright © 2012 Elsevier Inc. All rights reserved.

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

PubMed

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).

Biometeorology - a science supporting adaptation strategies

NASA Astrophysics Data System (ADS)

Matzarakis, A.; Cegnar, T.

2010-09-01

Biometeorology as an interdisciplinary science deals with the interactions between atmospheric processes and living organisms (plants, animals and humans). If and in what way weather and climate affect the well-being of all the living creatures? This is the most important question biometeorology is answering. The International Society of Biometeorology (ISB) has built an international forum for the promotion of interdisciplinary collaboration between meteorologists, health professionals, biologists, climatologists, ecologists and other scientists. The Society acts as a community of scientists with similar interests, and fulfills an important role in providing information, expertise and advice for international organizations requiring this assistance. The ISB represents the most comprehensive organization, which brings together people with expertise in these areas. Another specific aim of the ISB is the stimulation of research. Therefore, groups of members are working on several topics organized in commissions for specific targets. The recent five commissions are working in the several fields including climate change issues. Some of examples will be presented, which have been initiated by the members of the ISB and how they can be included as a solid scientific basis to develop efficient adaptation strategies. One such example is a project combining natural and social sciences (in the fields of cooperation processes, tourism analysis and strategy, weather and climate change analysis, information and communication and knowledge transfer) in a transdisciplinary approach that includes players from tourism policy and business and which focuses on the North Sea Coast and the Black Forest. The project "Climate trends and sustainable development of tourism in coastal and mountain range regions was divided into four phases - diagnosis, assessment, strategy/design of solutions, and evaluation - where scientific subprojects and practical partners meet regularly to discuss the

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

PubMed

Xie, Jianbo; Yang, Xiaohui; Song, Yuepeng; Du, Qingzhang; Li, Ying; Chen, Jinhui; Zhang, Deqiang

2017-01-01

Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Adaptive Management as an Effective Strategy: Interdisciplinary Perceptions for Natural Resources Management

NASA Astrophysics Data System (ADS)

Dreiss, Lindsay M.; Hessenauer, Jan-Michael; Nathan, Lucas R.; O'Connor, Kelly M.; Liberati, Marjorie R.; Kloster, Danielle P.; Barclay, Janet R.; Vokoun, Jason C.; Morzillo, Anita T.

2017-02-01

Adaptive management is a well-established approach to managing natural resources, but there is little evidence demonstrating effectiveness of adaptive management over traditional management techniques. Peer-reviewed literature attempts to draw conclusions about adaptive management effectiveness using social perceptions, but those studies are largely restricted to employees of US federal organizations. To gain a more comprehensive insight into perceived adaptive management effectiveness, this study aimed to broaden the suite of disciplines, professional affiliations, and geographic backgrounds represented by both practitioners and scholars. A questionnaire contained a series of questions concerning factors that lead to or inhibit effective management, followed by another set of questions focused on adaptive management. Using a continuum representing strategies of both adaptive management and traditional management, respondents selected those strategies that they perceived as being effective. Overall, characteristics (i.e., strategies, stakeholders, and barriers) identified by respondents as contributing to effective management closely aligned with adaptive management. Responses were correlated to the type of adaptive management experience rather than an individual's discipline, occupational, or regional affiliation. In particular, perceptions of characteristics contributing to adaptive management effectiveness varied between respondents who identified as adaptive management scholars (i.e., no implementation experience) and adaptive management practitioners. Together, these results supported two concepts that make adaptive management effective: practitioners emphasized adaptive management's value as a long-term approach and scholars noted the importance of stakeholder involvement. Even so, more communication between practitioners and scholars regarding adaptive management effectiveness could promote interdisciplinary learning and problem solving for improved

Adaptive Management as an Effective Strategy: Interdisciplinary Perceptions for Natural Resources Management.

PubMed

Dreiss, Lindsay M; Hessenauer, Jan-Michael; Nathan, Lucas R; O'Connor, Kelly M; Liberati, Marjorie R; Kloster, Danielle P; Barclay, Janet R; Vokoun, Jason C; Morzillo, Anita T

2017-02-01

Adaptive management is a well-established approach to managing natural resources, but there is little evidence demonstrating effectiveness of adaptive management over traditional management techniques. Peer-reviewed literature attempts to draw conclusions about adaptive management effectiveness using social perceptions, but those studies are largely restricted to employees of US federal organizations. To gain a more comprehensive insight into perceived adaptive management effectiveness, this study aimed to broaden the suite of disciplines, professional affiliations, and geographic backgrounds represented by both practitioners and scholars. A questionnaire contained a series of questions concerning factors that lead to or inhibit effective management, followed by another set of questions focused on adaptive management. Using a continuum representing strategies of both adaptive management and traditional management, respondents selected those strategies that they perceived as being effective. Overall, characteristics (i.e., strategies, stakeholders, and barriers) identified by respondents as contributing to effective management closely aligned with adaptive management. Responses were correlated to the type of adaptive management experience rather than an individual's discipline, occupational, or regional affiliation. In particular, perceptions of characteristics contributing to adaptive management effectiveness varied between respondents who identified as adaptive management scholars (i.e., no implementation experience) and adaptive management practitioners. Together, these results supported two concepts that make adaptive management effective: practitioners emphasized adaptive management's value as a long-term approach and scholars noted the importance of stakeholder involvement. Even so, more communication between practitioners and scholars regarding adaptive management effectiveness could promote interdisciplinary learning and problem solving for improved

Loss of control eating in adolescents: Associations with adaptive and maladaptive emotion regulation strategies.

PubMed

Goossens, Lien; Van Malderen, Eva; Van Durme, Kim; Braet, Caroline

2016-08-01

To examine differences in the use of emotion regulation strategies in adolescents with and without loss of control over eating (LOC). A community-based sample of 524 adolescents from 12 to 18years old (70.6% girls; Mage=15.08; SD=1.59) reported on LOC and the use of several maladaptive and adaptive emotion regulation strategies. Adolescents who experience LOC (28%) report more use of maladaptive strategies. With regard to adaptive strategies a significant group X gender interaction effect was found with girls who report LOC using less adaptive strategies. More specifically, based on the FEEL-KJ less problem-oriented action, distraction, humor enhancement, acceptance and cognitive problem solving were observed in girls who report LOC compared to those who do not report LOC. Boys with LOC report more use of adaptive strategies compared to those who do not report LOC. LOC in adolescents is associated with increased use of maladaptive emotion regulation strategies as well as a decreased use of adaptive strategies although the latter is only specific for girls. These results may inform prevention and treatment of emotion regulation problems in adolescents with LOC. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adaptive mesh strategies for the spectral element method

NASA Technical Reports Server (NTRS)

Mavriplis, Catherine

1992-01-01

An adaptive spectral method was developed for the efficient solution of time dependent partial differential equations. Adaptive mesh strategies that include resolution refinement and coarsening by three different methods are illustrated on solutions to the 1-D viscous Burger equation and the 2-D Navier-Stokes equations for driven flow in a cavity. Sharp gradients, singularities, and regions of poor resolution are resolved optimally as they develop in time using error estimators which indicate the choice of refinement to be used. The adaptive formulation presents significant increases in efficiency, flexibility, and general capabilities for high order spectral methods.

Coping and adaptive strategies of traumatic brain injury survivors and primary caregivers.

PubMed

Adams, Deana; Dahdah, Marie

2016-06-27

Qualitative research methods allowed the investigator to contribute to the development of new theories and to examine change in processes over time, which added rich detail to existing knowledge of the use of coping and adaptive strategies by traumatic brain injury survivors and their primary caregivers (Ponsford, Sloan, & Snow, 2013). The advantages of phenomenological study were that it allows flexibility to explore and understand meanings attached by people to well-studied concepts such as coping, resiliency, and adaptation or compensation. Phenomenological study was sensitive to contextual factors. It also permitted the study of in-depth dynamics of coping and adaptive strategies of TBI survivors and primary caregivers, while understanding the social and psychological implications of the phenomenon. To explore the needs and deficits of adult traumatic brain injury (TBI) survivors and primary caregivers; and to identify their self-initiated coping and adaptive strategies. Significant to this study was the development of coping and adaptive strategies by the participants after their discharge from inpatient and rehabilitation treatment. The compensatory skills taught in treatment settings did not transfer to the home environment. Therefore, these strategies developed independently from previous treatment recommendations contributed to the development of theory related to rehabilitation and counseling. Distinctive to this study was the similarity of coping and adaptive strategies developed from both mild and severe traumatic brain injury survivors. This study consisted of eleven with TBI and six primary caregivers (N = 17), who participated in a series of semi-structured interviews aimed at discovering the coping and adaptive strategies utilized in dealing with the effects of brain injury. A Qualitative Phenomenological design was employed. Patience and understanding, support, and professional help were identified by TBI survivors and caregivers as being their

Sleep Strategies of Night-Shift Nurses on Days Off: Which Ones are Most Adaptive?

PubMed

Petrov, Megan E; Clark, C Brendan; Molzof, Hylton E; Johnson, Russell L; Cropsey, Karen L; Gamble, Karen L

2014-01-01

To determine the off-shift sleep strategies of bi-ethnic night-shift nurses, the relationship between these sleep strategies and adaptation to shift work, and identify the participant-level characteristics associated with a given sleep strategy. African-American and non-Hispanic White female, night-shift nurses from an academic hospital were recruited to complete a survey on sleep-wake patterns (n = 213). Participants completed the standard shiftwork index and the biological clocks questionnaire to determine sleep strategies and adaptation to night-shift work. In addition, chronotype was determined quantitatively with a modified version of the Munich ChronoType Questionnaire. Most participants worked ~3 consecutive 12-h night-shifts followed by several days off. Five sleep strategies used on days off were identified: (a) night stay, (b) nap proxy, (c) switch sleeper, (d) no sleep, and (e) incomplete switcher. Nap proxy and no sleep types were associated with poorer adaptation to night-shift work. The switch sleeper and incomplete switcher types were identified as more adaptive strategies that were associated with less sleep disturbance, a later chronotype, and less cardiovascular problems. Behavioral sleep strategies are related to adaptation to a typical night-shift schedule among hospital nurses. Nurses are crucial to the safety and well-being of their patients. Therefore, adoption of more adaptive sleep strategies may reduce sleep/wake dysregulation in this population, and improve cardiovascular outcomes.

Vulnerability of maize production under future climate change: possible adaptation strategies.

PubMed

Bannayan, Mohammad; Paymard, Parisa; Ashraf, Batool

2016-10-01

Climate change can affect the productivity and geographic distribution of crops. Therefore, evaluation of adaptive management options is crucial in dealing with negative impacts of climate change. The objectives of this study were to simulate the impacts of climate change on maize production in the north-east of Iran. Moreover, vulnerability index which indicated that how much of the crop yield loss is related to the drought was computed for each location to identify where adaptation and mitigation strategies are effective. Different sowing dates were also applied as an adaptation approach to decrease the negative impacts of climate change in study area. The results showed that the maize yield would decline during the 21st century from -2.6% to -82% at all study locations in comparison with the baseline. The result of vulnerability index also indicated that using the adaptation strategies could be effective in all of the study areas. Using different sowing dates as an adaptation approach showed that delaying the sowing date will be advantageous in order to obtain higher yield in all study locations in future. This study provided insight regarding the climate change impacts on maize production and the efficacy of adaptation strategies. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Adaptive strategies to climate change in Southern Malawi

NASA Astrophysics Data System (ADS)

Chidanti-Malunga, J.

Climate change poses a big challenge to rural livelihoods in the Shire Valley area of Southern Malawi, where communities have depended almost entirely on rain-fed agriculture for generations. The Shire Valley area comprises of low-altitude dambo areas and uplands which have been the main agricultural areas. Since early to mid 1980s, the uplands have experienced prolonged droughts and poor rainfall distribution, while the dambos have experienced recurrent seasonal floods. This study assessed some of the adaptive strategies exercised by small-scale rural farmers in response to climate change in the Shire Valley. The methodology used in collecting information includes group discussions, household surveys in the area, secondary data, and field observations. The results show that small-scale rural farmers exercise a number of adaptive strategies in response to climate change. These adaptive strategies include: increased use of water resources for small-scale irrigation or wetland farming, mostly using simple delivery techniques; increased management of residual moisture; and increased alternative sources of income such as fishing and crop diversity. It was also observed that government promoted the use of portable motorized pumps for small-scale irrigation in order to mitigate the effects of climate change. However, these external interventions were not fully adopted; instead the farmers preferred local interventions which mostly had indigenous elements.

Adaptive Strategies, Gender Ideology, and Work-Family Balance among Dutch Dual Earners

ERIC Educational Resources Information Center

Wierda-Boer, Hilde H.; Gerris, Jan R. M.; Vermulst, Ad A.

2008-01-01

Using questionnaire data on 149 Dutch dual-earner couples with young children participating in the European Famwork study, we examine how adaptive strategies and gender ideology relate to parents' perceived success in balancing work and family. Path analysis indicates that some adaptive strategies may harm individuals' work-family balance,…

Cloud computing task scheduling strategy based on improved differential evolution algorithm

NASA Astrophysics Data System (ADS)

Ge, Junwei; He, Qian; Fang, Yiqiu

2017-04-01

In order to optimize the cloud computing task scheduling scheme, an improved differential evolution algorithm for cloud computing task scheduling is proposed. Firstly, the cloud computing task scheduling model, according to the model of the fitness function, and then used improved optimization calculation of the fitness function of the evolutionary algorithm, according to the evolution of generation of dynamic selection strategy through dynamic mutation strategy to ensure the global and local search ability. The performance test experiment was carried out in the CloudSim simulation platform, the experimental results show that the improved differential evolution algorithm can reduce the cloud computing task execution time and user cost saving, good implementation of the optimal scheduling of cloud computing tasks.

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

PubMed

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

Evolution of dispersal and life history strategies – Tetrahymena ciliates

PubMed Central

Fjerdingstad, Else J; Schtickzelle, Nicolas; Manhes, Pauline; Gutierrez, Arnaud; Clobert, Jean

2007-01-01

Background Considerable attention has focused on how selection on dispersal and other core life-history strategies (reproductive effort, survival ability, colonization capacity) may lead to so-called dispersal syndromes. Studies on genetic variation in these syndromes within species could importantly increase our understanding of their evolution, by revealing whether traits co-vary across genetic lineages in the manner predicted by theoretical models, and by stimulating further hypotheses for experimental testing. Yet such studies remain scarce. Here we studied the ciliated protist Tetrahymena thermophila, a particularly interesting organism due to cells being able to transform into morphs differing dramatically in swim-speed. We investigated dispersal, morphological responses, reproductive performance, and survival in ten different clonal strains. Then, we examined whether life history traits co-varied in the manner classically predicted for ruderal species, examined the investment of different strains into short- and putative long-distance dispersal, while considering also the likely impact of semi-sociality (cell aggregation, secretion of 'growth factors') on dispersal strategies. Results Very significant among-strain differences were found with regard to dispersal rate, morphological commitment and plasticity, and almost all core life-history traits (e.g. survival, growth performance and strategy), with most of these traits being significantly intercorrelated. Some strains showed high short-distance dispersal rates, high colonization capacity, bigger cell size, elevated growth performance, and good survival abilities. These well performing strains, however, produced fewer fast-swimming dispersal morphs when subjected to environmental degradation than did philopatric strains performing poorly under normal conditions. Conclusion Strong evidence was found for a genetic covariation between dispersal strategies and core life history traits in T. thermophila, with a

Assessment of the effectiveness of participatory developed adaptation strategies for HCMC

NASA Astrophysics Data System (ADS)

Lasage, R.; Veldkamp, T. I. E.; de Moel, H.; Van, T. C.; Phi, H. L.; Vellinga, P.; Aerts, J. C. J. H.

2014-01-01

Coastal cities are vulnerable to flooding, and flood risk to coastal cities will increase due to sea-level rise. Moreover, especially Asian cities are subject to considerable population growth and associated urban developments, increasing this risk even more. Empirical data on vulnerability and the cost and benefits of flood risk reducing measures are therefore paramount for sustainable development of these cities. This paper presents an approach to explore the impacts of sea level rise and socio-economic developments on flood risk for the flood prone District 4 in Ho Chi Minh City, Vietnam, and to develop and evaluate the effects of different adaptation strategies (new levees, dry- and wet flood proofing of buildings). A flood damage model was developed to simulate current and future flood risk using the results from a household survey to establish stage-damage curves for residential buildings. the model has been used to assess the effects of several participatory developed adaptation strategies to reduce flood risk, expressed in Expected Annual Damage (EAD). Adaptation strategies were evaluated assuming combinations of both sea level scenarios and land use scenarios. Together with information on costs of these strategies, we calculated the benefit-cost ratio and net present value for the adaptation strategies until 2100, taking into account depreciation rates of 2.5% and 5%. The results of this modeling study indicate that the current flood risk in District 4 is 0.31 million USD yr-1, increasing up to 0.78 million USD yr-1 in 2100. The net present value and benefit-cost ratios using a discount rate of 5% range from USD -107 to -1.5 million, and from 0.086 to 0.796 for the different strategies. Using a discount rate of 2.5% leads to an increase in both net present value and benefit cost ratio. The adaptation strategies wet proofing and dry proofing generate the best results using these economic indicators. The information on different strategies will be used by

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

PubMed

Bailey, Susan F; Bataillon, Thomas

2016-01-01

There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have 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 these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs 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. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution.

PubMed

Erickson, Keesha E; Otoupal, Peter B; Chatterjee, Anushree

2017-01-01

response processes known as adaptive resistance. Adaptive resistance fosters transient tolerance increases and the emergence of mutations conferring heritable drug resistance. In order to extend the applicable lifetime of new antibiotics, we must seek to hinder the occurrence of bacterial adaptive resistance; however, the regulation of adaptation is difficult to identify due to immense heterogeneity emerging during evolution. This study specifically seeks to generate heterogeneity by adapting bacteria to different stresses and then examines gene expression trends across the disparate populations in order to pinpoint key genes and pathways associated with adaptive resistance. The targets identified here may eventually inform strategies for impeding adaptive resistance and prolonging the effectiveness of antibiotic treatment.

Sleep Strategies of Night-Shift Nurses on Days Off: Which Ones are Most Adaptive?

PubMed Central

Petrov, Megan E.; Clark, C. Brendan; Molzof, Hylton E.; Johnson, Russell L.; Cropsey, Karen L.; Gamble, Karen L.

2014-01-01

Objectives: To determine the off-shift sleep strategies of bi-ethnic night-shift nurses, the relationship between these sleep strategies and adaptation to shift work, and identify the participant-level characteristics associated with a given sleep strategy. Methods: African-American and non-Hispanic White female, night-shift nurses from an academic hospital were recruited to complete a survey on sleep–wake patterns (n = 213). Participants completed the standard shiftwork index and the biological clocks questionnaire to determine sleep strategies and adaptation to night-shift work. In addition, chronotype was determined quantitatively with a modified version of the Munich ChronoType Questionnaire. Most participants worked ~3 consecutive 12-h night-shifts followed by several days off. Results: Five sleep strategies used on days off were identified: (a) night stay, (b) nap proxy, (c) switch sleeper, (d) no sleep, and (e) incomplete switcher. Nap proxy and no sleep types were associated with poorer adaptation to night-shift work. The switch sleeper and incomplete switcher types were identified as more adaptive strategies that were associated with less sleep disturbance, a later chronotype, and less cardiovascular problems. Conclusion: Behavioral sleep strategies are related to adaptation to a typical night-shift schedule among hospital nurses. Nurses are crucial to the safety and well-being of their patients. Therefore, adoption of more adaptive sleep strategies may reduce sleep/wake dysregulation in this population, and improve cardiovascular outcomes. PMID:25566182

Adaptation and the evolution of parasite virulence in a connected world.

PubMed

Wild, Geoff; Gardner, Andy; West, Stuart A

2009-06-18

Adaptation is conventionally regarded as occurring at the level of the individual organism, where it functions to maximize the individual's inclusive fitness. However, it has recently been argued that empirical studies on the evolution of parasite virulence in spatial populations show otherwise. In particular, it has been claimed that the evolution of lower virulence in response to limited parasite dispersal provides proof of Wynne-Edwards's idea of adaptation at the group level. Although previous theoretical work has shown that limited dispersal can favour lower virulence, it has not clarified why, with five different suggestions having been given. Here we show that the effect of dispersal on parasite virulence can be understood entirely within the framework of inclusive fitness theory. Limited parasite dispersal favours lower parasite growth rates and, hence, reduced virulence because it (1) decreases the direct benefit of producing offspring (dispersers are worth more than non-dispersers, because they can go to patches with no or fewer parasites), and (2) increases the competition for hosts experienced by both the focal individual ('self-shading') and their relatives ('kin shading'). This demonstrates that reduced virulence can be understood as an individual-level adaptation by the parasite to maximize its inclusive fitness, and clarifies the links with virulence theory more generally.

Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates.

PubMed

Kaufman, Jim

2018-04-26

The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system. Then it considers what the original antigen-specific receptor and MHC molecule might have looked like, how peptide binding might have evolved, and finally the importance of adaptive immunity in general.

Adaptation and colonization history affect the evolution of clines in two introduced species.

PubMed

Keller, Stephen R; Sowell, Dexter R; Neiman, Maurine; Wolfe, Lorne M; Taylor, Douglas R

2009-08-01

Phenotypic and genetic clines have long been synonymous with adaptive evolution. However, other processes (for example, migration, range expansion, invasion) may generate clines in traits or loci across geographical and environmental gradients. It is therefore important to distinguish between clines that represent adaptive evolution and those that result from selectively neutral demographic or genetic processes. We tested for the differentiation of phenotypic traits along environmental gradients using two species in the genus Silene, whilst statistically controlling for colonization history and founder effects. We sampled seed families from across the native and introduced ranges, genotyped individuals and estimated phenotypic differentiation in replicated common gardens. The results suggest that post-glacial expansion of S. vulgaris and S. latifolia involved both neutral and adaptive genetic differentiation (clines) of life history traits along major axes of environmental variation in Europe and North America. Phenotypic clines generally persisted when tested against the neutral expectation, although some clines disappeared (and one cline emerged) when the effects of genetic ancestry were statistically removed. Colonization history, estimated using genetic markers, is a useful null model for tests of adaptive trait divergence, especially during range expansion and invasion when selection and gene flow may not have reached equilibrium.

Strategies of Mesenchymal Invasion of Patient-derived Brain Tumors: Microenvironmental Adaptation.

PubMed

Cha, Junghwa; Kang, Seok-Gu; Kim, Pilnam

2016-04-25

The high mortality in glioblastoma multiforme (GBM) patients is primarily caused by extensive infiltration into adjacent tissue and subsequent rapid recurrence. There are no clear therapeutic strategies that target the infiltrative subpopulation of GBM mass. Using mesenchymal mode of invasion, the GBM is known to widely infiltrate by interacting with various unique components within brain microenvironment such as hyaluronic acid (HA)-rich matrix and white matter tracts. However, it is unclear how these GBM microenvironments influence the strategies of mesenchymal invasion. We hypothesize that GBM has different strategies to facilitate such invasion through adaptation to their local microenvironment. Using our in vitro biomimetic microenvironment platform for three-dimensional GBM tumorspheres (TSs), we found that the strategies of GBM invasion were predominantly regulated by the HA-rich ECM microenvironment, showing marked phenotypic changes in the presence of HA, which were mainly mediated by HA synthase (HAS). Interestingly, after inhibition of the HAS gene, GBM switched their invasion strategies to a focal adhesion (FA)-mediated invasion. These results demonstrate that the microenvironmental adaptation allowed a flexible invasion strategy for GBM. Using our model, we suggest a new inhibitory pathway for targeting infiltrative GBM and propose an importance of multi-target therapy for GBM, which underwent microenvironmental adaptation.

Adaptive Strategy Selection in Decision Making.

DTIC Science & Technology

1986-07-31

information processing capabilities of a decision maker, given any " reasonable " time limit for making the decision. If use of a more normative rule...DECISION MAKING JOHN W. PAYNE DTIC DUKE UNIVERSITY L.CT E AUG 13 JAMES R. BETTMAN DUKE. UNIVERSITY ERIC J. JOHNSON CARNEGIE-MELLON UNIVERSITY...REPORT & PERIOD COVERED ADAPTIVE STRATEGY SELECTION IN DECISION MAKING Research 6. PERFORMING ORO. REPORT NUMSER 7. AUTNORfe) e. CONTRACT ON GRANT

Multilevel Optimization Framework for Hierarchical Stiffened Shells Accelerated by Adaptive Equivalent Strategy

NASA Astrophysics Data System (ADS)

Wang, Bo; Tian, Kuo; Zhao, Haixin; Hao, Peng; Zhu, Tianyu; Zhang, Ke; Ma, Yunlong

2017-06-01

In order to improve the post-buckling optimization efficiency of hierarchical stiffened shells, a multilevel optimization framework accelerated by adaptive equivalent strategy is presented in this paper. Firstly, the Numerical-based Smeared Stiffener Method (NSSM) for hierarchical stiffened shells is derived by means of the numerical implementation of asymptotic homogenization (NIAH) method. Based on the NSSM, a reasonable adaptive equivalent strategy for hierarchical stiffened shells is developed from the concept of hierarchy reduction. Its core idea is to self-adaptively decide which hierarchy of the structure should be equivalent according to the critical buckling mode rapidly predicted by NSSM. Compared with the detailed model, the high prediction accuracy and efficiency of the proposed model is highlighted. On the basis of this adaptive equivalent model, a multilevel optimization framework is then established by decomposing the complex entire optimization process into major-stiffener-level and minor-stiffener-level sub-optimizations, during which Fixed Point Iteration (FPI) is employed to accelerate convergence. Finally, the illustrative examples of the multilevel framework is carried out to demonstrate its efficiency and effectiveness to search for the global optimum result by contrast with the single-level optimization method. Remarkably, the high efficiency and flexibility of the adaptive equivalent strategy is indicated by compared with the single equivalent strategy.

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

PubMed

Franks, Steven J; Munshi-South, Jason

2014-05-01

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

Adaptation and Convergent Evolution within the Jamesonia-Eriosorus Complex in High-Elevation Biodiverse Andean Hotspots

PubMed Central

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. PMID:25340770

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

PubMed

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.

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

Reactive strategies in indirect reciprocity.

PubMed

Ohtsuki, Hisashi

2004-04-07

Evolution of reactive strategy of indirect reciprocity is discussed, where individuals interact with others through the one-shot Prisoner's Dilemma game, changing their partners in every round. We investigate all of the reactive strategies that are stochastic, including deterministic ones as special cases. First we study adaptive dynamics of reactive strategies by assuming monomorphic population. Results are very similar to the corresponding evolutionary dynamics of direct reciprocity. The discriminating strategy, which prescribes cooperation only with those who cooperated in the previous round, cannot be an outcome of the evolution. Next we examine the case where the population includes a diversity of strategies. We find that only the mean 'discriminatoriness' in the population is the parameter that affects the evolutionary dynamics. The discriminating strategy works as a promoter of cooperation there. However, it is again not the end point of the evolution. This is because retaliatory defection, which was prescribed by the discriminating strategy, is regarded as another defection toward the society. These results caution that we have to reconsider the role of retaliatory defection much more carefully.

Evolution of State Outreach Efforts Under SCHIP

PubMed Central

Williams, Susan R.; Rosenbach, Margo L.

2007-01-01

States have shown creativity and adaptability in developing outreach strategies to promote State Children's Health Insurance Program (SCHIP) enrollment. As the program has matured and the fiscal environment has tightened, States have learned what efforts are successful and have tailored their approaches accordingly This article reviews the evolution of State outreach strategies under SCHIP, using qualitative information from all 50 States and the District of Columbia. Early campaigns were aimed at building broad awareness of SCHIP. Over time, States have adapted their outreach campaigns to close the gaps in enrolling hard-to-reach populations, by modifying their target populations, messages, methods, organizational strategies, and emphasis. PMID:17722754

Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance.

PubMed

McGlothlin, Joel W; Kobiela, Megan E; Feldman, Chris R; Castoe, Todd A; Geffeney, Shana L; Hanifin, Charles T; Toledo, Gabriela; Vonk, Freek J; Richardson, Michael K; Brodie, Edmund D; Pfrender, Michael E; Brodie, Edmund D

2016-06-20

Novel adaptations must originate and function within an already established genome [1]. As a result, the ability of a species to adapt to new environmental challenges is predicted to be highly contingent on the evolutionary history of its lineage [2-6]. Despite a growing appreciation of the importance of historical contingency in the adaptive evolution of single proteins [7-11], we know surprisingly little about its role in shaping complex adaptations that require evolutionary change in multiple genes. One such adaptation, extreme resistance to tetrodotoxin (TTX), has arisen in several species of snakes through coevolutionary arms races with toxic amphibian prey, which select for TTX-resistant voltage-gated sodium channels (Nav) [12-16]. Here, we show that the relatively recent origins of extreme toxin resistance, which involve the skeletal muscle channel Nav1.4, were facilitated by ancient evolutionary changes in two other members of the same gene family. A substitution conferring TTX resistance to Nav1.7, a channel found in small peripheral neurons, arose in lizards ∼170 million years ago (mya) and was present in the common ancestor of all snakes. A second channel found in larger myelinated neurons, Nav1.6, subsequently evolved resistance in four different snake lineages beginning ∼38 mya. Extreme TTX resistance has evolved at least five times within the past 12 million years via changes in Nav1.4, but only within lineages that previously evolved resistant Nav1.6 and Nav1.7. Our results show that adaptive protein evolution may be contingent upon enabling substitutions elsewhere in the genome, in this case, in paralogs of the same gene family. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Linking Individual and Collective Behavior in Adaptive Social Networks

NASA Astrophysics Data System (ADS)

Pinheiro, Flávio L.; Santos, Francisco C.; Pacheco, Jorge M.

2016-03-01

Adaptive social structures are known to promote the evolution of cooperation. However, up to now the characterization of the collective, population-wide dynamics resulting from the self-organization of individual strategies on a coevolving, adaptive network has remained unfeasible. Here we establish a (reversible) link between individual (micro)behavior and collective (macro)behavior for coevolutionary processes. We demonstrate that an adaptive network transforms a two-person social dilemma locally faced by individuals into a collective dynamics that resembles that associated with an N -person coordination game, whose characterization depends sensitively on the relative time scales between the entangled behavioral and network evolutions. In particular, we show that the faster the relative rate of adaptation of the network, the smaller the critical fraction of cooperators required for cooperation to prevail, thus establishing a direct link between network adaptation and the evolution of cooperation. The framework developed here is general and may be readily applied to other dynamical processes occurring on adaptive networks, notably, the spreading of contagious diseases or the diffusion of innovations.

Evolution Of The Operational Energy Strategy And Its Consideration In The Defense Acquisition Process

DTIC Science & Technology

2016-09-01

OPERATIONAL ENERGY STRATEGY AND ITS CONSIDERATION IN THE DEFENSE ACQUISITION PROCESS by Richard J. Kendig Ashley D. Seaton Robert J. Rodgers...project 4. TITLE AND SUBTITLE EVOLUTION OF THE OPERATIONAL ENERGY STRATEGY AND ITS CONSIDERATION IN THE DEFENSE ACQUISITION PROCESS 5. FUNDING...looked at the DOD Operational Energy Strategy evolution and how it applies to new and modified weapon systems, considering the three-legged table of the

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

PubMed

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

2012-11-01

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

Adaptive strategies for materials design using uncertainties

DOE PAGES

Balachandran, Prasanna V.; Xue, Dezhen; Theiler, James; ...

2016-01-21

Here, we compare several adaptive design strategies using a data set of 223 M2AX family of compounds for which the elastic properties [bulk (B), shear (G), and Young’s (E) modulus] have been computed using density functional theory. The design strategies are decomposed into an iterative loop with two main steps: machine learning is used to train a regressor that predicts elastic properties in terms of elementary orbital radii of the individual components of the materials; and a selector uses these predictions and their uncertainties to choose the next material to investigate. The ultimate goal is to obtain a material withmore » desired elastic properties in as few iterations as possible. We examine how the choice of data set size, regressor and selector impact the design. We find that selectors that use information about the prediction uncertainty outperform those that don’t. Our work is a step in illustrating how adaptive design tools can guide the search for new materials with desired properties.« less

Adaptive strategies for materials design using uncertainties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balachandran, Prasanna V.; Xue, Dezhen; Theiler, James

Here, we compare several adaptive design strategies using a data set of 223 M2AX family of compounds for which the elastic properties [bulk (B), shear (G), and Young’s (E) modulus] have been computed using density functional theory. The design strategies are decomposed into an iterative loop with two main steps: machine learning is used to train a regressor that predicts elastic properties in terms of elementary orbital radii of the individual components of the materials; and a selector uses these predictions and their uncertainties to choose the next material to investigate. The ultimate goal is to obtain a material withmore » desired elastic properties in as few iterations as possible. We examine how the choice of data set size, regressor and selector impact the design. We find that selectors that use information about the prediction uncertainty outperform those that don’t. Our work is a step in illustrating how adaptive design tools can guide the search for new materials with desired properties.« less

A Model for Designing Adaptive Laboratory Evolution Experiments.

PubMed

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

2017-04-15

The occurrence of mutations is a cornerstone of the evolutionary theory of adaptation, capitalizing on the rare chance that a mutation confers a fitness benefit. Natural selection is increasingly being leveraged in laboratory settings for industrial and basic science applications. Despite increasing deployment, there are no standardized procedures available for designing and performing adaptive laboratory evolution (ALE) experiments. Thus, there is a need to optimize the experimental design, specifically for determining when to consider an experiment complete and for balancing outcomes with available resources (i.e., laboratory supplies, personnel, and time). To design and to better understand ALE experiments, a simulator, ALEsim, was developed, validated, and applied to the optimization of ALE experiments. The effects of various passage sizes were experimentally determined and subsequently evaluated with ALEsim, to explain differences in experimental outcomes. Furthermore, a beneficial mutation rate of 10 -6.9 to 10 -8.4 mutations per cell division was derived. A retrospective analysis of ALE experiments revealed that passage sizes typically employed in serial passage batch culture ALE experiments led to inefficient production and fixation of beneficial mutations. ALEsim and the results described here will aid in the design of ALE experiments to fit the exact needs of a project while taking into account the resources required and will lower the barriers to entry for this experimental technique. IMPORTANCE ALE is a widely used scientific technique to increase scientific understanding, as well as to create industrially relevant organisms. The manner in which ALE experiments are conducted is highly manual and uniform, with little optimization for efficiency. Such inefficiencies result in suboptimal experiments that can take multiple months to complete. With the availability of automation and computer simulations, we can now perform these experiments in an optimized

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

PubMed

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.

Transitions in optimal adaptive strategies for populations in fluctuating environments

NASA Astrophysics Data System (ADS)

Mayer, Andreas; Mora, Thierry; Rivoire, Olivier; Walczak, Aleksandra M.

2017-09-01

Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist phenotype that compromises between conditions, or population-wise diversification (bet hedging). Which strategy provides the largest selective advantage in the long run depends on the range of accessible phenotypes and the statistics of the environmental fluctuations. Here, we analyze this problem in a simple mathematical model of population growth. First, we review and extend a graphical method to identify the nature of the optimal strategy when the environmental fluctuations are uncorrelated. Temporal correlations in environmental fluctuations open up new strategies that rely on memory but are mathematically challenging to study: We present analytical results to address this challenge. We illustrate our general approach by analyzing optimal adaptive strategies in the presence of trade-offs that constrain the range of accessible phenotypes. Our results extend several previous studies and have applications to a variety of biological phenomena, from antibiotic resistance in bacteria to immune responses in vertebrates.

Management of Computer-Based Instruction: Design of an Adaptive Control Strategy.

ERIC Educational Resources Information Center

Tennyson, Robert D.; Rothen, Wolfgang

1979-01-01

Theoretical and research literature on learner, program, and adaptive control as forms of instructional management are critiqued in reference to the design of computer-based instruction. An adaptive control strategy using an online, iterative algorithmic model is proposed. (RAO)

Evolution of social learning does not explain the origin of human cumulative culture.

PubMed

Enquist, Magnus; Ghirlanda, Stefano

2007-05-07

Because culture requires transmission of information between individuals, thinking about the origin of culture has mainly focused on the genetic evolution of abilities for social learning. Current theory considers how social learning affects the adaptiveness of a single cultural trait, yet human culture consists of the accumulation of very many traits. Here we introduce a new modeling strategy that tracks the adaptive value of many cultural traits, showing that genetic evolution favors only limited social learning owing to the accumulation of maladaptive as well as adaptive culture. We further show that culture can be adaptive, and refined social learning can evolve, if individuals can identify and discard maladaptive culture. This suggests that the evolution of such "adaptive filtering" mechanisms may have been crucial for the birth of human culture.

The importance of training strategy adaptation: a learner-oriented approach for improving older adults' memory and transfer.

PubMed

Bottiroli, Sara; Cavallini, Elena; Dunlosky, John; Vecchi, Tomaso; Hertzog, Christopher

2013-09-01

We investigated the benefits of strategy-adaptation training for promoting transfer effects. This learner-oriented approach--which directly encourages the learner to generalize strategic behavior to new tasks--helps older adults appraise new tasks and adapt trained strategies to them. In Experiment 1, older adults in a strategy-adaptation training group used 2 strategies (imagery and sentence generation) while practicing 2 tasks (list and associative learning); they were then instructed on how to do a simple task analysis to help them adapt the trained strategies for 2 different unpracticed tasks (place learning and text learning) that were discussed during training. Two additional criterion tasks (name-face associative learning and grocery-list learning) were never mentioned during training. Two other groups were included: A strategy training group (who received strategy training and transfer instructions but not strategy-adaptation training) and a waiting-list control group. Both training procedures enhanced older adults' performance on the trained tasks and those tasks that were discussed during training, but transfer was greatest after strategy-adaptation training. Experiment 2 found that strategy-adaptation training conducted via a manual that older adults used at home also promoted transfer. These findings demonstrate the importance of adopting a learner-oriented approach to promote transfer of strategy training. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Distinct motor strategies underlying split-belt adaptation in human walking and running.

PubMed

Ogawa, Tetsuya; Kawashima, Noritaka; Obata, Hiroki; Kanosue, Kazuyuki; Nakazawa, Kimitaka

2015-01-01

The aim of the present study was to elucidate the adaptive and de-adaptive nature of human running on a split-belt treadmill. The degree of adaptation and de-adaptation was compared with those in walking by calculating the antero-posterior component of the ground reaction force (GRF). Adaptation to walking and running on a split-belt resulted in a prominent asymmetry in the movement pattern upon return to the normal belt condition, while the two components of the GRF showed different behaviors depending on the gaits. The anterior braking component showed prominent adaptive and de-adaptive behaviors in both gaits. The posterior propulsive component, on the other hand, exhibited such behavior only in running, while that in walking showed only short-term aftereffect (lasting less than 10 seconds) accompanied by largely reactive responses. These results demonstrate a possible difference in motor strategies (that is, the use of reactive feedback and adaptive feedforward control) by the central nervous system (CNS) for split-belt locomotor adaptation between walking and running. The present results provide basic knowledge on neural control of human walking and running as well as possible strategies for gait training in athletic and rehabilitation scenes.

Distinct Motor Strategies Underlying Split-Belt Adaptation in Human Walking and Running

PubMed Central

Ogawa, Tetsuya; Kawashima, Noritaka; Obata, Hiroki; Kanosue, Kazuyuki; Nakazawa, Kimitaka

2015-01-01

The aim of the present study was to elucidate the adaptive and de-adaptive nature of human running on a split-belt treadmill. The degree of adaptation and de-adaptation was compared with those in walking by calculating the antero-posterior component of the ground reaction force (GRF). Adaptation to walking and running on a split-belt resulted in a prominent asymmetry in the movement pattern upon return to the normal belt condition, while the two components of the GRF showed different behaviors depending on the gaits. The anterior braking component showed prominent adaptive and de-adaptive behaviors in both gaits. The posterior propulsive component, on the other hand, exhibited such behavior only in running, while that in walking showed only short-term aftereffect (lasting less than 10 seconds) accompanied by largely reactive responses. These results demonstrate a possible difference in motor strategies (that is, the use of reactive feedback and adaptive feedforward control) by the central nervous system (CNS) for split-belt locomotor adaptation between walking and running. The present results provide basic knowledge on neural control of human walking and running as well as possible strategies for gait training in athletic and rehabilitation scenes. PMID:25775426

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

PubMed

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

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

PubMed Central

Overbeck, Tom J.; Welker, Dennis L.; Hughes, Joanne E.; Steele, James L.

2017-01-01

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

[Insulin resistance as a mechanism of adaptation during human evolution].

PubMed

Ricart, W; Fernández-Real, J M

2010-10-01

The recent application of concepts of evolution to human disease is proving useful to understand certain pathophysiological mechanisms of different entities that span genomic alterations of immunity, respiratory and hormone function, and the circulatory and neural systems. However, effort has concentrated on explaining the keys to adaptation that define human metabolism and, since the early 1960s, several theories have been developed. This article reviews some of the hypotheses postulated in recent years on the potential benefit of insulin resistance and discusses the most recent knowledge. The concept of the thrifty gene seems to have been definitively refuted by current knowledge. The current paradigm describes an interaction between the metabolic and the immune systems resulting from their coevolution, promoted by evolutionary pressures triggered by fasting, infection and intake of different foods. The activation and regulation of these ancient mechanisms in integrated and interdependent areas defines insulin resistance as a survival strategy that is critical during fasting and in the fight against infection. The relationship with some components of the diet and, particularly, with the symbiotic intestinal microflora points to new paradigms in understanding the pathophysiology of obesity, metabolic syndrome and type 2 diabetes mellitus. Copyright © 2010 SEEN. Published by Elsevier Espana. All rights reserved.

Sex speeds adaptation by altering the dynamics of molecular evolution.

PubMed

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.

Adaptive Control Based Harvesting Strategy for a Predator-Prey Dynamical System.

PubMed

Sen, Moitri; Simha, Ashutosh; Raha, Soumyendu

2018-04-23

This paper deals with designing a harvesting control strategy for a predator-prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory. In order to account for unknown parameters, an adaptive control strategy has been proposed in which the control law depends on an adaptive variable which tracks the unknown parameter. Further, a switching component has been incorporated to robustify the control performance against bounded disturbances. Proofs have been provided to show that the proposed adaptive control strategy ensures asymptotic stability of the dynamics at a desired operating point, as well as exact parameter learning in the disturbance-free case and learning with bounded error in the disturbance prone case. The dynamics, with uncertainty in the death rate of the predator, subjected to a bounded disturbance has been simulated with the proposed control strategy.

Siderophore production and the evolution of investment in a public good: An adaptive dynamics approach to kin selection.

PubMed

Lee, William; van Baalen, Minus; Jansen, Vincent A A

2016-01-07

Like many other bacteria, Pseudomonas aeruginosa sequesters iron from the environment through the secretion, and subsequent uptake, of iron-binding molecules. As these molecules can be taken up by other bacteria in the population than those who secreted them, this is a form of cooperation through a public good. Traditionally, this problem has been studied by comparing the relative fitnesses of siderophore-producing and non-producing strains, but this gives no information about the fate of strains that do produce intermediate amounts of siderophores. Here, we investigate theoretically how the amount invested in this form of cooperation evolves. We use a mechanistic description of the laboratory protocols used in experimental evolution studies to describe the competition and cooperation of the bacteria. From this dynamical model we derive the fitness following the adaptive dynamics method. The results show how selection is driven by local siderophore production and local competition. Because siderophore production reduces the growth rate, local competition decreases with the degree of relatedness (which is a dynamical variable in our model). Our model is not restricted to the analysis of small phenotypic differences and allows for theoretical exploration of the effects of large phenotypic differences between cooperators and cheats. We predict that an intermediate ESS level of cooperation (molecule production) should exist. The adaptive dynamics approach allows us to assess evolutionary stability, which is often not possible in other kin-selection models. We found that selection can lead to an intermediate strategy which in our model is always evolutionarily stable, yet can allow invasion of strategies that are much more cooperative. Our model describes the evolution of a public good in the context of the ecology of the microorganism, which allows us to relate the extent of production of the public good to the details of the interactions. Copyright © 2015 Elsevier

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

PubMed

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.

Intelligent fault recognition strategy based on adaptive optimized multiple centers

NASA Astrophysics Data System (ADS)

Zheng, Bo; Li, Yan-Feng; Huang, Hong-Zhong

2018-06-01

For the recognition principle based optimized single center, one important issue is that the data with nonlinear separatrix cannot be recognized accurately. In order to solve this problem, a novel recognition strategy based on adaptive optimized multiple centers is proposed in this paper. This strategy recognizes the data sets with nonlinear separatrix by the multiple centers. Meanwhile, the priority levels are introduced into the multi-objective optimization, including recognition accuracy, the quantity of optimized centers, and distance relationship. According to the characteristics of various data, the priority levels are adjusted to ensure the quantity of optimized centers adaptively and to keep the original accuracy. The proposed method is compared with other methods, including support vector machine (SVM), neural network, and Bayesian classifier. The results demonstrate that the proposed strategy has the same or even better recognition ability on different distribution characteristics of data.

Automatic Clustering Using FSDE-Forced Strategy Differential Evolution

NASA Astrophysics Data System (ADS)

Yasid, A.

2018-01-01

Clustering analysis is important in datamining for unsupervised data, cause no adequate prior knowledge. One of the important tasks is defining the number of clusters without user involvement that is known as automatic clustering. This study intends on acquiring cluster number automatically utilizing forced strategy differential evolution (AC-FSDE). Two mutation parameters, namely: constant parameter and variable parameter are employed to boost differential evolution performance. Four well-known benchmark datasets were used to evaluate the algorithm. Moreover, the result is compared with other state of the art automatic clustering methods. The experiment results evidence that AC-FSDE is better or competitive with other existing automatic clustering algorithm.

Strategy evolution driven by switching probabilities in structured multi-agent systems

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Chen, Zengqiang; Li, Zhiqi

2017-10-01

Evolutionary mechanism driving the commonly seen cooperation among unrelated individuals is puzzling. Related models for evolutionary games on graphs traditionally assume that players imitate their successful neighbours with higher benefits. Notably, an implicit assumption here is that players are always able to acquire the required pay-off information. To relax this restrictive assumption, a contact-based model has been proposed, where switching probabilities between strategies drive the strategy evolution. However, the explicit and quantified relation between a player's switching probability for her strategies and the number of her neighbours remains unknown. This is especially a key point in heterogeneously structured system, where players may differ in the numbers of their neighbours. Focusing on this, here we present an augmented model by introducing an attenuation coefficient and evaluate its influence on the evolution dynamics. Results show that the individual influence on others is negatively correlated with the contact numbers specified by the network topologies. Results further provide the conditions under which the coexisting strategies can be calculated analytically.

Exposure to Stressful Environments: Strategy of Adaptive Responses

NASA Technical Reports Server (NTRS)

Farhi, Leon E.

1991-01-01

Any new natural environment may generate a number of stresses (such as hypoxia, water lack, and heat exposure), each of which can produce strains in more than a single organ system. Every strain may in turn stimulate the body to adapt in multiple ways. Nevertheless, a general strategy of the various adaptive responses emerges when the challenges are divided into three groups. The first category includes conditions that affect the supply of essential molecules, while the second is made up by those stresses that prevent the body from regulating properly the output of waste products, such as CO2 and heat. In both classes, there is a small number of responses, similar in principle, regardless of the specific situation. The third unit is created by environments that disrupt body transport systems. Problems may arise when there is a conflict between two stresses requiring conflicting adaptive changes. An alternative to adaptation, creation of micro-environment, is often favored by the animal.

An adaptation strategy of sandland peasants in Yogyakarta toward climate change

NASA Astrophysics Data System (ADS)

Rusdiyana, E.; Suminah

2018-03-01

This study aims to explore and describe the adaptation strategies of sandland peasants toward climate change. Qualitative research method was employed and the data were collected through observation. In addition, the recording of the data, interview and the validity of data were determined by triangulation of sources. The results of the research showed that the adaptation strategies of sandland peasants toward climate change were; (1) the adjustment of crop varieties, (2) the utilization of productive crops as wind breaking, and (3) the irrigation system using “sumur panthek”.

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

PubMed

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.

Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution

PubMed Central

Arbour, Jessica Hilary; López-Fernández, Hernán

2013-01-01

Diversity and disparity are unequally distributed both phylogenetically and geographically. This uneven distribution may be owing to differences in diversification rates between clades resulting from processes such as adaptive radiation. We examined the rate and distribution of evolution in feeding biomechanics in the extremely diverse and continentally distributed South American geophagine cichlids. Evolutionary patterns in multivariate functional morphospace were examined using a phylomorphospace approach, disparity-through-time analyses and by comparing Brownian motion (BM) and adaptive peak evolutionary models using maximum likelihood. The most species-rich and functionally disparate clade (CAS) expanded more efficiently in morphospace and evolved more rapidly compared with both BM expectations and its sister clade (GGD). Members of the CAS clade also exhibited an early burst in functional evolution that corresponds to the development of modern ecological roles and may have been related to the colonization of a novel adaptive peak characterized by fast oral jaw mechanics. Furthermore, reduced ecological opportunity following this early burst may have restricted functional evolution in the GGD clade, which is less species-rich and more ecologically specialized. Patterns of evolution in ecologically important functional traits are consistent with a pattern of adaptive radiation within the most diverse clade of Geophagini. PMID:23740780

Climate change adaptation strategies and mitigation policies

NASA Astrophysics Data System (ADS)

García Fernández, Cristina

2015-04-01

The pace of climate change and the consequent warming of the Earth's surface is increasing vulnerability and decreasing adaptive capacity. Achieving a successful adaptation depends on the development of technology, institutional organization, financing availability and the exchange of information. Populations living in arid and semi-arid zones, low-lying coastal areas, land with water shortages or at risk of overflow or small islands are particularly vulnerable to climate change. Due to increasing population density in sensitive areas, some regions have become more vulnerable to events such as storms, floods and droughts, like the river basins and coastal plains. Human activities have fragmented and increased the vulnerability of ecosystems, which limit both, their natural adaptation and the effectiveness of the measures adopted. Adaptation means to carry out the necessary modifications for society to adapt to new climatic conditions in order to reduce their vulnerability to climate change. Adaptive capacity is the ability of a system to adjust to climate change (including climate variability and extremes) and to moderate potential damages, to take advantage of opportunities or face the consequences. Adaptation reduces the adverse impacts of climate change and enhance beneficial impacts, but will not prevent substantial cost that are produced by all damages. The performances require adaptation actions. These are defined and implemented at national, regional or local levels since many of the impacts and vulnerabilities depend on the particular economic, geographic and social circumstances of each country or region. We will present some adaptation strategies at national and local level and revise some cases of its implementation in several vulnerable areas. However, adaptation to climate change must be closely related to mitigation policies because the degree of change planned in different climatic variables is a function of the concentration levels that are achieved

Sequential causal inference: Application to randomized trials of adaptive treatment strategies

PubMed Central

Dawson, Ree; Lavori, Philip W.

2009-01-01

SUMMARY Clinical trials that randomize subjects to decision algorithms, which adapt treatments over time according to individual response, have gained considerable interest as investigators seek designs that directly inform clinical decision making. We consider designs in which subjects are randomized sequentially at decision points, among adaptive treatment options under evaluation. We present a sequential method to estimate the comparative effects of the randomized adaptive treatments, which are formalized as adaptive treatment strategies. Our causal estimators are derived using Bayesian predictive inference. We use analytical and empirical calculations to compare the predictive estimators to (i) the ‘standard’ approach that allocates the sequentially obtained data to separate strategy-specific groups as would arise from randomizing subjects at baseline; (ii) the semi-parametric approach of marginal mean models that, under appropriate experimental conditions, provides the same sequential estimator of causal differences as the proposed approach. Simulation studies demonstrate that sequential causal inference offers substantial efficiency gains over the standard approach to comparing treatments, because the predictive estimators can take advantage of the monotone structure of shared data among adaptive strategies. We further demonstrate that the semi-parametric asymptotic variances, which are marginal ‘one-step’ estimators, may exhibit significant bias, in contrast to the predictive variances. We show that the conditions under which the sequential method is attractive relative to the other two approaches are those most likely to occur in real studies. PMID:17914714

Paradoxical cardiovascular effects of implementing adaptive emotion regulation strategies in generalized anxiety disorder.

PubMed

Aldao, Amelia; Mennin, Douglas S

2012-02-01

Recent models of generalized anxiety disorder (GAD) have expanded on Borkovec's avoidance theory by delineating emotion regulation deficits associated with the excessive worry characteristic of this disorder (see Behar, DiMarco, Hekler, Mohlman, & Staples, 2009). However, it has been difficult to determine whether emotion regulation is simply a useful heuristic for the avoidant properties of worry or an important extension to conceptualizations of GAD. Some of this difficulty may arise from a focus on purported maladaptive regulation strategies, which may be confounded with symptomatic distress components of the disorder (such as worry). We examined the implementation of adaptive regulation strategies by participants with and without a diagnosis of GAD while watching emotion-eliciting film clips. In a between-subjects design, participants were randomly assigned to accept, reappraise, or were not given specific regulation instructions. Implementation of adaptive regulation strategies produced differential effects in the physiological (but not subjective) domain across diagnostic groups. Whereas participants with GAD demonstrated lower cardiac flexibility when implementing adaptive regulation strategies than when not given specific instructions on how to regulate, healthy controls showed the opposite pattern, suggesting they benefited from the use of adaptive regulation strategies. We discuss the implications of these findings for the delineation of emotion regulation deficits in psychopathology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Role of environmental variability in the evolution of life history strategies.

PubMed

Hastings, A; Caswell, H

1979-09-01

We reexamine the role of environmental variability in the evolution of life history strategies. We show that normally distributed deviations in the quality of the environment should lead to normally distributed deviations in the logarithm of year-to-year survival probabilities, which leads to interesting consequences for the evolution of annual and perennial strategies and reproductive effort. We also examine the effects of using differing criteria to determine the outcome of selection. Some predictions of previous theory are reversed, allowing distinctions between r and K theory and a theory based on variability. However, these distinctions require information about both the environment and the selection process not required by current theory.

On the adaptivity and complexity embedded into differential evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman

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 performedmore » 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.« less

Cycles of adaptive strategies over the life course.

PubMed

Cooper, Margaret; Bigby, Christine

2014-01-01

An increasing number of Australia's ageing population are aging with long-term physical impairments. This study explored the life experiences of this group using a qualitative approach. In-depth interviews were conducted with 10 disabled Victorians, aged between 51 and 84 years, and an inductive thematic analysis undertaken. A relationship was found between the adaptive strategies that participants developed as they moved through life phases and the impairment stages. The implications of the emergence of a cyclical process of adaptation across the life course. and particularly in respect of aging, delivery of aged-care services and social workers in this sector are discussed.

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

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.

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution.

PubMed

Peabody, George; Winkler, James; Fountain, Weston; Castro, David A; Leiva-Aravena, Enzo; Kao, Katy C

2016-11-15

Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution

PubMed Central

Peabody, George; Winkler, James; Fountain, Weston; Castro, David A.; Leiva-Aravena, Enzo

2016-01-01

ABSTRACT Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. PMID:27613685

An adaptive deep Q-learning strategy for handwritten digit recognition.

PubMed

Qiao, Junfei; Wang, Gongming; Li, Wenjing; Chen, Min

2018-02-22

Handwritten digits recognition is a challenging problem in recent years. Although many deep learning-based classification algorithms are studied for handwritten digits recognition, the recognition accuracy and running time still need to be further improved. In this paper, an adaptive deep Q-learning strategy is proposed to improve accuracy and shorten running time for handwritten digit recognition. The adaptive deep Q-learning strategy combines the feature-extracting capability of deep learning and the decision-making of reinforcement learning to form an adaptive Q-learning deep belief network (Q-ADBN). First, Q-ADBN extracts the features of original images using an adaptive deep auto-encoder (ADAE), and the extracted features are considered as the current states of Q-learning algorithm. Second, Q-ADBN receives Q-function (reward signal) during recognition of the current states, and the final handwritten digits recognition is implemented by maximizing the Q-function using Q-learning algorithm. Finally, experimental results from the well-known MNIST dataset show that the proposed Q-ADBN has a superiority to other similar methods in terms of accuracy and running time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes

PubMed Central

Ponce de León, Inés; Montesano, Marcos

2017-01-01

Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens. PMID:28360923

Cuckoos versus hosts in insects and birds: adaptations, counter-adaptations and outcomes.

PubMed

Kilner, Rebecca M; Langmore, Naomi E

2011-11-01

arms race but depends more on whether hosts or parasites control the co-evolutionary trajectory: tolerance is an outcome that parasites inflict on hosts, whereas the other three outcomes are more dependent on properties intrinsic to the host species. Finally, our review highlights considerable interspecific variation in the complexity and depth of host defence portfolios. Whether this variation is adaptive or merely reflects evolutionary lag is unclear. We propose an adaptive explanation, which centres on the relative strength of two opposing processes: strategy-facilitation, in which one line of host defence promotes the evolution of another form of resistance, and strategy-blocking, in which one line of defence may relax selection on another so completely that it causes it to decay. We suggest that when strategy-facilitation outweighs strategy-blocking, hosts will possess complex defence portfolios and we identify selective conditions in which this is likely to be the case. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

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

PubMed

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.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

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

Evaluation of delivered dose for a clinical daily adaptive plan selection strategy for bladder cancer radiotherapy.

PubMed

Lutkenhaus, Lotte J; Visser, Jorrit; de Jong, Rianne; Hulshof, Maarten C C M; Bel, Arjan

2015-07-01

To account for variable bladder size during bladder cancer radiotherapy, a daily plan selection strategy was implemented. The aim of this study was to calculate the actually delivered dose using an adaptive strategy, compared to a non-adaptive approach. Ten patients were treated to the bladder and lymph nodes with an adaptive full bladder strategy. Interpolated delineations of bladder and tumor on a full and empty bladder CT scan resulted in five PTVs for which VMAT plans were created. Daily cone beam CT (CBCT) scans were used for plan selection. Bowel, rectum and target volumes were delineated on these CBCTs, and delivered dose for these was calculated using both the adaptive plan, and a non-adaptive plan. Target coverage for lymph nodes improved using an adaptive strategy. The full bladder strategy spared the healthy part of the bladder from a high dose. Average bowel cavity V30Gy and V40Gy significantly reduced with 60 and 69ml, respectively (p<0.01). Other parameters for bowel and rectum remained unchanged. Daily plan selection compared to a non-adaptive strategy yielded similar bladder coverage and improved coverage for lymph nodes, with a significant reduction in bowel cavity V30Gy and V40Gy only, while other sparing was limited. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

PubMed

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

2015-07-28

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

ADAPT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reynolds, John; Jankovsky, Zachary; Metzroth, Kyle G

2018-04-04

The purpose of the ADAPT code is to generate Dynamic Event Trees (DET) using a user specified set of simulators. ADAPT can utilize any simulation tool which meets a minimal set of requirements. ADAPT is based on the concept of DET which uses explicit modeling of the deterministic dynamic processes that take place during a nuclear reactor plant system (or other complex system) evolution along with stochastic modeling. When DET are used to model various aspects of Probabilistic Risk Assessment (PRA), all accident progression scenarios starting from an initiating event are considered simultaneously. The DET branching occurs at user specifiedmore » times and/or when an action is required by the system and/or the operator. These outcomes then decide how the dynamic system variables will evolve in time for each DET branch. Since two different outcomes at a DET branching may lead to completely different paths for system evolution, the next branching for these paths may occur not only at separate times, but can be based on different branching criteria. The computational infrastructure allows for flexibility in ADAPT to link with different system simulation codes, parallel processing of the scenarios under consideration, on-line scenario management (initiation as well as termination), analysis of results, and user friendly graphical capabilities. The ADAPT system is designed for a distributed computing environment; the scheduler can track multiple concurrent branches simultaneously. The scheduler is modularized so that the DET branching strategy can be modified (e.g. biasing towards the worst-case scenario/event). Independent database systems store data from the simulation tasks and the DET structure so that the event tree can be constructed and analyzed later. ADAPT is provided with a user-friendly client which can easily sort through and display the results of an experiment, precluding the need for the user to manually inspect individual simulator runs.« less

Acculturation Strategies, Social Support, and Cross-Cultural Adaptation: A Mediation Analysis

ERIC Educational Resources Information Center

Ng, Ting Kin; Tsang, Kwok Kuen; Lian, Yi

2013-01-01

Previous acculturation research has established the influences of acculturation strategies and social support on cross-cultural adaptation. The present study attempted to elaborate these direct associations by proposing that social support and the use of the integration and marginalization strategies might affect psychological adaptation…

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

PubMed

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.

Adaptive evolution of baker's yeast in a dough‐like environment enhances freeze and salinity tolerance

PubMed Central

Aguilera, Jaime; Andreu, Pasqual; Randez‐Gil, Francisca; Prieto, Jose Antonio

2010-01-01

Summary We used adaptive evolution to improve freeze tolerance of industrial baker's yeast. Our hypothesis was that adaptation to low temperature is accompanied by enhanced resistance of yeast to freezing. Based on this hypothesis, yeast was propagated in a flour‐free liquid dough model system, which contained sorbitol and NaCl, by successive batch refreshments maintained constantly at 12°C over at least 200 generations. Relative to the parental population, the maximal growth rate (µmax) under the restrictive conditions, increased gradually over the time course of the experiment. This increase was accompanied by enhanced freeze tolerance. However, these changes were not the consequence of genetic adaptation to low temperature, a fact that was confirmed by prolonged selection of yeast cells in YPD at 12°C. Instead, the experimental populations showed a progressive increase in NaCl tolerance. This phenotype was likely achieved at the expense of others traits, since evolved cells showed a ploidy reduction, a defect in the glucose derepression mechanism and a loss in their ability to utilize gluconeogenic carbon sources. We discuss the genetic flexibility of S. cerevisiae in terms of adaptation to the multiple constraints of the experimental design applied to drive adaptive evolution and the technologically advantageous phenotype of the evolved population. PMID:21255321

The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

PubMed

Moore, Jason R; Varricchio, David J

2016-01-01

Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

Ten Adaptive Strategies for Family and Work Balance: Advice from Successful Families.

ERIC Educational Resources Information Center

Haddock, Shelley A.; Zimmerman, Toni Schindler; Ziemba, Scott J.; Current, Lisa R.

2001-01-01

Investigated adaptive strategies of middle class, dual earner couples (N=47) with children that are successfully managing family and work. Guided by grounded-theory methodology, analysis of interview data revealed these successful couples structured their lives around 10 major strategies. Each strategy is defined and illustrated through the…

Adapting qualitative research strategies to technology savvy adolescents.

PubMed

Mason, Deanna Marie; Ide, Bette

2014-05-01

To adapt research strategies involving adolescents in a grounded theory qualitative research study by conducting email rather than face-to-face interviews. Adolescent culture relies heavily on text-based communication and teens prefer interactions mediated through technology. Traditional qualitative research strategies need to be rethought when working with adolescents. Adapting interviewing strategies to electronic environments is timely and relevant for researching adolescents. Twenty three adolescents (aged 16-21) were interviewed by email. A letter of invitation was distributed. Potential participants emailed the researcher to convey interest in participating. If the inclusion criteria were met, email interviews were initiated. Participants controlled the interviews through their rate of response to interview questions. A grounded theory methodology was employed. Initial contact with participants reiterated confidentiality and the ability to withdraw from the study at any time. Interviews began with the collection of demographic information and a broad opening based on a semi-structured interview guide. All data were permissible, including text, photos, music, videos or outside media, for example YouTube. The participant was allowed to give direction to the interview after initial questions were posed. Email interviews continued until saturation was reached in the data. Participants were enthusiastic about email interviewing. Attrition did not occur. Email interviewing gave participants more control over the research, decreased power differentials between the adolescent and researcher, allowed the study to be adapted to cultural, linguistic and developmental needs, and maintained confidentiality. As participants said that email communication was slow and they preferred instant messaging, replication in faster-paced media is recommended. Repetition in face-to-face settings is warranted to evaluate how technology may have influenced the findings. Implications for

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

PubMed

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.

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

PubMed

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.

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

PubMed

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.

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

PubMed Central

Hope, Elyse A.; Amorosi, Clara J.; Miller, Aaron W.; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J.

2017-01-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. PMID:28450459

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

PubMed

Hope, Elyse A; Amorosi, Clara J; Miller, Aaron W; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J

2017-06-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1 , and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1 , which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. Copyright © 2017 Hope et al.

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

PubMed Central

2011-01-01

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 evolution of this

THE EVOLUTION OF BET-HEDGING ADAPTATIONS TO RARE SCENARIOS

PubMed Central

King, Oliver D.

2007-01-01

When faced with a variable environment, organisms may switch between different strategies according to some probabilistic rule. In an infinite population, evolution is expected to favor the rule that maximizes geometric mean fitness. If some environments are encountered only rarely, selection may not be strong enough for optimal switching probabilities to evolve. Here we calculate the evolution of switching probabilities in a finite population by analyzing fixation probabilities of alleles specifying switching rules. We calculate the conditions required for the evolution of phenotypic switching as a form of bet-hedging as a function of the population size N, the rateθ at which a rare environment is encountered, and the selective advantage s associated with switching in the rare environment. We consider a simplified model in which environmental switching and phenotypic switching are one-way processes, and mutation is symmetric and rare with respect to the timescale of fixation events. In this case, the approximate requirements for bet-hedging to be favored by a ratio of at least R are that sN > log(R) and θN>R. PMID:17915273

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

NASA Astrophysics Data System (ADS)

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.

Using a Social Justice and Health Framework to Assess European Climate Change Adaptation Strategies

PubMed Central

Boeckmann, Melanie; Zeeb, Hajo

2014-01-01

Climate change puts pressure on existing health vulnerabilities through higher frequency of extreme weather events, changes in disease vector distribution or exacerbated air pollution. Climate change adaptation policies may hold potential to reduce societal inequities. We assessed the role of public health and social justice in European climate change adaptation using a three-fold approach: a document analysis, a critical discourse analysis of a subgroup of strategies, and a ranking of strategies against our social justice framework. The ranking approach favored planning that includes various adaptation types, social issues and infrastructure changes. Themes on values identified in the five subgroup documents showed that risks are perceived as contradictory, technology is viewed as savior, responsibilities need to be negotiated, and social justice is advocated by only a few countries. Of 21 strategy documents assessed overall, those from Austria, England and Sweden received the highest scores in the ranking. Our qualitative assessment showed that in European adaptation planning, progress could still be made through community involvement into adaptation decisions, consistent consideration of social and demographic determinants, and a stronger link between infrastructural adaptation and the health sector. Overall, a social justice framework can serve as an evaluation guideline for adaptation policy documents. PMID:25464133

Using a social justice and health framework to assess European climate change adaptation strategies.

PubMed

Boeckmann, Melanie; Zeeb, Hajo

2014-11-28

Climate change puts pressure on existing health vulnerabilities through higher frequency of extreme weather events, changes in disease vector distribution or exacerbated air pollution. Climate change adaptation policies may hold potential to reduce societal inequities. We assessed the role of public health and social justice in European climate change adaptation using a three-fold approach: a document analysis, a critical discourse analysis of a subgroup of strategies, and a ranking of strategies against our social justice framework. The ranking approach favored planning that includes various adaptation types, social issues and infrastructure changes. Themes on values identified in the five subgroup documents showed that risks are perceived as contradictory, technology is viewed as savior, responsibilities need to be negotiated, and social justice is advocated by only a few countries. Of 21 strategy documents assessed overall, those from Austria, England and Sweden received the highest scores in the ranking. Our qualitative assessment showed that in European adaptation planning, progress could still be made through community involvement into adaptation decisions, consistent consideration of social and demographic determinants, and a stronger link between infrastructural adaptation and the health sector. Overall, a social justice framework can serve as an evaluation guideline for adaptation policy documents.

An experimental comparison of two adaptation strategies in an adaptive-walls wind-tunnel

NASA Astrophysics Data System (ADS)

Russo, G. P.; Zuppardi, G.; Basciani, M.

1995-08-01

In the present work an experimental comparison is made between two adaptation strategies: the Judd's method and the Everhart's method. A NACA 0012 airfoil has been tested at Mach numbers up to 0.4: models with chords up to 200 mm have been tested in a 200 mm × 200 mm test section. The two strategies, though based on different theoretical approaches, show a fairly good agreement as far as c p distribution on the model, lift and drag curves and residual interference are concerned and agree, in terms of lift curve slope and drag coefficient at zero lift, with the McCroskey correlation.

A Structure-Adaptive Hybrid RBF-BP Classifier with an Optimized Learning Strategy

PubMed Central

Wen, Hui; Xie, Weixin; Pei, Jihong

2016-01-01

This paper presents a structure-adaptive hybrid RBF-BP (SAHRBF-BP) classifier with an optimized learning strategy. SAHRBF-BP is composed of a structure-adaptive RBF network and a BP network of cascade, where the number of RBF hidden nodes is adjusted adaptively according to the distribution of sample space, the adaptive RBF network is used for nonlinear kernel mapping and the BP network is used for nonlinear classification. The optimized learning strategy is as follows: firstly, a potential function is introduced into training sample space to adaptively determine the number of initial RBF hidden nodes and node parameters, and a form of heterogeneous samples repulsive force is designed to further optimize each generated RBF hidden node parameters, the optimized structure-adaptive RBF network is used for adaptively nonlinear mapping the sample space; then, according to the number of adaptively generated RBF hidden nodes, the number of subsequent BP input nodes can be determined, and the overall SAHRBF-BP classifier is built up; finally, different training sample sets are used to train the BP network parameters in SAHRBF-BP. Compared with other algorithms applied to different data sets, experiments show the superiority of SAHRBF-BP. Especially on most low dimensional and large number of data sets, the classification performance of SAHRBF-BP outperforms other training SLFNs algorithms. PMID:27792737

A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation, population viability and genetic variation.

PubMed

Gomez-Mestre, Ivan; Jovani, Roger

2013-11-22

An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion.

PubMed

Twyford, Alex D; Friedman, Jannice

2015-06-01

Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

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

PubMed

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.

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

PubMed Central

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

A Climate Change Adaptation Strategy for Management of ...

EPA Pesticide Factsheets

Sea level rise is causing shoreline erosion, increased coastal flooding, and marsh vulnerability to the impact of storms. Coastal marshes provide flood abatement, carbon and nutrient sequestration, water quality maintenance, and habitat for fish, shellfish, and wildlife, including species of concern, such as the saltmarsh sparrow (Ammodramus caudacutus). We present a climate change adaptation strategy (CCAS) adopted by scientific, management, and policy stakeholders for managing coastal marshes and enhancing system resiliency. A common adaptive management approach previously used for restoration projects was modified to identify climate-related vulnerabilities and plan climate change adaptive actions. As an example of implementation of the CCAS, we describe the stakeholder plans and management actions the US Fish and Wildlife Service and partners developed to build coastal resiliency in the Narrow River Estuary, RI, in the aftermath of Superstorm Sandy. When possible, an experimental BACI (before-after, control-impact) design, described as pre- and post-sampling at the impact site and one or more control sites, was incorporated into the climate change adaptation and implementation plans. Specific climate change adaptive actions and monitoring plans are described and include shoreline stabilization, restoring marsh drainage, increasing marsh elevation, and enabling upland marsh migration. The CCAS provides a framework and methodology for successfully managing coa

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

PubMed

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.

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

PubMed Central

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

2014-01-01

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. PMID:25415197

Evolution of active host-attraction strategies in the freshwater mussel tribe Lampsilini (Bivalvia: Unionidae).

PubMed

Zanatta, David T; Murphy, Robert W

2006-10-01

Most freshwater mussels (Bivalvia: Unionoida) require a host, usually a fish, to complete their life cycle. Most species of mussels show adaptations that increase the chances of glochidia larvae contacting a host. We investigated the evolutionary relationships of the freshwater mussel tribe Lampsilini including 49 of the approximately 100 extant species including 21 of the 24 recognized genera. Mitochondrial DNA sequence data (COI, 16S, and ND1) were used to create a molecular phylogeny for these species. Parsimony and Bayesian likelihood topologies revealed that the use of an active lure arose early in the evolution of the Lampsiline mussels. The mantle flap lure appears to have been the first to evolve with other lure types being derived from this condition. Apparently, lures were lost independently in several clades. Hypotheses are discussed as to how some of these lure strategies may have evolved in response to host fish prey preferences.

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

PubMed Central

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

2017-01-01

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

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

PubMed

Verin, Mélissa; Tellier, Aurélien

2018-04-20

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Evolution of individual versus social learning on social networks

PubMed Central

Tamura, Kohei; Kobayashi, Yutaka; Ihara, Yasuo

2015-01-01

A number of studies have investigated the roles played by individual and social learning in cultural phenomena and the relative advantages of the two learning strategies in variable environments. Because social learning involves the acquisition of behaviours from others, its utility depends on the availability of ‘cultural models’ exhibiting adaptive behaviours. This indicates that social networks play an essential role in the evolution of learning. However, possible effects of social structure on the evolution of learning have not been fully explored. Here, we develop a mathematical model to explore the evolutionary dynamics of learning strategies on social networks. We first derive the condition under which social learners (SLs) are selectively favoured over individual learners in a broad range of social network. We then obtain an analytical approximation of the long-term average frequency of SLs in homogeneous networks, from which we specify the condition, in terms of three relatedness measures, for social structure to facilitate the long-term evolution of social learning. Finally, we evaluate our approximation by Monte Carlo simulations in complete graphs, regular random graphs and scale-free networks. We formally show that whether social structure favours the evolution of social learning is determined by the relative magnitudes of two effects of social structure: localization in competition, by which competition between learning strategies is evaded, and localization in cultural transmission, which slows down the spread of adaptive traits. In addition, our estimates of the relatedness measures suggest that social structure disfavours the evolution of social learning when selection is weak. PMID:25631568

More efficient evolutionary strategies for model calibration with watershed model for demonstration

NASA Astrophysics Data System (ADS)

Baggett, J. S.; Skahill, B. E.

2008-12-01

Evolutionary strategies allow automatic calibration of more complex models than traditional gradient based approaches, but they are more computationally intensive. We present several efficiency enhancements for evolution strategies, many of which are not new, but when combined have been shown to dramatically decrease the number of model runs required for calibration of synthetic problems. To reduce the number of expensive model runs we employ a surrogate objective function for an adaptively determined fraction of the population at each generation (Kern et al., 2006). We demonstrate improvements to the adaptive ranking strategy that increase its efficiency while sacrificing little reliability and further reduce the number of model runs required in densely sampled parts of parameter space. Furthermore, we include a gradient individual in each generation that is usually not selected when the search is in a global phase or when the derivatives are poorly approximated, but when selected near a smooth local minimum can dramatically increase convergence speed (Tahk et al., 2007). Finally, the selection of the gradient individual is used to adapt the size of the population near local minima. We show, by incorporating these enhancements into the Covariance Matrix Adaption Evolution Strategy (CMAES; Hansen, 2006), that their synergetic effect is greater than their individual parts. This hybrid evolutionary strategy exploits smooth structure when it is present but degrades to an ordinary evolutionary strategy, at worst, if smoothness is not present. Calibration of 2D-3D synthetic models with the modified CMAES requires approximately 10%-25% of the model runs of ordinary CMAES. Preliminary demonstration of this hybrid strategy will be shown for watershed model calibration problems. Hansen, N. (2006). The CMA Evolution Strategy: A Comparing Review. In J.A. Lozano, P. Larrañga, I. Inza and E. Bengoetxea (Eds.). Towards a new evolutionary computation. Advances in estimation of

Adapting to Adaptations: Behavioural Strategies that are Robust to Mutations and Other Organisational-Transformations

PubMed Central

Egbert, Matthew D.; Pérez-Mercader, Juan

2016-01-01

Genetic mutations, infection by parasites or symbionts, and other events can transform the way that an organism’s internal state changes in response to a given environment. We use a minimalistic computational model to support an argument that by behaving “interoceptively,” i.e. responding to internal state rather than to the environment, organisms can be robust to these organisational-transformations. We suggest that the robustness of interoceptive behaviour is due, in part, to the asymmetrical relationship between an organism and its environment, where the latter more substantially influences the former than vice versa. This relationship means that interoceptive behaviour can respond to the environment, the internal state and the interaction between the two, while exteroceptive behaviour can only respond to the environment. We discuss the possibilities that (i) interoceptive behaviour may play an important role of facilitating adaptive evolution (especially in the early evolution of primitive life) and (ii) interoceptive mechanisms could prove useful in efforts to create more robust synthetic life-forms. PMID:26743579

Battery parameterisation based on differential evolution via a boundary evolution strategy

NASA Astrophysics Data System (ADS)

Yang, Guangya

2014-01-01

Attention has been given to the battery modelling in the electric engineering field following the current development of renewable energy and electrification of transportation. The establishment of the equivalent circuit model of the battery requires data preparation and parameterisation. Besides, as the equivalent circuit model is an abstract map of the battery electric characteristics, the determination of the possible ranges of parameters can be a challenging task. In this paper, an efficient yet easy to implement method is proposed to parameterise the equivalent circuit model of batteries utilising the advances of evolutionary algorithms (EAs). Differential evolution (DE) is selected and modified to parameterise an equivalent circuit model of lithium-ion batteries. A boundary evolution strategy (BES) is developed and incorporated into the DE to update the parameter boundaries during the parameterisation. The method can parameterise the model without extensive data preparation. In addition, the approach can also estimate the initial SOC and the available capacity. The efficiency of the approach is verified through two battery packs, one is an 8-cell battery module and one from an electrical vehicle.

Computational model for behavior shaping as an adaptive health intervention strategy.

PubMed

Berardi, Vincent; Carretero-González, Ricardo; Klepeis, Neil E; Ghanipoor Machiani, Sahar; Jahangiri, Arash; Bellettiere, John; Hovell, Melbourne

2018-03-01

Adaptive behavioral interventions that automatically adjust in real-time to participants' changing behavior, environmental contexts, and individual history are becoming more feasible as the use of real-time sensing technology expands. This development is expected to improve shortcomings associated with traditional behavioral interventions, such as the reliance on imprecise intervention procedures and limited/short-lived effects. JITAI adaptation strategies often lack a theoretical foundation. Increasing the theoretical fidelity of a trial has been shown to increase effectiveness. This research explores the use of shaping, a well-known process from behavioral theory for engendering or maintaining a target behavior, as a JITAI adaptation strategy. A computational model of behavior dynamics and operant conditioning was modified to incorporate the construct of behavior shaping by adding the ability to vary, over time, the range of behaviors that were reinforced when emitted. Digital experiments were performed with this updated model for a range of parameters in order to identify the behavior shaping features that optimally generated target behavior. Narrowing the range of reinforced behaviors continuously in time led to better outcomes compared with a discrete narrowing of the reinforcement window. Rapid narrowing followed by more moderate decreases in window size was more effective in generating target behavior than the inverse scenario. The computational shaping model represents an effective tool for investigating JITAI adaptation strategies. Model parameters must now be translated from the digital domain to real-world experiments so that model findings can be validated.

Size variation, growth strategies, and the evolution of modularity in the mammalian skull.

PubMed

Porto, Arthur; Shirai, Leila Teruko; de Oliveira, Felipe Bandoni; Marroig, Gabriel

2013-11-01

Allometry is a major determinant of within-population patterns of association among traits and, therefore, a major component of morphological integration studies. Even so, the influence of size variation over evolutionary change has been largely unappreciated. Here, we explore the interplay between allometric size variation, modularity, and life-history strategies in the skull from representatives of 35 mammalian families. We start by removing size variation from within-species data and analyzing its influence on integration magnitudes, modularity patterns, and responses to selection. We also carry out a simulation in which we artificially alter the influence of size variation in within-taxa matrices. Finally, we explore the relationship between size variation and different growth strategies. We demonstrate that a large portion of the evolution of modularity in the mammalian skull is associated to the evolution of growth strategies. Lineages with highly altricial neonates have adult variation patterns dominated by size variation, leading to high correlations among traits regardless of any underlying modular process and impacting directly their potential to respond to selection. Greater influence of size variation is associated to larger intermodule correlations, less individualized modules, and less flexible responses to natural selection. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

2016-09-01

A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be restricted to uniform time scales associated with the game interaction and strategy adaption evolution. In this study, we remove this restricting assumption by dividing the population into fast and slow groups according to the players' strategy updating frequencies and investigate how different strategy compositions of one group influence the evolutionary outcome of the other's fixation probabilities of strategies within its own group. Analytical analysis and numerical calculations are performed to study the evolutionary dynamics of strategies in typical classes of two-player games (prisoner's dilemma game, snowdrift game, and stag-hunt game). The introduction of the heterogeneity in strategy-update time scales leads to substantial changes in the evolution dynamics of strategies. We provide an approximation formula for the fixation probability of mutant types in finite populations and study the outcome of strategy evolution under the weak selection. We find that although heterogeneity in time scales makes the collective evolutionary dynamics more complicated, the possible long-run evolutionary outcome can be effectively predicted under technical assumptions when knowing the population composition and payoff parameters.

Adapting Strategies of Effective Instruction for Culturally Diverse Preschoolers

ERIC Educational Resources Information Center

Yamauchi, Lois A.; Im, Seongah; Schonleber, Nanette S.

2012-01-01

This article describes collaboration between preschool and university educators focused on adapting the Center for Research on Education, Diversity, and Excellence (CREDE) standards for Effective Pedagogy for use in early childhood (EC) settings. The CREDE standards are strategies of best practices for culturally diverse K-12 students. Teachers…

Simulation of the evolution of root water foraging strategies in dry and shallow soils

PubMed Central

Renton, Michael; Poot, Pieter

2014-01-01

Background and Aims The dynamic structural development of plants can be seen as a strategy for exploiting the limited resources available within their environment, and we would expect that evolution would lead to efficient strategies that reduce costs while maximizing resource acquisition. In particular, perennial species endemic to habitats with shallow soils in seasonally dry environments have been shown to have a specialized root system morphology that may enhance access to water resources in the underlying rock. This study aimed to explore these hypotheses by applying evolutionary algorithms to a functional–structural root growth model. Methods A simulation model of a plant's root system was developed, which represents the dynamics of water uptake and structural growth. The model is simple enough for evolutionary optimization to be computationally feasible, yet flexible enough to allow a range of structural development strategies to be explored. The model was combined with an evolutionary algorithm in order to investigate a case study habitat with a highly heterogeneous distribution of resources, both spatially and temporally – the situation of perennial plants occurring on shallow soils in seasonally dry environments. Evolution was simulated under two contrasting fitness criteria: (1) the ability to find wet cracks in underlying rock, and (2) maximizing above-ground biomass. Key Results The novel approach successfully resulted in the evolution of more efficient structural development strategies for both fitness criteria. Different rooting strategies evolved when different criteria were applied, and each evolved strategy made ecological sense in terms of the corresponding fitness criterion. Evolution selected for root system morphologies which matched those of real species from corresponding habitats. Conclusions Specialized root morphology with deeper rather than shallower lateral branching enhances access to water resources in underlying rock. More

Simulation of the evolution of root water foraging strategies in dry and shallow soils.

PubMed

Renton, Michael; Poot, Pieter

2014-09-01

The dynamic structural development of plants can be seen as a strategy for exploiting the limited resources available within their environment, and we would expect that evolution would lead to efficient strategies that reduce costs while maximizing resource acquisition. In particular, perennial species endemic to habitats with shallow soils in seasonally dry environments have been shown to have a specialized root system morphology that may enhance access to water resources in the underlying rock. This study aimed to explore these hypotheses by applying evolutionary algorithms to a functional-structural root growth model. A simulation model of a plant's root system was developed, which represents the dynamics of water uptake and structural growth. The model is simple enough for evolutionary optimization to be computationally feasible, yet flexible enough to allow a range of structural development strategies to be explored. The model was combined with an evolutionary algorithm in order to investigate a case study habitat with a highly heterogeneous distribution of resources, both spatially and temporally--the situation of perennial plants occurring on shallow soils in seasonally dry environments. Evolution was simulated under two contrasting fitness criteria: (1) the ability to find wet cracks in underlying rock, and (2) maximizing above-ground biomass. The novel approach successfully resulted in the evolution of more efficient structural development strategies for both fitness criteria. Different rooting strategies evolved when different criteria were applied, and each evolved strategy made ecological sense in terms of the corresponding fitness criterion. Evolution selected for root system morphologies which matched those of real species from corresponding habitats. Specialized root morphology with deeper rather than shallower lateral branching enhances access to water resources in underlying rock. More generally, the approach provides insights into both

Adaptive evolution of centromere proteins in plants and animals.

PubMed

Talbert, Paul B; Bryson, Terri D; Henikoff, Steven

2004-01-01

Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif). Whereas we find no evidence that mammalian CenH3 (CENP-A) has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p) is under negative selection. CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi.

Determinants of climate change adaptation strategies used by fish farmers in Epe Local Government Area of Lagos State, Nigeria.

PubMed

Arimi, Kayode S

2014-05-01

Undesirable impacts of climate change have been a common occurrence that has made fish farmers in developing countries adopt some climate-change adaptation strategies. However, little is known about determinants of climate-change adaptation strategies used by these fish farmers. This study, therefore, articulates novelties on adaptation to climate change, as well ascertains determinants of adaptation strategies used by fish farmers in Epe, Lagos State, Nigeria. Climate change adaptation strategies mostly used by fish farmers include frequent seeking for early warning information about climate change (76.7%) and avoidance of areas susceptible to flooding (60.0%). Climate-change adaptation strategies used by fish farmers were significantly influenced by access to early warning information (β = 7.21), knowledge of farmers about climate change adaptation strategies (β = 8.86), access to capital (β = 28.25), and participation in workshop and conferences (β = 37.19) but were reduced by number of fish stocking (β = -2.06). The adaptation strategies used by fish farmers were autonomous and mostly determined by the access to credit facilities and information. Development policy should focus on carbon capture and storage technology in order to reduce adverse impacts of climate change, as well as making early warning information on climate change available to fish farmers. These will enhance adaptation to climate change. © 2013 Society of Chemical Industry.

Chromosome rearrangements and the evolution of genome structuring and adaptability.

PubMed

Crombach, Anton; Hogeweg, Paulien

2007-05-01

Eukaryotes appear to evolve by micro and macro rearrangements. This is observed not only for long-term evolutionary adaptation, but also in short-term experimental evolution of yeast, Saccharomyces cerevisiae. Moreover, based on these and other experiments it has been postulated that repeat elements, retroposons for example, mediate such events. We study an evolutionary model in which genomes with retroposons and a breaking/repair mechanism are subjected to a changing environment. We show that retroposon-mediated rearrangements can be a beneficial mutational operator for short-term adaptations to a new environment. But simply having the ability of rearranging chromosomes does not imply an advantage over genomes in which only single-gene insertions and deletions occur. Instead, a structuring of the genome is needed: genes that need to be amplified (or deleted) in a new environment have to cluster. We show that genomes hosting retroposons, starting with a random order of genes, will in the long run become organized, which enables (fast) rearrangement-based adaptations to the environment. In other words, our model provides a "proof of principle" that genomes can structure themselves in order to increase the beneficial effect of chromosome rearrangements.

Are winter and summer dormancy symmetrical seasonal adaptive strategies? The case of temperate herbaceous perennials

PubMed Central

Gillespie, Lauren M.; Volaire, Florence A.

2017-01-01

Background Dormancy in higher plants is an adaptive response enabling plant survival during the harshest seasons and has been more explored in woody species than in herbaceous species. Nevertheless, winter and summer shoot meristem dormancy are adaptive strategies that could play a major role in enhancing seasonal stress tolerance and resilience of widespread herbaceous plant communities. Scope This review outlines the symmetrical aspects of winter and summer dormancy in order to better understand plant adaptation to severe stress, and highlight research priorities in a changing climate. Seasonal dormancy is a good model to explore the growth–stress survival trade-off and unravel the relationships between growth potential and stress hardiness. Although photoperiod and temperature are known to play a crucial, though reversed, role in the induction and release of both types of dormancy, the thresholds and combined effects of these environmental factors remain to be identified. The biochemical compounds involved in induction or release in winter dormancy (abscisic acid, ethylene, sugars, cytokinins and gibberellins) could be a priority research focus for summer dormancy. To address these research priorities, herbaceous species, being more tractable than woody species, are excellent model plants for which both summer and winter dormancy have been clearly identified. Conclusions Summer and winter dormancy, although responding to inverse conditions, share many characteristics. This analogous nature can facilitate research as well as lead to insight into plant adaptations to extreme conditions and the evolution of phenological patterns of species and communities under climate change. The development of phenotypes showing reduced winter and/or enhanced summer dormancy may be expected and could improve adaptation to less predictable environmental stresses correlated with future climates. To this end, it is suggested to explore the inter- and intraspecific genotypic

Adaptive Control Strategies for Interlimb Coordination in Legged Robots: A Review

PubMed Central

Aoi, Shinya; Manoonpong, Poramate; Ambe, Yuichi; Matsuno, Fumitoshi; Wörgötter, Florentin

2017-01-01

Walking animals produce adaptive interlimb coordination during locomotion in accordance with their situation. Interlimb coordination is generated through the dynamic interactions of the neural system, the musculoskeletal system, and the environment, although the underlying mechanisms remain unclear. Recently, investigations of the adaptation mechanisms of living beings have attracted attention, and bio-inspired control systems based on neurophysiological findings regarding sensorimotor interactions are being developed for legged robots. In this review, we introduce adaptive interlimb coordination for legged robots induced by various factors (locomotion speed, environmental situation, body properties, and task). In addition, we show characteristic properties of adaptive interlimb coordination, such as gait hysteresis and different time-scale adaptations. We also discuss the underlying mechanisms and control strategies to achieve adaptive interlimb coordination and the design principle for the control system of legged robots. PMID:28878645

Risk evaluation mitigation strategies: the evolution of risk management policy.

PubMed

Hollingsworth, Kristen; Toscani, Michael

2013-04-01

The United States Food and Drug Administration (FDA) has the primary regulatory responsibility to ensure that medications are safe and effective both prior to drug approval and while the medication is being actively marketed by manufacturers. The responsibility for safe medications prior to marketing was signed into law in 1938 under the Federal Food, Drug, and Cosmetic Act; however, a significant risk management evolution has taken place since 1938. Additional federal rules, entitled the Food and Drug Administration Amendments Act, were established in 2007 and extended the government's oversight through the addition of a Risk Evaluation and Mitigation Strategy (REMS) for certain drugs. REMS is a mandated strategy to manage a known or potentially serious risk associated with a medication or biological product. Reasons for this extension of oversight were driven primarily by the FDA's movement to ensure that patients and providers are better informed of drug therapies and their specific benefits and risks prior to initiation. This article provides an historical perspective of the evolution of medication risk management policy and includes a review of REMS programs, an assessment of the positive and negative aspects of REMS, and provides suggestions for planning and measuring outcomes. In particular, this publication presents an overview of the evolution of the REMS program and its implications.

Climate change impacts and adaptive strategies: lessons from the grapevine.

PubMed

Mosedale, Jonathan R; Abernethy, Kirsten E; Smart, Richard E; Wilson, Robert J; Maclean, Ilya M D

2016-11-01

The cultivation of grapevines for winemaking, known as viticulture, is widely cited as a climate-sensitive agricultural system that has been used as an indicator of both historic and contemporary climate change. Numerous studies have questioned the viability of major viticulture regions under future climate projections. We review the methods used to study the impacts of climate change on viticulture in the light of what is known about the effects of climate and weather on the yields and quality of vineyard harvests. Many potential impacts of climate change on viticulture, particularly those associated with a change in climate variability or seasonal weather patterns, are rarely captured. Key biophysical characteristics of viticulture are often unaccounted for, including the variability of grapevine phenology and the exploitation of microclimatic niches that permit successful cultivation under suboptimal macroclimatic conditions. We consider how these same biophysical characteristics permit a variety of strategies by which viticulture can adapt to changing climatic conditions. The ability to realize these strategies, however, is affected by uneven exposure to risks across the winemaking sector, and the evolving capacity for decision-making within and across organizational boundaries. The role grape provenance plays in shaping perceptions of wine value and quality illustrates how conflicts of interest influence decisions about adaptive strategies within the industry. We conclude by considering what lessons can be taken from viticulture for studies of climate change impacts and the capacity for adaptation in other agricultural and natural systems. © 2016 John Wiley & Sons Ltd.

An innovative cross-sectoral method for implementation of trade-off adaptation strategy assessment under climate change

NASA Astrophysics Data System (ADS)

Tsao, Jung-Hsuan; Tung, Ching-Pin; Liu, Tzu-Ming

2014-05-01

Climate change will increase sharp risks to the water and food supply in coming decades. Although impact assessment and adaptation evaluation has been discussed a lot in recent years, the importance of adaptation implement should not be ignored. In Taiwan, and elsewhere, fallow is an option of adaptation strategy under climate change. Fallow would improve the water scarcity of domestic use, but the food security might be threatened. The trade-off effects of adaptation actions are just like the side effects of medicine which cannot be avoided. Thus, managing water resources with an integrated approach will be urgent. This study aims to establish a cross-sectoral framework for implementation the trade-off adaptation strategy. Not only fallow, but also other trade-off strategy like increasing the percentage of national grain self-sufficiency would be analyzed by a rational decision process. The recent percentage of grain self-sufficiency in Taiwan is around 32, which was decreasing from 53 thirty years ago. Yet, the goal of increasing grain self-sufficiency means much more water must be used in agriculture. In that way, domestic users may face the water shortage situation. Considering the conflicts between water supply and food security, the concepts from integrative negotiation are appropriate to apply. The implementation of trade-off adaptation strategies needs to start by quantifying the utility of water supply and food security were be quantified. Next, each side's bottom line can be found by BATNA (Best Alternative to a Negotiated Agreement) and ZOPA (Zone of Possible Agreement). ZOPA provides the entire possible outcomes, and BATNA ensures the efficiency of adaptation actions by moving along with Pareto frontier. Therefore, the optimal percentage of fallow and grain self-sufficiency can be determined. Furthermore, BATNA also provides the pathway step by step which can be a guideline of adaptation strategies. This framework allows analysts and stakeholder to

Ten adaptive strategies for family and work balance: advice from successful families.

PubMed

Haddock, S A; Zimmerman, T S; Ziemba, S J; Current, L R

2001-10-01

Despite negative media images and social dynamics insensitive to the lives of many dual-career couples, research shows that these families are largely healthy and thriving. In this study, we investigated the adaptive strategies of middle-class, dual-earner couples (N = 47) with children that are successfully managing family and work. Guided by grounded-theory methodology, analysis of interview data revealed that these successful couples structured their lives around 10 major strategies: Valuing family, striving for partnership, deriving meaning from work, maintaining work boundaries, focusing and producing at work, taking pride in dual earning, prioritizing family fun, living simply, making decisions proactively, and valuing time. Each adaptive strategy is defined and illustrated through the participants' own words. Clinical applications for therapists working with dual-earner couples are offered.

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

PubMed

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.

Alternate pathways of body shape evolution translate into common patterns of locomotor evolution in two clades of lizards.

PubMed

Bergmann, Philip J; Irschick, Duncan J

2010-06-01

Body shape has a fundamental impact on organismal function, but it is unknown how functional morphology and locomotor performance and kinematics relate across a diverse array of body shapes. We showed that although patterns of body shape evolution differed considerably between lizards of the Phrynosomatinae and Lerista, patterns of locomotor evolution coincided between clades. Specifically, we found that the phrynosomatines evolved a stocky phenotype through body widening and limb shortening, whereas Lerista evolved elongation through body lengthening and limb shortening. In both clades, relative limb length played a key role in locomotor evolution and kinematic strategies, with long-limbed species moving faster and taking longer strides. In Lerista, the body axis also influenced locomotor evolution. Similar patterns of locomotor evolution were likely due to constraints on how the body can move. However, these common patterns of locomotor evolution between the two clades resulted in different kinematic strategies and levels of performance among species because of their morphological differences. Furthermore, we found no evidence that distinct body shapes are adaptations to different substrates, as locomotor kinematics did not change on loose or solid substrates. Our findings illustrate the importance of studying kinematics to understand the mechanisms of locomotor evolution and phenotype-function relationships.

A review of climate-change adaptation strategies for wildlife management and biodiversity conservation.

PubMed

Mawdsley, Jonathan R; O'Malley, Robin; Ojima, Dennis S

2009-10-01

The scientific literature contains numerous descriptions of observed and potential effects of global climate change on species and ecosystems. In response to anticipated effects of climate change, conservation organizations and government agencies are developing "adaptation strategies" to facilitate the adjustment of human society and ecological systems to altered climate regimes. We reviewed the literature and climate-change adaptation plans that have been developed in United States, Canada, England, México, and South Africa and found 16 general adaptation strategies that relate directly to the conservation of biological diversity. These strategies can be grouped into four broad categories: land and water protection and management; direct species management; monitoring and planning; and law and policy. Tools for implementing these strategies are similar or identical to those already in use by conservationists worldwide (land and water conservation, ecological restoration, agrienvironment schemes, species translocation, captive propagation, monitoring, natural resource planning, and legislation/regulation). Although our review indicates natural resource managers already have many tools that can be used to address climate-change effects, managers will likely need to apply these tools in novel and innovative ways to meet the unprecedented challenges posed by climate change.

Accuracy in strategy imitations promotes the evolution of fairness in the spatial ultimatum game

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž; Szabó, György

2012-10-01

Spatial structure has a profound effect on the outcome of evolutionary games. In the ultimatum game, it leads to the dominance of much fairer players than those predicted to evolve in well-mixed settings. Here we show that spatiality leads to fair ultimatums only if the intervals from which the players are able to choose how much to offer and how little to accept are sufficiently fine-grained. Small sets of discrete strategies lead to the stable coexistence of the two most rational strategies in the set, while larger sets lead to the dominance of a single yet not necessarily the fairest strategy. The fairest outcome is obtained for the most accurate strategy imitation, that is in the limit of a continuous strategy set. Having a multitude of choices is thus crucial for the evolution of fairness, but not necessary for the evolution of empathy.

Adaptive governance and institutional strategies for climate-induced community relocations in Alaska.

PubMed

Bronen, Robin; Chapin, F Stuart

2013-06-04

This article presents governance and institutional strategies for climate-induced community relocations. In Alaska, repeated extreme weather events coupled with climate change-induced coastal erosion impact the habitability of entire communities. Community residents and government agencies concur that relocation is the only adaptation strategy that can protect lives and infrastructure. Community relocation stretches the financial and institutional capacity of existing governance institutions. Based on a comparative analysis of three Alaskan communities, Kivalina, Newtok, and Shishmaref, which have chosen to relocate, we examine the institutional constraints to relocation in the United States. We identify policy changes and components of a toolkit that can facilitate community-based adaptation when environmental events threaten people's lives and protection in place is not possible. Policy changes include amendment of the Stafford Act to include gradual geophysical processes, such as erosion, in the statutory definition of disaster and the creation of an adaptive governance framework to allow communities a continuum of responses from protection in place to community relocation. Key components of the toolkit are local leadership and integration of social and ecological well-being into adaptation planning.

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

PubMed Central

Henrich, Joseph; Henrich, Natalie

2010-01-01

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

Evolution of individual versus social learning on social networks.

PubMed

Tamura, Kohei; Kobayashi, Yutaka; Ihara, Yasuo

2015-03-06

A number of studies have investigated the roles played by individual and social learning in cultural phenomena and the relative advantages of the two learning strategies in variable environments. Because social learning involves the acquisition of behaviours from others, its utility depends on the availability of 'cultural models' exhibiting adaptive behaviours. This indicates that social networks play an essential role in the evolution of learning. However, possible effects of social structure on the evolution of learning have not been fully explored. Here, we develop a mathematical model to explore the evolutionary dynamics of learning strategies on social networks. We first derive the condition under which social learners (SLs) are selectively favoured over individual learners in a broad range of social network. We then obtain an analytical approximation of the long-term average frequency of SLs in homogeneous networks, from which we specify the condition, in terms of three relatedness measures, for social structure to facilitate the long-term evolution of social learning. Finally, we evaluate our approximation by Monte Carlo simulations in complete graphs, regular random graphs and scale-free networks. We formally show that whether social structure favours the evolution of social learning is determined by the relative magnitudes of two effects of social structure: localization in competition, by which competition between learning strategies is evaded, and localization in cultural transmission, which slows down the spread of adaptive traits. In addition, our estimates of the relatedness measures suggest that social structure disfavours the evolution of social learning when selection is weak. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

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

PubMed

Radke, David W; Lee, Charles

2015-09-01

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

Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

PubMed

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-05-19

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Adaptive evolution of centromere proteins in plants and animals

PubMed Central

Talbert, Paul B; Bryson, Terri D; Henikoff, Steven

2004-01-01

Background Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif). Results Whereas we find no evidence that mammalian CenH3 (CENP-A) has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p) is under negative selection. Conclusions CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi. PMID:15345035

An adaptive radiotherapy planning strategy for bladder cancer using deformation vector fields.

PubMed

Vestergaard, Anne; Kallehauge, Jesper Folsted; Petersen, Jørgen Breede Baltzer; Høyer, Morten; Søndergaard, Jimmi; Muren, Ludvig Paul

2014-09-01

Adaptive radiotherapy (ART) has considerable potential in treatment of bladder cancer due to large inter-fractional changes in shape and size of the target. The aim of this study was to compare our clinically applied method for plan library creation that involves manual bladder delineations (Clin-ART) with a method using the deformation vector fields (DVFs) resulting from intensity-based deformable image registrations (DVF-based ART). The study included thirteen patients with urinary bladder cancer who had daily cone beam CTs (CBCTs) acquired for set-up. In both ART strategies investigated, three plan selection volumes were generated using the CBCTs from the first four fractions; in Clin-ART boolean combinations of delineated bladders were used, while the DVF-based strategy applied combinations of the mean and standard deviation of patient-specific DVFs. The volume ratios (VRs) of the course-averaged PTV for the two ART strategies relative the non-adaptive PTV were calculated. Both Clin-ART and DVF-based ART considerably reduced the course-averaged PTV, compared to non-adaptive RT. The VR for DVF-based ART was lower than for Clin-ART (0.65 vs. 0.73; p<0.01). DVF-based ART for bladder irradiation has a considerable normal tissue sparing potential surpassing our already highly conformal clinically applied ART strategy. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Adaptive Evolution of Mitochondrial Energy Metabolism Genes Associated with Increased Energy Demand in Flying Insects

PubMed Central

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. PMID:24918926

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

PubMed

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.

Relationships Among Adaptive and Maladaptive Emotion Regulation Strategies and Psychopathology During the Treatment of Comorbid Anxiety and Alcohol Use Disorders

PubMed Central

Conklin, Laren R.; Cassiello-Robbins, Clair; Brake, C. Alex; Sauer-Zavala, Shannon; Farchione, Todd J.; Ciraulo, Domenic A.; Barlow, David H.

2015-01-01

Both maladaptive and adaptive emotion regulation strategies have been linked with psychopathology. However, previous studies have largely examined them separately, and little research has examined the interplay of these strategies cross-sectionally or longitudinally in patients undergoing psychological treatment. This study examined the use and interplay of adaptive and maladaptive emotion regulation strategies in 81 patients receiving cognitive-behavioral interventions for comorbid alcohol use and anxiety disorders. Patients completed measures of emotion regulation strategy use and symptoms of psychopathology pre- and post-treatment. Cross-sectionally, higher use of maladaptive strategies (e.g., denial) was significantly related to higher psychopathology pre- and post-treatment, whereas higher use of adaptive strategies (e.g., acceptance) only significantly related to lower psychopathology post-treatment. Prospectively, changes in maladaptive strategies, but not changes in adaptive strategies, were significantly associated with post-treatment psychopathology. However, for patients with higher pre-treatment maladaptive strategy use, gains in adaptive strategies were significantly associated with lower post-treatment psychopathology. These findings suggest that psychological treatments may maximize efficacy by considering patient skill use at treatment outset. By better understanding a patient's initial emotion regulation skills, clinicians may be better able to optimize treatment outcomes by emphasizing maladaptive strategy use reduction predominately, or in conjunction with increasing adaptive skill use. PMID:26310363

Self-guided strategy-adaption training for older adults: Transfer effects to everyday tasks.

PubMed

Bottiroli, Sara; Cavallini, Elena; Dunlosky, John; Vecchi, Tomaso; Hertzog, Christopher

2017-09-01

The goal of the present research was to examine the potential of a learner-oriented approach to improving older adults' performance in tasks that are similar to real-life situations that require strategic deployment of cognitive resources. A crucial element of this approach involves encouraging older adults to explicitly analyze tasks to consider how to adapt trained skills to a new task context. In an earlier study, a specialist-directed intervention produced training gains and transfer to some untrained memory tasks. In the present study, older adults received a manual instructing them about principles of task analysis, two memory strategies, and strategy adaptation. Self-guided strategy-adaption training involved practicing some memory tasks as well as instructions on how the trained skills could be applied to new tasks that were not practiced. The criterion tasks involved practice tasks, non-practiced tasks that were discussed in the manual, and transfer tasks that were never mentioned in the manual. Two of the tests were from the Everyday Cognition Battery (inductive reasoning and working memory). As compared to a waiting-list control group, older adults assigned to self-guided strategy-adaption training showed memory improvements on tasks that were practiced or discussed during training. Most important, the learner-oriented approach produced transfer to the everyday tasks. Our findings show the potential of instructing task appraisal processes as a basis for fostering transfer, including improving older adults' performance in simulated everyday tasks. Copyright © 2017 Elsevier B.V. All rights reserved.

Dual-phase evolution in complex adaptive systems.

PubMed

Paperin, Greg; Green, David G; Sadedin, Suzanne

2011-05-06

Understanding the origins of complexity is a key challenge in many sciences. Although networks are known to underlie most systems, showing how they contribute to well-known phenomena remains an issue. Here, we show that recurrent phase transitions in network connectivity underlie emergent phenomena in many systems. We identify properties that are typical of systems in different connectivity phases, as well as characteristics commonly associated with the phase transitions. We synthesize these common features into a common framework, which we term dual-phase evolution (DPE). Using this framework, we review the literature from several disciplines to show that recurrent connectivity phase transitions underlie the complex properties of many biological, physical and human systems. We argue that the DPE framework helps to explain many complex phenomena, including perpetual novelty, modularity, scale-free networks and criticality. Our review concludes with a discussion of the way DPE relates to other frameworks, in particular, self-organized criticality and the adaptive cycle.

Dual-phase evolution in complex adaptive systems

PubMed Central

Paperin, Greg; Green, David G.; Sadedin, Suzanne

2011-01-01

Understanding the origins of complexity is a key challenge in many sciences. Although networks are known to underlie most systems, showing how they contribute to well-known phenomena remains an issue. Here, we show that recurrent phase transitions in network connectivity underlie emergent phenomena in many systems. We identify properties that are typical of systems in different connectivity phases, as well as characteristics commonly associated with the phase transitions. We synthesize these common features into a common framework, which we term dual-phase evolution (DPE). Using this framework, we review the literature from several disciplines to show that recurrent connectivity phase transitions underlie the complex properties of many biological, physical and human systems. We argue that the DPE framework helps to explain many complex phenomena, including perpetual novelty, modularity, scale-free networks and criticality. Our review concludes with a discussion of the way DPE relates to other frameworks, in particular, self-organized criticality and the adaptive cycle. PMID:21247947

Adaptive evolution of newly emerged micro-RNA genes in Drosophila.

PubMed

Lu, Jian; Fu, Yonggui; Kumar, Supriya; Shen, Yang; Zeng, Kai; Xu, Anlong; Carthew, Richard; Wu, Chung-I

2008-05-01

How often micro-RNA (miRNA) genes emerged and how fast they evolved soon after their emergence are some of the central questions in the evolution of miRNAs. Because most known miRNA genes are ancient and highly conserved, these questions can be best answered by identifying newly emerged miRNA genes. Among the 78 miRNA genes in Drosophila reported before 2007, only 5 are confirmed to be newly emerged in the genus (although many more can be found in the newly reported data set; e.g., Ruby et al. 2007; Stark et al. 2007; Lu et al. 2008). These new miRNA genes have undergone numerous changes, even in the normally invariant mature sequences. Four of them (the miR-310/311/312/313 cluster, denoted miR-310s) were duplicated from other conserved miRNA genes. The fifth one (miR-303) appears to be a very young gene, originating de novo from a non-miRNA sequence recently. We sequenced these 5 miRNA genes and their neighboring regions from a worldwide collection of Drosophila melanogaster lines. The levels of divergence and polymorphism in these miRNA genes, vis-à-vis those of the neighboring DNA sequences, suggest that these 5 genes are evolving adaptively. Furthermore, the polymorphism pattern of miR-310s in D. melanogaster is indicative of hitchhiking under positive selection. Thus, a large number of adaptive changes over a long period of time may be essential for the evolution of newly emerged miRNA genes.

Phenotype adjustment promotes adaptive evolution in a game without conflict.

PubMed

Yamaguchi, Sachi; Iwasa, Yoh

2015-06-01

Organisms may adjust their phenotypes in response to social and physical environments. Such phenotypic plasticity is known to help or retard adaptive evolution. Here, we study the evolutionary outcomes of adaptive phenotypic plasticity in an evolutionary game involving two players who have no conflicts of interest. A possible example is the growth and sex allocation of a lifelong pair of shrimps entrapped in the body of a sponge. We consider random pair formation, the limitation of total resources for growth, and the needs of male investment to fertilize eggs laid by the partner. We compare the following three different evolutionary dynamics: (1) No adjustment: each individual develops a phenotype specified by its own genotype; (2) One-player adjustment: the phenotype of the first player is specified by its own genotype, and the second player chooses the phenotype that maximizes its own fitness; (3) Two-player adjustment: the first player exhibits an initial phenotype specified by its own genotype, the second player chooses a phenotype given that of the first player, and finally, the first player readjusts its phenotype given that of the second player. We demonstrate that both one-player and two-player adjustments evolve to achieve maximum fitness. In contrast, the dynamics without adjustment fails in some cases to evolve outcomes with the highest fitness. For an intermediate range of male cost, the evolution of no adjustment realizes two hermaphrodites with equal size, whereas the one-player and two-player adjustments realize a small male and a large female. Copyright © 2015 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2016-01-01

In recent years, laboratory studies of cultural evolution have become increasingly prevalent as a means of identifying and understanding the effects of cultural transmission on the form and functionality of transmitted material. The datasets generated by these studies may provide insights into the conditions encouraging, or inhibiting, high rates of innovation, as well as the effect that this has on measures of adaptive cultural change. Here we review recent experimental studies of cultural evolution with a view to elucidating the role of innovation in generating observed trends. We first consider how tasks are presented to participants, and how the corresponding conceptualization of task success is likely to influence the degree of intent underlying any deviations from perfect reproduction. We then consider the measures of interest used by the researchers to track the changes that occur as a result of transmission, and how these are likely to be affected by differing rates of retention. We conclude that considering studies of cultural evolution from the perspective of innovation provides us with valuable insights that help to clarify important differences in research designs, which have implications for the likely effects of variation in retention rates on measures of cultural adaptation. PMID:26926283

Convergence of an hp-Adaptive Finite Element Strategy in Two and Three Space-Dimensions

NASA Astrophysics Data System (ADS)

Bürg, Markus; Dörfler, Willy

2010-09-01

We show convergence of an automatic hp-adaptive refinement strategy for the finite element method on the elliptic boundary value problem. The strategy is a generalization of a refinement strategy proposed for one-dimensional situations to problems in two and three space-dimensions.

Faster-X evolution of gene expression is driven by recessive adaptive cis-regulatory variation in Drosophila.

PubMed

Llopart, Ana

2018-05-01

The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genomewide test of this hypothesis is still missing. Here, I use whole genome sequence data in Drosophila yakuba and D. santomea to evaluate this hypothesis and report positive correlations between sequence divergence at 5' noncoding sequences and gene expression divergence. I also examine polymorphism and divergence in 9,279 noncoding sequences located at the 5' end of annotated genes and detected multiple signals of positive selection. Notably, I used the traditional synonymous sites as neutral reference to test for adaptive evolution, but I also used bases 8-30 of introns <65 bp, which have been proposed to be a better neutral choice. X-linked genes with high degree of male-biased expression show the most extreme adaptive pattern at 5' noncoding regions, in agreement with faster-X evolution for gene expression divergence and a higher incidence of positively selected recessive mutations. © 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Sexual selection expedites the evolution of pesticide resistance.

PubMed

Jacomb, Frances; Marsh, Jason; Holman, Luke

2016-12-01

The evolution of insecticide resistance by crop pests and disease vectors causes serious problems for agriculture and health. Sexual selection can accelerate or hinder adaptation to abiotic challenges in a variety of ways, but the effect of sexual selection on resistance evolution is little studied. Here, we examine this question using experimental evolution in the pest insect Tribolium castaneum. The experimental removal of sexual selection slowed the evolution of resistance in populations treated with pyrethroid pesticide, and also reduced the rate at which resistance was lost from pesticide-free populations. These results suggest that selection arising from variance in mating and fertilization success can augment natural selection on pesticide resistance, meaning that sexual selection should be considered when designing strategies to limit the evolution of pesticide resistance. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Strategies for the Evolution of Sex

NASA Astrophysics Data System (ADS)

Erzan, Ayse

2002-03-01

Using a bit-string model of evolution we find a successful route to diploidy and sex in simple organisms, for a step-like fitness function. Assuming that an excess of deleterious mutations triggers the conversion of haploids to diploidy and sex, we find that only one pair of sexual organisms can take over a finite population, if they engage in sexual reproduction under unfavorable conditions, and otherwise perform mitosis. Then, a haploid-diploid (HD) cycle is established, with an abbreviated haploid phase, as in present day sexual reproduction. If crossover is allowed during meiosis, HD cycles of arbitrary duration can be maintained. We find that the sexual population has a higher mortality rate than asexual diploids, but also a relaxation rate that is an order of magnitude higher. As a result, sexuals have a higher adaptability and lower mutational load on the average, since they can select out the undesirable genes much faster.

[An increase in efficiency of adaptations and a weakening of organism protective reactions in the process of biological evolution].

PubMed

Ivanov, K P

2014-01-01

The main direction of evolution of living organisms is development of the central nervous system and sense organ, an increase of energy exchange development of homoiothermia, development of the more and more complex forms of behavior, an increase in energy expenditure in connection with an increase of the organism activity, and development of adaptation to the habitat. Such fundamental processes were subjected and have been subjected to numerous studies and discussions. However, in different animals there exist different species peculiarities of evolution of physiological functions, from which finally formed are fundamental evolutionary processes. We studied some of these specific processes by dividing them into two categories. The first category is "Increase of efficiency of adaptation" in development of biological evolution. By this term we mean development of amazing by perfection specific physiological mechanisms of adaptive character. The second category is "Weakening of protective organism reactions". By this we understand disturbance of protective mechanisms of the organism immune system, discoordination of movement of leukocytes along microvessels, the absence of efficient collateral circulation in brain and in heart, etc.

Sex differences, sexual selection, and ageing: an experimental evolution approach.

PubMed

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

2009-10-01

Life-history (LH) theory predicts that selection will optimize the trade-off between reproduction and somatic maintenance. Reproductive ageing and finite life span are direct consequences of such optimization. Sexual selection and conflict profoundly affect the reproductive strategies of the sexes and thus can play an important role in the evolution of life span and ageing. In theory, sexual selection can favor the evolution of either faster or slower ageing, but the evidence is equivocal. We used a novel selection experiment to investigate the potential of sexual selection to influence the adaptive evolution of age-specific LH traits. We selected replicate populations of the seed beetle Callosobruchus maculatus for age at reproduction ("Young" and "Old") either with or without sexual selection. We found that LH selection resulted in the evolution of age-specific reproduction and mortality but these changes were largely unaffected by sexual selection. Sexual selection depressed net reproductive performance and failed to promote adaptation. Nonetheless, the evolution of several traits differed between males and females. These data challenge the importance of current sexual selection in promoting rapid adaptation to environmental change but support the hypothesis that sex differences in LH-a historical signature of sexual selection-are key in shaping trait responses to novel selection.

Sex-biased dispersal promotes adaptive parental effects

PubMed Central

2010-01-01

Background In heterogeneous environments, sex-biased dispersal could lead to environmental adaptive parental effects, with offspring selected to perform in the same way as the parent dispersing least, because this parent is more likely to be locally adapted. We investigate this hypothesis by simulating varying levels of sex-biased dispersal in a patchy environment. The relative advantage of a strategy involving pure maternal (or paternal) inheritance is then compared with a strategy involving classical biparental inheritance in plants and in animals. Results We find that the advantage of the uniparental strategy over the biparental strategy is maximal when dispersal is more strongly sex-biased and when dispersal distances of the least mobile sex are much lower than the size of the environmental patches. In plants, only maternal effects can be selected for, in contrast to animals where the evolution of either paternal or maternal effects can be favoured. Moreover, the conditions for environmental adaptive maternal effects to be selected for are more easily fulfilled in plants than in animals. Conclusions The study suggests that sex-biased dispersal can help predict the direction and magnitude of environmental adaptive parental effects. However, this depends on the scale of dispersal relative to that of the environment and on the existence of appropriate mechanisms of transmission of environmentally induced traits. PMID:20637098

Adaptive Dynamics of Extortion and Compliance

PubMed Central

Hilbe, Christian; Nowak, Martin A.; Traulsen, Arne

2013-01-01

Direct reciprocity is a mechanism for the evolution of cooperation. For the iterated prisoner’s dilemma, a new class of strategies has recently been described, the so-called zero-determinant strategies. Using such a strategy, a player can unilaterally enforce a linear relationship between his own payoff and the co-player’s payoff. In particular the player may act in such a way that it becomes optimal for the co-player to cooperate unconditionally. In this way, a player can manipulate and extort his co-player, thereby ensuring that the own payoff never falls below the co-player’s payoff. However, using a compliant strategy instead, a player can also ensure that his own payoff never exceeds the co-player’s payoff. Here, we use adaptive dynamics to study when evolution leads to extortion and when it leads to compliance. We find a remarkable cyclic dynamics: in sufficiently large populations, extortioners play a transient role, helping the population to move from selfish strategies to compliance. Compliant strategies, however, can be subverted by altruists, which in turn give rise to selfish strategies. Whether cooperative strategies are favored in the long run critically depends on the size of the population; we show that cooperation is most abundant in large populations, in which case average payoffs approach the social optimum. Our results are not restricted to the case of the prisoners dilemma, but can be extended to other social dilemmas, such as the snowdrift game. Iterated social dilemmas in large populations do not lead to the evolution of strategies that aim to dominate their co-player. Instead, generosity succeeds. PMID:24223739

Strategies for adding adaptive learning mechanisms to rule-based diagnostic expert systems

NASA Technical Reports Server (NTRS)

Stclair, D. C.; Sabharwal, C. L.; Bond, W. E.; Hacke, Keith

1988-01-01

Rule-based diagnostic expert systems can be used to perform many of the diagnostic chores necessary in today's complex space systems. These expert systems typically take a set of symptoms as input and produce diagnostic advice as output. The primary objective of such expert systems is to provide accurate and comprehensive advice which can be used to help return the space system in question to nominal operation. The development and maintenance of diagnostic expert systems is time and labor intensive since the services of both knowledge engineer(s) and domain expert(s) are required. The use of adaptive learning mechanisms to increment evaluate and refine rules promises to reduce both time and labor costs associated with such systems. This paper describes the basic adaptive learning mechanisms of strengthening, weakening, generalization, discrimination, and discovery. Next basic strategies are discussed for adding these learning mechanisms to rule-based diagnostic expert systems. These strategies support the incremental evaluation and refinement of rules in the knowledge base by comparing the set of advice given by the expert system (A) with the correct diagnosis (C). Techniques are described for selecting those rules in the in the knowledge base which should participate in adaptive learning. The strategies presented may be used with a wide variety of learning algorithms. Further, these strategies are applicable to a large number of rule-based diagnostic expert systems. They may be used to provide either immediate or deferred updating of the knowledge base.

Impacts of adaptive flood management strategies on the Socio-Hydrological system in Ganges - Brahmaputra river basin, Bangladesh

NASA Astrophysics Data System (ADS)

Sung, K.; Jeong, H.; Sangwan, N.; Yu, D. J.

2017-12-01

Human societies have tried to prevent floods by building robust infrastructure such as levees or dams. However, some scholars raise a doubt to this approach because of a lack of adaptiveness to environmental and societal changes in a long-term. Thus, a growing number of studies now suggest adopting new strategies in flood management to reinforce an adapt capacity to the long-term flood risk. This study addresses this issue by developing a conceptual mathematical model exploring how flood management strategies effect to the dynamics human-flood interaction, ultimately the flood resilience in a long-term. Especially, our model is motivated by the community-based flood protection system in southwest coastal area in Bangladesh. We developed several conceptual flood management strategies and investigated the interplay between those strategies and community's capacity to cope with floods. We additionally analyzed how external disturbances (sea level rise, water tide level change, and outside economic development) alter the adaptive capacity to flood risks. The results of this study reveal that the conventional flood management has potential vulnerabilities as external disturbances increase. Our results also highlight the needs of the adaptive strategy as a new paradigm in flood management which is able to feedback to the social and hydrological conditions. These findings provide insights on the resilience-based, adaptive strategies which can build flood resilience under global change.

Adaptive landscapes: Top-down and bottom-up perspectives

NASA Astrophysics Data System (ADS)

Kerr, Benjamin

Sewall Wright introduced the metaphor of the adaptive landscape, a map from genotype to fitness, more than 80 years ago to help describe his view of adaptive evolution. This metaphor has been immensely popular and has been used in a variety of incarnations. However, a systematic study of the genotype-fitness map presents significant problems. The space of possible genotypes is vast, and the mapping is likely dependent on both environment and the composition of genotypes in a population. In this talk, I will discuss some of these problems and present experimental strategies for uncovering features of adaptive landscapes. In particular, I will discuss how population structure can be used as an experimental variable to elucidate landscape topography and how a combination of experimental evolution and genetic engineering can reveal important landscape features in changing environments. I will also present some potential applications of this work to the problem of antibiotic resistance and potential implications for evolutionary rescue in the face of global climate change. For some of these topics, the classic notion of the adaptive landscape must itself be adapted; however, I propose that there are fruitful ways to continue to apply this metaphor.

Socio-economic vulnerability of coastal communities in southern Thailand: the development of adaptation strategies

NASA Astrophysics Data System (ADS)

Willroth, P.; Massmann, F.; Wehrhahn, R.; Revilla Diez, J.

2012-08-01

The tsunami of December 2004 impacted large areas of Thailand's coastline and caused severe human and economic losses. The recovery period revealed differences in the vulnerabilities of communities affected. An understanding of the causal factors of vulnerability is crucial for minimising the negative effects of future threats and developing adaptive capacities. This paper analyses the vulnerabilities and the development of adaptation strategies in the booming tourist area of Khao Lak and in the predominantly fishing and agricultural area of Ban Nam Khem through a comprehensive vulnerability framework. The results show that social networks played a crucial role in coping with the disaster. Social cohesion is important for strengthening the community and developing successful adaptation strategies. The development of tourism and the turning away from traditional activities have a significant positive influence on the income situation, but create a dependency on a single business sector. It could be shown that households generating their income in the tourism sector were vulnerable unless they had diversified their income previously. Income diversification decreased the vulnerability in the study areas. Adaptation strategies and processes developed in the aftermath clearly address these issues.

An adapted yield criterion for the evolution of subsequent yield surfaces

NASA Astrophysics Data System (ADS)

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.

Functional Evolution of Leptin of Ochotona curzoniae in Adaptive Thermogenesis Driven by Cold Environmental Stress

PubMed Central

Yang, Jie; Bromage, Timothy G.; Zhao, Qian; Xu, Bao Hong; Gao, Wei Li; Tian, Hui Fang; Tang, Hui Jun; Liu, Dian Wu; Zhao, Xin Quan

2011-01-01

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. PMID:21698227

Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations.

PubMed

Sandberg, Troy E; Pedersen, Margit; LaCroix, Ryan A; Ebrahim, Ali; Bonde, Mads; Herrgard, Markus J; Palsson, Bernhard O; Sommer, Morten; Feist, Adam M

2014-10-01

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 conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths. Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across two or more strains. This mutational recurrence pointed to the key genetic targets underlying the evolved fitness increase. Genome engineering was used to introduce the novel ALE-acquired alleles in random combinations into the ancestral strain, and competition between these engineered strains reaffirmed the impact of the key mutations on the growth rate at 42 °C. Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype. Additionally, transcriptomic analysis of the ancestral and evolved strains revealed a general trend for restoration of the global expression state back toward preheat stressed levels. This restorative effect was previously documented following evolution to metabolic perturbations, and thus may represent a general feature of ALE experiments. The widespread evolved expression shifts were enabled by a comparatively scant number of regulatory mutations, providing a net fitness benefit but causing suboptimal expression levels for certain genes, such as those governing flagellar formation, which then became targets for additional ameliorating mutations. Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future

Recruitment of hard-to-reach population subgroups via adaptations of the snowball sampling strategy.

PubMed

Sadler, Georgia Robins; Lee, Hau-Chen; Lim, Rod Seung-Hwan; Fullerton, Judith

2010-09-01

Nurse researchers and educators often engage in outreach to narrowly defined populations. This article offers examples of how variations on the snowball sampling recruitment strategy can be applied in the creation of culturally appropriate, community-based information dissemination efforts related to recruitment to health education programs and research studies. Examples from the primary author's program of research are provided to demonstrate how adaptations of snowball sampling can be used effectively in the recruitment of members of traditionally underserved or vulnerable populations. The adaptation of snowball sampling techniques, as described in this article, helped the authors to gain access to each of the more-vulnerable population groups of interest. The use of culturally sensitive recruitment strategies is both appropriate and effective in enlisting the involvement of members of vulnerable populations. Adaptations of snowball sampling strategies should be considered when recruiting participants for education programs or for research studies when the recruitment of a population-based sample is not essential.

Testing directed evolution strategies for space exploration: genetic modification of photosystem II to increase stress tolerance under space conditions

NASA Astrophysics Data System (ADS)

Bertalan, I.; Giardi, M. T.; Johanningmeier, U.

Plants and many microorganisms are able to convert and store solar energy in chemical bonds by a process called photosynthesis They remove CO 2 from the atmosphere fix it as carbohydrate and simultaneously evolve oxygen Oxygen evolution is of supreme relevance for all higher life forms and results from the splitting of water molecules This process is catalyzed by the so called photosystem II PSII complex and represents the very beginning of biomass production PS II is also a central point of regulation being responsive to various physical and physiological parameters Complex space radiation is damaging PS II and reduces photosynthetic efficiency Thus bioregenerative life-support systems are severely disturbed at this point Genetic manipulation of photosynthesis checkpoints offer the possibility to adjust biomass and oxygen production to changing environmental conditions As the photosynthetic apparatus has adapted to terrestrial and not to space conditions we are trying to adapt a central and particularly stress-susceptible element of the photosynthesis apparatus - the D1 subunit of PS II - to space radiation by a strategy of directed evolution The D1 subunit together with its sister subunit D2 form the reaction centre of PS II D1 presents a central weak point for radiation energy that hits the chloroplast We have constructed a mutant of the green alga Chlamydomonas reinhardtii with a defect D1 protein This mutant is easily transformable with D1-encoding PCR fragments without purification and cloning steps 1 When

Adaptive evolution of insect selective excitatory β-type sodium channel neurotoxins from scorpion venom.

PubMed

Wu, Wenlan; Li, Zhongjie; Ma, Yibao

2017-06-01

Insect selective excitatory β-type sodium channel neurotoxins from scorpion venom (β-NaScTxs) are composed of about 70-76 amino acid residues and share a common scaffold stabilized by four unique disulfide bonds. The phylogenetic analysis of these toxins was hindered by limited sequence data. In our recent study, two new insect selective excitatory β-NaScTxs, LmIT and ImIT, were isolated from Lychas mucronatus and Isometrus maculatus, respectively. With the sequences previously reported, we examined the adaptive molecular evolution of insect selective excitatory β-NaScTxs by estimating the nonsynonymous-to-synonymous rate ratio (ω=d N /d S ). The results revealed 12 positively selected sites in the genes of insect selective excitatory β-NaScTxs. Moreover, these positively selected sites match well with the sites important for interacting with sodium channels, as demonstrated in previous mutagenesis study. These results reveal that adaptive evolution after gene duplication is one of the most important genetic mechanisms of scorpion neurotoxin diversification. Copyright © 2017 Elsevier Inc. All rights reserved.

Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant.

PubMed

Lee, Chien-Yueh; Hsieh, Ping-Han; Chiang, Li-Mei; Chattopadhyay, Amrita; Li, Kuan-Yi; Lee, Yi-Fang; Lu, Tzu-Pin; Lai, Liang-Chuan; Lin, En-Chung; Lee, Hsinyu; Ding, Shih-Torng; Tsai, Mong-Hsun; Chen, Chien-Yu; Chuang, Eric Y

2018-05-01

The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.

Adaptive Insecure Attachment and Resource Control Strategies during Middle Childhood

ERIC Educational Resources Information Center

Chen, Bin-Bin; Chang, Lei

2012-01-01

By integrating the life history theory of attachment with resource control theory, the current study examines the hypothesis that insecure attachment styles reorganized in middle childhood are alternative adaptive strategies used to prepare for upcoming competition with the peer group. A sample of 654 children in the second through seventh grades…

Compromise-based Robust Prioritization of Climate Change Adaptation Strategies for Watershed Management

NASA Astrophysics Data System (ADS)

Kim, Y.; Chung, E. S.

2014-12-01

This study suggests a robust prioritization framework for climate change adaptation strategies under multiple climate change scenarios with a case study of selecting sites for reusing treated wastewater (TWW) in a Korean urban watershed. The framework utilizes various multi-criteria decision making techniques, including the VIKOR method and the Shannon entropy-based weights. In this case study, the sustainability of TWW use is quantified with indicator-based approaches with the DPSIR framework, which considers both hydro-environmental and socio-economic aspects of the watershed management. Under the various climate change scenarios, the hydro-environmental responses to reusing TWW in potential alternative sub-watersheds are determined using the Hydrologic Simulation Program in Fortran (HSPF). The socio-economic indicators are obtained from the statistical databases. Sustainability scores for multiple scenarios are estimated individually and then integrated with the proposed approach. At last, the suggested framework allows us to prioritize adaptation strategies in a robust manner with varying levels of compromise between utility-based and regret-based strategies.

Are winter and summer dormancy symmetrical seasonal adaptive strategies? The case of temperate herbaceous perennials.

PubMed

Gillespie, Lauren M; Volaire, Florence A

2017-02-01

Dormancy in higher plants is an adaptive response enabling plant survival during the harshest seasons and has been more explored in woody species than in herbaceous species. Nevertheless, winter and summer shoot meristem dormancy are adaptive strategies that could play a major role in enhancing seasonal stress tolerance and resilience of widespread herbaceous plant communities. This review outlines the symmetrical aspects of winter and summer dormancy in order to better understand plant adaptation to severe stress, and highlight research priorities in a changing climate. Seasonal dormancy is a good model to explore the growth-stress survival trade-off and unravel the relationships between growth potential and stress hardiness. Although photoperiod and temperature are known to play a crucial, though reversed, role in the induction and release of both types of dormancy, the thresholds and combined effects of these environmental factors remain to be identified. The biochemical compounds involved in induction or release in winter dormancy (abscisic acid, ethylene, sugars, cytokinins and gibberellins) could be a priority research focus for summer dormancy. To address these research priorities, herbaceous species, being more tractable than woody species, are excellent model plants for which both summer and winter dormancy have been clearly identified. Summer and winter dormancy, although responding to inverse conditions, share many characteristics. This analogous nature can facilitate research as well as lead to insight into plant adaptations to extreme conditions and the evolution of phenological patterns of species and communities under climate change. The development of phenotypes showing reduced winter and/or enhanced summer dormancy may be expected and could improve adaptation to less predictable environmental stresses correlated with future climates. To this end, it is suggested to explore the inter- and intraspecific genotypic variability of dormancy and its

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

PubMed Central

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-01-01

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

Light adaptation and the evolution of vertebrate photoreceptors.

PubMed

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

Adaptive evolution of osmoregulatory-related genes provides insight into salinity adaptation in Chinese mitten crab, Eriocheir sinensis.

PubMed

Wang, Zhengfei; Bai, Yuze; Zhang, Daizhen; Tang, Boping

2018-06-01

Osmoregulation is an important mechanism by which euryhaline crustaceans regulate osmotic and ionic concentrations. The Chinese mitten crab (Eriocheir sinensis) is a strong osmoregulating animal model among crustacean species, as it can maintain its hemolymph composition and survives well in either seawater or freshwater. Osmoregulation by E. sinensis during physiological adaptation has been studied extensively. However, the genetic basis of osmoregulation in E. sinensis for acclimating to changing salinities remains unclear. The current study investigated five genes involved in E. sinensis osmoregulation and compared them with a representative marine crab Portunus trituberculatus to test whether adaptive evolution has occurred changing salinity conditions. The results showed that carbonic anhydrase (CA), cytochrome P450 4C (CYP4C), glutamate dehydrogenase (GDH), and the Na + /H + exchanger (NHE) have undergone positive selection (i.e., directional selection) in E. sinensis. Thus, the positive selection in CA and NHE suggests that E. sinensis has enhanced capacity for maintaining systemic acid-base balance and ion regulation. GDH and CYP4C also demonstrated positive selection in E. sinensis, suggesting that E. sinensis might have acquired an enhanced capacity to metabolize glutamate and synthesize ecdysteroids in response to a change in osmotic concentration. The present study provides new insight into the molecular genetic basis of salinity adaption in E. sinensis.

Stakeholders' participatory diagnosis of climate change impacts on subsistence agriculture in Sikkim, India, for identifying adaptation strategies

NASA Astrophysics Data System (ADS)

Azhoni, A.; Goyal, M. K.

2017-12-01

Narrowing the gap between research, policy making and implementing adaptation remains a challenge in many parts of the world where climate change is likely to severely impact subsistence agriculture. This research aims to narrow this gap by matching the adaptation strategies being framed by policy makers and perspectives of consultants and researchers which are expected to be implemented by development agencies farmers in the state of Sikkim in India. Our case study examined the framing and implementation of State Action Plan on Climate Change through semi-structured interviews carried out with decision makers in the State Government, Scientific Organisations, consultants, local academia, implementing and development agencies, and farmers for whom the adaptation strategies are targeted. Using Social Network and Stakeholder Analysis approach, this research unravels the complexities of perceiving climate change impacts, identifying adaptation strategies, and implementing climate change adaptation strategies. While farmers are less aware about the global phenomenon of climate change impacts for their subsistence livelihood, their knowledge of the local conditions and their close interaction with the State Government Agriculture Department provides them an access to new and high value crops. Although important steps are initiated through the Sikkim State Action Plan on Climate Change it is yet to deliver effective means of adaptation implementation and identifying the networks of close coordination between the various implementing agencies will likely to pay rich dividends. While Sikkim being a small and hilly state with specific contextual challenges of climate change impacts, the results from this study highlights how the internal and external networks between various types of stakeholders informs decision makers in identifying local impacts of climate change and plan adaptation strategies.

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution

PubMed Central

Price, Christopher T. D.; Richards, Ashley M.; Von Dwingelo, Juanita E.; Samara, Hala A.; Kwaik, Yousef Abu

2013-01-01

Summary Legionella pneumophila, the causative agent of Legionnaires’ disease, invades and proliferates within a diverse range of free-living amoeba in the environment but upon transmission to humans the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. L. pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. PMID:24112119

Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.

PubMed

Flegr, Jaroslav

2010-01-13

Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years. The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct. Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).

Dosimetric evaluation of three adaptive strategies for prostate cancer treatment including pelvic lymph nodes irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantin, Audrey; Gingras, Luc; Archambault, Louis, E-mail: louis.archambault@phy.ulaval.ca

Purpose: The movements of the prostate relative to the pelvic lymph nodes during intensity-modulated radiation therapy treatment can limit margin reduction and affect the protection of the organs at risk (OAR). In this study, the authors performed an analysis of three adaptive treatment strategies that combine information from both bony and gold marker registrations. The robustness of those treatments against the interfraction prostate movements was evaluated. Methods: A retrospective study was conducted on five prostate cancer patients with 7–13 daily cone-beam CTs (CBCTs). The clinical target volumes (CTVs) consisting of pelvic lymph nodes, prostate, and seminal vesicles as well asmore » the OARs were delineated on each CBCT and the initial CT. Three adaptive strategies were analyzed. Two of these methods relied on a two-step patient positioning at each fraction. First step: a bony registration was used to deliver the nodal CTV prescription. Second step: a gold marker registration was then used either to (1) complete the dose delivered to the prostate (complement); (2) or give almost the entire prescription to the prostate with a weak dose gradient between the targets to compensate for possible motions (gradient). The third method (COR) used a pool of precalculated plans based on images acquired at previous treatment fractions. At each new fraction, a plan is selected from that pool based on the daily position of prostate center-of-mass. The dosimetric comparison was conducted and results are presented with and without the systematic shift in the prostate position on the CT planning. The adaptive strategies were compared to the current clinical standard where all fractions are treated with the initial nonadaptive plan. Results: The minimum daily prostate D{sub 95%} is improved by 2%, 9%, and 6% for the complement, the gradient, and the COR approaches, respectively, compared to the nonadaptive method. The average nodal CTV D{sub 95%} remains constant across

Dosimetric evaluation of three adaptive strategies for prostate cancer treatment including pelvic lymph nodes irradiation.

PubMed

Cantin, Audrey; Gingras, Luc; Lachance, Bernard; Foster, William; Goudreault, Julie; Archambault, Louis

2015-12-01

The movements of the prostate relative to the pelvic lymph nodes during intensity-modulated radiation therapy treatment can limit margin reduction and affect the protection of the organs at risk (OAR). In this study, the authors performed an analysis of three adaptive treatment strategies that combine information from both bony and gold marker registrations. The robustness of those treatments against the interfraction prostate movements was evaluated. A retrospective study was conducted on five prostate cancer patients with 7-13 daily cone-beam CTs (CBCTs). The clinical target volumes (CTVs) consisting of pelvic lymph nodes, prostate, and seminal vesicles as well as the OARs were delineated on each CBCT and the initial CT. Three adaptive strategies were analyzed. Two of these methods relied on a two-step patient positioning at each fraction. First step: a bony registration was used to deliver the nodal CTV prescription. Second step: a gold marker registration was then used either to (1) complete the dose delivered to the prostate (complement); (2) or give almost the entire prescription to the prostate with a weak dose gradient between the targets to compensate for possible motions (gradient). The third method (COR) used a pool of precalculated plans based on images acquired at previous treatment fractions. At each new fraction, a plan is selected from that pool based on the daily position of prostate center-of-mass. The dosimetric comparison was conducted and results are presented with and without the systematic shift in the prostate position on the CT planning. The adaptive strategies were compared to the current clinical standard where all fractions are treated with the initial nonadaptive plan. The minimum daily prostate D95% is improved by 2%, 9%, and 6% for the complement, the gradient, and the COR approaches, respectively, compared to the nonadaptive method. The average nodal CTV D95% remains constant across the strategies, except for the gradient approach

Climate change adaptation strategies for resource management and conservation planning.

PubMed

Lawler, Joshua J

2009-04-01

Recent rapid changes in the Earth's climate have altered ecological systems around the globe. Global warming has been linked to changes in physiology, phenology, species distributions, interspecific interactions, and disturbance regimes. Projected future climate change will undoubtedly result in even more dramatic shifts in the states of many ecosystems. These shifts will provide one of the largest challenges to natural resource managers and conservation planners. Managing natural resources and ecosystems in the face of uncertain climate requires new approaches. Here, the many adaptation strategies that have been proposed for managing natural systems in a changing climate are reviewed. Most of the recommended approaches are general principles and many are tools that managers are already using. What is new is a turning toward a more agile management perspective. To address climate change, managers will need to act over different spatial and temporal scales. The focus of restoration will need to shift from historic species assemblages to potential future ecosystem services. Active adaptive management based on potential future climate impact scenarios will need to be a part of everyday operations. And triage will likely become a critical option. Although many concepts and tools for addressing climate change have been proposed, key pieces of information are still missing. To successfully manage for climate change, a better understanding will be needed of which species and systems will likely be most affected by climate change, how to preserve and enhance the evolutionary capacity of species, how to implement effective adaptive management in new systems, and perhaps most importantly, in which situations and systems will the general adaptation strategies that have been proposed work and how can they be effectively applied.

77 FR 2996 - National Fish, Wildlife, and Plants Climate Adaptation Strategy

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-20

... (Strategy). The adverse impacts of climate change transcend political and administrative boundaries. No... principles and science-based practices--for reducing the negative impacts of climate change on fish, wildlife... resource adaptation to climate change, and will describe mechanisms that will foster collaboration among...

Developing Rational-Empirical Views of Intelligent Adaptive Behavior

DTIC Science & Technology

2004-08-01

biological frame to the information processing model and outline our understanding of intentions and beliefs that co-exist with rational and...notion that the evolution of cognition has produced memory/ knowledge systems that specialize in the processing of particular types of information ...1 PERMIS 2004 Developing Rational-Empirical Views of Intelligent Adaptive Behavior Gary Berg-Cross, Knowledge Strategies Potomac, Maryland

A driver-adaptive stability control strategy for sport utility vehicles

NASA Astrophysics Data System (ADS)

Zhu, Shenjin; He, Yuping

2017-08-01

Conventional vehicle stability control (VSC) systems are designed for average drivers. For a driver with a good driving skill, the VSC systems may be redundant; for a driver with a poor driving skill, the VSC intervention may be inadequate. To increase safety of sport utility vehicles (SUVs), this paper proposes a novel driver-adaptive VSC (DAVSC) strategy based on scaling the target yaw rate commanded by the driver. The DAVSC system is adaptive to drivers' driving skills. More control effort would be exerted for drivers with poor driving skills, and vice versa. A sliding mode control (SMC)-based differential braking (DB) controller is designed using a three degrees of freedom (DOF) yaw-plane model. An eight DOF nonlinear yaw-roll model is used to simulate the SUV dynamics. Two driver models, namely longitudinal and lateral, are used to 'drive' the virtual SUV. By integrating the virtual SUV, the DB controller, and the driver models, the performance of the DAVSC system is investigated. The simulations demonstrate the effectiveness of the DAVSC strategy.

Farmers' perceptions of climate change and agricultural adaptation strategies in rural Sahel.

PubMed

Mertz, Ole; Mbow, Cheikh; Reenberg, Anette; Diouf, Awa

2009-05-01

Farmers in the Sahel have always been facing climatic variability at intra- and inter-annual and decadal time scales. While coping and adaptation strategies have traditionally included crop diversification, mobility, livelihood diversification, and migration, singling out climate as a direct driver of changes is not so simple. Using focus group interviews and a household survey, this study analyzes the perceptions of climate change and the strategies for coping and adaptation by sedentary farmers in the savanna zone of central Senegal. Households are aware of climate variability and identify wind and occasional excess rainfall as the most destructive climate factors. Households attribute poor livestock health, reduced crop yields and a range of other problems to climate factors, especially wind. However, when questions on land use and livelihood change are not asked directly in a climate context, households and groups assign economic, political, and social rather than climate factors as the main reasons for change. It is concluded that the communities studied have a high awareness of climate issues, but climatic narratives are likely to influence responses when questions mention climate. Change in land use and livelihood strategies is driven by adaptation to a range of factors of which climate appears not to be the most important. Implications for policy-making on agricultural and economic development will be to focus on providing flexible options rather than specific solutions to uncertain climate.

Experimental evolution in biofilm populations

PubMed Central

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

Experimental evolution in biofilm populations.

PubMed

Steenackers, Hans P; Parijs, Ilse; Dubey, Akanksha; Foster, Kevin R; Vanderleyden, Jozef

2016-05-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. © FEMS 2016.

Directed evolution: tailoring biocatalysts for industrial applications.

PubMed

Kumar, Ashwani; Singh, Suren

2013-12-01

Current challenges and promises of white biotechnology encourage protein engineers to use a directed evolution approach to generate novel and useful biocatalysts for various sets of applications. Different methods of enzyme engineering have been used in the past in an attempt to produce enzymes with improved functions and properties. Recent advancement in the field of random mutagenesis, screening, selection and computational design increased the versatility and the rapid development of enzymes under strong selection pressure with directed evolution experiments. Techniques of directed evolution improve enzymes fitness without understanding them in great detail and clearly demonstrate its future role in adapting enzymes for use in industry. Despite significant advances to date regarding biocatalyst improvement, there still remains a need to improve mutagenesis strategies and development of easy screening and selection tools without significant human intervention. This review covers fundamental and major development of directed evolution techniques, and highlights the advances in mutagenesis, screening and selection methods with examples of enzymes developed by using these approaches. Several commonly used methods for creating molecular diversity with their advantages and disadvantages including some recently used strategies are also discussed.

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

PubMed

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

2013-04-01

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

Adaptive sampling strategies with high-throughput molecular dynamics

NASA Astrophysics Data System (ADS)

Clementi, Cecilia

Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.

Metabolic evolution of Corynebacterium glutamicum for increased production of L-ornithine

PubMed Central

2013-01-01

Background L-ornithine is effective in the treatment of liver diseases and helps strengthen the heart. The commercial applications mean that efficient biotechnological production of L-ornithine has become increasingly necessary. Adaptive evolution strategies have been proven a feasible and efficient technique to achieve improved cellular properties without requiring metabolic or regulatory details of the strain. The evolved strains can be further optimised by metabolic engineering. Thus, metabolic evolution strategy was used for engineering Corynebacterium glutamicum to enhance L-ornithine production. Results A C. glutamicum strain was engineered by using a combination of gene deletions and adaptive evolution with 70 passages of growth-based selection. The metabolically evolved C. glutamicum strain, named ΔAPE6937R42, produced 24.1 g/L of L-ornithine in a 5-L bioreactor. The mechanism used by C. glutamicum ΔAPE6937R42 to produce L-ornithine was investigated by analysing transcriptional levels of select genes and NADPH contents. The upregulation of the transcription levels of genes involved in the upstream pathway of glutamate biosynthesis and the elevated NADPH concentration caused by the upregulation of the transcriptional level of the ppnK gene promoted L-ornithine production in C. glutamicum ΔAPE6937R42. Conclusions The availability of NADPH plays an important role in L-ornithine production in C. glutamicum. Our results demonstrated that the combination of growth-coupled evolution with analysis of transcript abundances provides a strategy to engineer microbial strains for improving production of target compounds. PMID:23725060

Recruiting hard-to-reach United States population sub-groups via adaptations of snowball sampling strategy

PubMed Central

Sadler, Georgia Robins; Lee, Hau-Chen; Seung-Hwan Lim, Rod; Fullerton, Judith

2011-01-01

Nurse researchers and educators often engage in outreach to narrowly defined populations. This article offers examples of how variations on the snowball sampling recruitment strategy can be applied in the creation of culturally appropriate, community-based information dissemination efforts related to recruitment to health education programs and research studies. Examples from the primary author’s program of research are provided to demonstrate how adaptations of snowball sampling can be effectively used in the recruitment of members of traditionally underserved or vulnerable populations. The adaptation of snowball sampling techniques, as described in this article, helped the authors to gain access to each of the more vulnerable population groups of interest. The use of culturally sensitive recruitment strategies is both appropriate and effective in enlisting the involvement of members of vulnerable populations. Adaptations of snowball sampling strategies should be considered when recruiting participants for education programs or subjects for research studies when recruitment of a population based sample is not essential. PMID:20727089

Neighbourhood reaction in the evolution of cooperation.

PubMed

Yang, Guoli; Zhang, Weiming; Xiu, Baoxin

2015-05-07

Combining evolutionary games with adaptive networks, an entangled model between strategy evolution and structure adaptation is researched in this paper. We consider a large population of cooperators C and defectors D placed in the networks, playing the repeated prisoner׳s dilemma (PD) games. Because of the conflicts between social welfare and personal rationality, both strategy and structure are allowed to change. In this paper, the dynamics of strategy originates form the partner imitation based on social learning and the dynamics of structure is driven by the active linking and neighbourhood reaction. Notably, the neighbourhood reaction is investigated considering the changes of interfaces between cooperators and defectors, where some neighbours may get away from the interface once the focal agent changes to different strategy. A rich landscape is demonstrated by changing various embedding parameters, which sheds light upon that reacting promptly to the shifted neighbour will promote the prevalence of cooperation. Our model encapsulates the dynamics of strategy, reaction and structure into the evolutionary games, which manifests some intriguing principles in the competition between two groups in natural populations, artificial systems and even human societies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental evolution: Assortative mating and sexual selection, independent of local adaptation, lead to reproductive isolation in the nematode Caenorhabditis remanei.

PubMed

Castillo, Dean M; Burger, Melissa K; Lively, Curtis M; Delph, Lynda F

2015-12-01

Using experimental evolution, we investigated the contributions of ecological divergence, sexual selection, and genetic drift to the evolution of reproductive isolation in Caenorhabditis remanei. The nematodes were reared on two different environments for 100 generations. They were assayed for fitness on both environments after 30, 64, and 100 generations, and hybrid fitness were analyzed after 64 and 100 generations. Mating propensity within and between populations was also analyzed. The design allowed us to determine whether local adaptation was synchronous with pre- and postzygotic reproductive isolation. Prezygotic isolation evolved quickly but was unconnected with adaptation to the divergent environments. Instead, prezygotic isolation was driven by mate preferences favoring individuals from the same replicate population. A bottleneck treatment, meant to enhance the opportunity for genetic drift, had no effect on prezygotic isolation. Postzygotic isolation occurred in crosses where at least one population had a large fitness advantage in its "home" environment. Taken together, our results suggest that prezygotic isolation did not depend on drift or adaptation to divergent environments, but instead resulted from differences in sexual interactions within individual replicates. Furthermore, our results suggest that postzygotic isolation can occur between populations even when only one population has greater fitness in its home environment. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Multi-type Childhood Abuse, Strategies of Coping, and Psychological Adaptations in Young Adults

PubMed Central

Sesar, Kristina; Šimić, Nataša; Barišić, Marijana

2010-01-01

Aim To retrospectively analyze the rate of multi-type abuse in childhood and the effects of childhood abuse and type of coping strategies on the psychological adaptation of young adults in a sample form the student population of the University of Mostar. Methods The study was conducted on a convenience sample of 233 students from the University of Mostar (196 female and 37 male), with a median age of 20 (interquartile range, 2). Exposure to abuse was determined using the Child Maltreatment Scales for Adults, which assesses emotional, physical, and sexual abuse, neglect, and witnessing family violence. Psychological adaptation was explored by the Trauma Symptom Checklist, which assesses anxiety/depression, sexual problems, trauma symptoms, and somatic symptoms. Strategies of coping with stress were explored by the Coping Inventory for Stressful Situations. Results Multi-type abuse in childhood was experienced by 172 participants (74%) and all types of abuse by 11 (5%) participants. Emotional and physical maltreatment were the most frequent types of abuse and mostly occurred together with other types of abuse. Significant association was found between all types of abuse (r = 0.436-0.778, P < 0.050). Exposure to sexual abuse in childhood and coping strategies were significant predictors of anxiety/depression (R2 = 0.3553), traumatic symptoms (R2 = 0.2299), somatic symptoms (R2 = 0.2173), and sexual problems (R2 = 0.1550, P < 0.001). Conclusion Exposure to multi-type abuse in childhood is a traumatic experience with long-term negative effects. Problem-oriented coping strategies ensure a better psychosocial adaptation than emotion-oriented strategies. PMID:20960590

Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress

PubMed Central

Yang, Jie; Wang, Zhen Long; Zhao, Xin Quan; Wang, De Peng; Qi, De Lin; Xu, Bao Hong; Ren, Yong Hong; Tian, Hui Fang

2008-01-01

Background Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism's fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. Methodology/Principal Findings To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase α and β subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. Conclusions/Significance Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas' ecological adaptation to extreme environmental

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

PubMed

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

2017-05-01

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

Are adaptation costs necessary to build up a local adaptation pattern?

PubMed

Magalhães, Sara; Blanchet, Elodie; Egas, Martijn; Olivieri, Isabelle

2009-08-03

Ecological specialization is pervasive in phytophagous arthropods. In such specialization mode, limits to host range are imposed by trade-offs preventing adaptation to several hosts. The occurrence of such trade-offs is inferred by a pattern of local adaptation, i.e., a negative correlation between relative performance on different hosts. To establish a causal link between local adaptation and trade-offs, we performed experimental evolution of spider mites on cucumber, tomato and pepper, starting from a population adapted to cucumber. Spider mites adapted to each novel host within 15 generations and no further evolution was observed at generation 25. A pattern of local adaptation was found, as lines evolving on a novel host performed better on that host than lines evolving on other hosts. However, costs of adaptation were absent. Indeed, lines adapted to tomato had similar or higher performance on pepper than lines evolving on the ancestral host (which represent the initial performance of all lines) and the converse was also true, e.g. negatively correlated responses were not observed on the alternative novel host. Moreover, adapting to novel hosts did not result in decreased performance on the ancestral host. Adaptation did not modify host ranking, as all lines performed best on the ancestral host. Furthermore, mites from all lines preferred the ancestral to novel hosts. Mate choice experiments indicated that crosses between individuals from the same or from a different selection regime were equally likely, hence development of reproductive isolation among lines adapted to different hosts is unlikely. Therefore, performance and preference are not expected to impose limits to host range in our study species. Our results show that the evolution of a local adaptation pattern is not necessarily associated with the evolution of an adaptation cost.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.

PubMed

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N

2014-03-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

PubMed Central

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N.

2014-01-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea. PMID:24371267

Stepping through treatment: reflections on an adaptive treatment strategy among methamphetamine users with depression.

PubMed

Kay-Lambkin, Frances J; Baker, Amanda L; McKetin, Rebecca; Lee, Nicole

2010-09-01

Stepped-care has been recommended in the alcohol and other drug field and adopted in a number of service settings, but few research projects have examined this approach. This article aims to describe a pilot trial of stepped-care methods in the treatment of methamphetamine use and depression comorbidity. An adaptive treatment strategy was developed based on recommendations for stepped-care among methamphetamine users, and incorporating cognitive behaviour therapy/motivational intervention for methamphetamine use and depression. The adaptive treatment strategy was compared with a fixed treatment, comprising an extended integrated cognitive behaviour therapy/motivational intervention treatment. Eighteen participants across two study sites were involved in the trial, and were current users of methamphetamines (at least once weekly) exhibiting at least moderate symptoms of depression (score of 17 or greater on the Beck Depression Inventory II). Treatment delivered via the adaptive treatment (stepped-care) model was associated with improvement in depression and methamphetamine use, however, was not associated with more efficient delivery of psychological treatment to this population relative to the comparison treatment. This pilot trial attests to the potential for adaptive treatment strategies to increase the evidence base for stepped-care approaches within the alcohol and other drug field. However, in order for stepped-care treatment in this trial to be delivered efficiently, specific training in the delivery and philosophy of the model is required.

Cultural adaptation of preschool PATHS (Promoting Alternative Thinking Strategies) curriculum for Pakistani children.

PubMed

Inam, Ayesha; Tariq, Pervaiz N; Zaman, Sahira

2015-06-01

Cultural adaptation of evidence-based programmes has gained importance primarily owing to its perceived impact on the established effectiveness of a programme. To date, many researchers have proposed different frameworks for systematic adaptation process. This article presents the cultural adaptation of preschool Promoting Alternative Thinking Strategies (PATHS) curriculum for Pakistani children using the heuristic framework of adaptation (Barrera & Castro, 2006). The study was completed in four steps: information gathering, preliminary adaptation design, preliminary adaptation test and adaptation refinement. Feedbacks on programme content suggested universality of the core programme components. Suggested changes were mostly surface structure: language, presentation of materials, conceptual equivalence of concepts, training needs of implementation staff and frequency of programme delivery. In-depth analysis was done to acquire cultural equivalence. Pilot testing of the outcome measures showed strong internal consistency. The results were further discussed with reference to similar work undertaken in other cultures. © 2014 International Union of Psychological Science.

Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.

PubMed

Win, Joe; Kamoun, Sophien

2008-04-01

Plant pathogenic microbes deliver effector proteins inside host cells to modulate plant defense circuitry and enable parasitic colonization. As genome sequences from plant pathogens become available, genome-wide evolutionary analyses will shed light on how pathogen effector genes evolved and adapted to the cellular environment of their host plants. In the August 2007 issue of Plant Cell, we described adaptive evolution (positive selection) in the cytoplasmic RXLR effectors of three recently sequenced oomycete plant pathogens. Here, we summarize our findings and describe additional data that further validate our approach.

A global analysis of adaptive evolution of operons in cyanobacteria.

PubMed

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

2013-02-01

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

The evolution of Rare Pride: using evaluation to drive adaptive management in a biodiversity conservation organization.

PubMed

Jenks, Brett; Vaughan, Peter W; Butler, Paul J

2010-05-01

Rare Pride is a social marketing program that stimulates human behavior change in order to promote biodiversity conservation in critically threatened regions in developing countries. A series of formal evaluation studies, networking strategies, and evaluative inquiries have driven a 20-year process of adaptive management that has resulted in extensive programmatic changes within Pride. This paper describes the types of evaluation that Rare used to drive adaptive management and the changes it caused in Pride's theory-of-change and programmatic structure. We argue that (a) qualitative data gathered from partners and staff through structured interviews is most effective at identifying problems with current programs and procedures, (b) networking with other organizations is the most effective strategy for learning of new management strategies, and (c) quantitative data gathered through surveys is effective at measuring program impact and quality. Adaptive management has allowed Rare to increase its Pride program from implementing about two campaigns per year in 2001 to more than 40 per year in 2009 while improving program quality and maintaining program impact. Copyright 2009 Elsevier Ltd. All rights reserved.

The evolution of flowering strategies in US weedy rice.

PubMed

Thurber, Carrie S; Reagon, Michael; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

2014-10-01

• Local adaptation in plants often involves changes in flowering time in response to day length and temperature. Many crops have been selected for uniformity in flowering time. In contrast, variable flowering may be important for increased competitiveness in weed species invading the agricultural environment. Given the shared species designation of cultivated rice (Oryza sativa) and its the invasive conspecific weed, weedy rice, we assessed the extent to which flowering time differed between these groups. We further assessed whether genes affecting flowering time variation in rice could play a role in the evolution of weedy rice in the United States.• We quantified flowering time under day-neutral conditions in weedy, cultivated, and wild Oryza groups. We also sequenced two candidate gene regions: Hd1, a locus involved in promotion of flowering under short days, and the promoter of Hd3a, a locus encoding the mobile signal that induces flowering.• We found that flowering time has diverged between two distinct weedy rice groups, such that straw-hull weeds tend to flower earlier and black-hull awned weeds tend to flower later than cultivated rice. These differences are consistent with weed Hd1 alleles. At both loci, weeds share haplotypes with their cultivated progenitors, despite significantly different flowering times.• Our phenotypic data indicate the existence of multiple flowering strategies in weedy rice. Flowering differences between weeds and ancestors suggest this trait has evolved rapidly. From a weed management standpoint, there is the potential for overlap in flowering of black-hull awned weeds and crops in the United States, permitting hybridization and the potential escape of genes from crops. © 2014 Botanical Society of America, Inc.

Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

PubMed Central

Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

2016-01-01

The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers. PMID:27336480

Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs.

PubMed

Montelli, Stefano; Peruffo, Antonella; Patarnello, Tomaso; Cozzi, Bruno; Negrisolo, Enrico

2016-01-01

The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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.).

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

PubMed Central

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

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

PubMed

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.

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

PubMed Central

Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.; Palsson, Bernhard O.; Antoniewicz, Maciek R.

2018-01-01

Adaptive laboratory evolution (ALE) is a widely-used method for improving the fitness of microorganisms in selected environmental conditions. It has been applied previously to Escherichia coli K-12 MG1655 during aerobic exponential growth on glucose minimal media, a frequently used model organism and growth condition, to probe the limits of E. coli growth rate and gain insights into fast growth phenotypes. Previous studies have described up to 1.6-fold increases in growth rate following ALE, and have identified key causal genetic mutations and changes in transcriptional patterns. Here, we report for the first time intracellular metabolic fluxes for six such adaptively evolved strains, as determined by high-resolution 13C-metabolic flux analysis. Interestingly, we found that intracellular metabolic pathway usage changed very little following adaptive evolution. Instead, at the level of central carbon metabolism the faster growth was facilitated by proportional increases in glucose uptake and all intracellular rates. Of the six evolved strains studied here, only one strain showed a small degree of flux rewiring, and this was also the strain with unique genetic mutations. A comparison of fluxes with two other wild-type (unevolved) E. coli strains, BW25113 and BL21, showed that inter-strain differences are greater than differences between the parental and evolved strains. Principal component analysis highlighted that nearly all flux differences (95%) between the nine strains were captured by only two principal components. The distance between measured and flux balance analysis predicted fluxes was also investigated. It suggested a relatively wide range of similar stoichiometric optima, which opens new questions about the path-dependency of adaptive evolution. PMID:28951266

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

PubMed Central

Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

2017-01-01

Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life. PMID:28178274

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2013-01-01

Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world. PMID:23188175

Forest adjacent households' voices on their perceptions and adaptation strategies to climate change in Kilombero District, Tanzania.

PubMed

Balama, Chelestino; Augustino, Suzana; Eriksen, Siri; Makonda, Fortunatus B S

2016-01-01

Climate change is a global and local challenge to both sustainable livelihoods and economic development. Tanzania as other countries of the world has been affected. Several studies have been conducted on farmers' perceptions and adaptation to climate change in the country, but little attention has been devoted to forest adjacent households in humid areas. This study assessed this gap through assessing forest adjacent households' voices on perceptions and adaptation strategies to climate change in Kilombero District, Tanzania. Data collection involved key informant interviews, focus group discussions and household questionnaires. Results showed that the majority of households perceived changed climate in terms of temperature increase, unpredictable rainfall, frequent occurrence of floods, increased dry spells during rainy season coupled with decreased water sources and emergence of new pests and diseases. The perceived change in climate has impacted agriculture productivity as the main livelihood source. Different coping and adaptation strategies are employed. These are; crop diversification, changing cropping calendar, adopting modern farming technologies, and increasing reliance on non-timber forest products. These strategies were positively and significantly influenced by socio-economic factors including household size, residence period, land ownership and household income. The study concludes that, there are changes in climatic conditions; and to respond to these climatic changes, forest adjacent households have developed numerous coping and adaptation strategies, which were positively and significantly influenced by some socio-economic factors. The study calls for actual implementation of local climate change policies and strategies in order to enhance adaptive capacity at household level.

The influence of gender and age on choice of flood adaptation strategies: A case study of Zambia and Namibia..

NASA Astrophysics Data System (ADS)

Mabuku, Monde

2017-04-01

It is reported that flood events will increase due to variability and change in climate, thus increasing the number of people exposed to flooding disasters. This exposure negatively impacts rural households' livelihoods. Women, men, young, old has distinctive vulnerability and this shapes the choice of flood adaptation strategies. This calls for a need to adopt group specific interventions to strengthen local adaptive capacity to flooding for the affected population. The purpose of this case study was to determine the adaptation strategies to floods adopted by rural households in the Zambezi region of Namibia and Mwandi district of Zambia. The study further examined how gender and age influenced the choice of different adaptation strategies. Six focus group meetings and a questionnaire survey of 207 randomly sampled households were conducted in the flood prone areas of the study. Descriptive statistics results on the adaptation strategies indicated that a majority of the households in Namibia learnt to live with floods (86%),practiced mafisa cattle trade (86%), flood water harvesting (68%), practiced early and late planting (63%), prayed (55%), practiced conservation agriculture (54%) and fish farming (53%). In Zambia the adaptation strategies were; conservation agriculture (91%), acquiring better skills on preparedness (66%), flood water harvesting (63%), praying (60%), and flood proofing (52%). Logistic regression analysis showed that age positively and significantly influenced the likelihood of taking up adaptation strategies such as tree planting, relocation to higher ground, flood water harvesting, early and late planting. The older the respondents the more likely they were to adopt the strategies mentioned. More young ones were more likely to adopt acquiring better skills on flood preparedness and mafisa cattle trading than the old ones. Gender positively and significantly influenced mafisa cattle trade (p<0.01), male headed households were more likely to

Comparative genomics reveals insights into avian genome evolution and adaptation

PubMed Central

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

Paradigms for adaptive statistical information designs: practical experiences and strategies.

PubMed

Wang, Sue-Jane; Hung, H M James; O'Neill, Robert

2012-11-10

design. We highlight the substantial risk of planning the sample size for confirmatory trials when information is very uninformative and stipulate the advantages of adaptive statistical information designs for planning exploratory trials. Practical experiences and strategies as lessons learned from more recent adaptive design proposals will be discussed to pinpoint the improved utilities of adaptive design clinical trials and their potential to increase the chance of a successful drug development. Published 2012. This article is a US Government work and is in the public domain in the USA.

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

PubMed

Klemm, Elizabeth J; Gkrania-Klotsas, Effrossyni; Hadfield, James; Forbester, Jessica L; Harris, Simon R; Hale, Christine; Heath, Jennifer N; Wileman, Thomas; Clare, Simon; Kane, Leanne; Goulding, David; Otto, Thomas D; Kay, Sally; Doffinger, Rainer; Cooke, Fiona J; Carmichael, Andrew; Lever, Andrew Ml; Parkhill, Julian; MacLennan, Calman A; Kumararatne, Dinakantha; Dougan, Gordon; Kingsley, Robert A

2016-03-01

Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts 1 . Host adaptation can potentially progress to host restriction where the pathogen is strictly limited to a single host species and is frequently associated with more severe symptoms. Host-adapted and host-restricted bacterial clades evolve from within a broader host-promiscuous species and sometimes target different niches within their specialist hosts, such as adapting from a mucosal to a systemic lifestyle. Genome degradation, marked by gene inactivation and deletion, is a key feature of host adaptation, although the triggers initiating genome degradation are not well understood. Here, we show that a chronic systemic non-typhoidal Salmonella infection in an immunocompromised human patient resulted in genome degradation targeting genes that are expendable for a systemic lifestyle. We present a genome-based investigation of a recurrent blood-borne Salmonella enterica serotype Enteritidis ( S . Enteritidis) infection covering 15 years in an interleukin (IL)-12 β-1 receptor-deficient individual that developed into an asymptomatic chronic infection. The infecting S. Enteritidis harbored a mutation in the mismatch repair gene mutS that accelerated the genomic mutation rate. Phylogenetic analysis and phenotyping of multiple patient isolates provides evidence for a remarkable level of within-host evolution that parallels genome changes present in successful host-restricted bacterial pathogens but never before observed on this timescale. Our analysis identifies common pathways of host adaptation and demonstrates the role that immunocompromised individuals can play in this process.

How Can Evolution Learn?

PubMed

Watson, Richard A; Szathmáry, Eörs

2016-02-01

The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the 'uninformed' process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles - the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Spatial Selection and Local Adaptation Jointly Shape Life-History Evolution during Range Expansion.

PubMed

Van Petegem, Katrien H P; Boeye, Jeroen; Stoks, Robby; Bonte, Dries

2016-11-01

In the context of climate change and species invasions, range shifts increasingly gain attention because the rates at which they occur in the Anthropocene induce rapid changes in biological assemblages. During range shifts, species experience multiple selection pressures. For poleward expansions in particular, it is difficult to interpret observed evolutionary dynamics because of the joint action of evolutionary processes related to spatial selection and to adaptation toward local climatic conditions. To disentangle the effects of these two processes, we integrated stochastic modeling and data from a common garden experiment, using the spider mite Tetranychus urticae as a model species. By linking the empirical data with those derived form a highly parameterized individual-based model, we infer that both spatial selection and local adaptation contributed to the observed latitudinal life-history divergence. Spatial selection best described variation in dispersal behavior, while variation in development was best explained by adaptation to the local climate. Divergence in life-history traits in species shifting poleward could consequently be jointly determined by contemporary evolutionary dynamics resulting from adaptation to the environmental gradient and from spatial selection. The integration of modeling with common garden experiments provides a powerful tool to study the contribution of these evolutionary processes on life-history evolution during range expansion.

Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance

PubMed Central

Zhang, Xiaolin; Reed, Jennifer L.

2014-01-01

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

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution.

PubMed

Price, Christopher T D; Richards, Ashley M; Von Dwingelo, Juanita E; Samara, Hala A; Abu Kwaik, Yousef

2014-02-01

Legionella pneumophila, the causative agent of Legionnaires' disease, invades and proliferates within a diverse range of free-living amoeba in the environment, but upon transmission to humans, the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host, but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. Legionella pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Consistent individual differences in human social learning strategies.

PubMed

Molleman, Lucas; van den Berg, Pieter; Weissing, Franz J

2014-04-04

Social learning has allowed humans to build up extensive cultural repertoires, enabling them to adapt to a wide variety of environmental and social conditions. However, it is unclear which social learning strategies people use, especially in social contexts where their payoffs depend on the behaviour of others. Here we show experimentally that individuals differ in their social learning strategies and that they tend to employ the same learning strategy irrespective of the interaction context. Payoff-based learners focus on their peers' success, while decision-based learners disregard payoffs and exclusively focus on their peers' past behaviour. These individual differences may be of considerable importance for cultural evolution. By means of a simple model, we demonstrate that groups harbouring individuals with different learning strategies may be faster in adopting technological innovations and can be more efficient through successful role differentiation. Our study highlights the importance of individual variation for human interactions and sheds new light on the dynamics of cultural evolution.

Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout, Oncorhynchus mykiss.

PubMed

Phillis, Corey C; Moore, Jonathan W; Buoro, Mathieu; Hayes, Sean A; Garza, John Carlos; Pearse, Devon E

2016-01-01

Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. We created 9 families and 917 offspring from 14 parents collected from the above- and below-barrier populations. After 1 year of common garden-rearing above-barrier offspring were 11% smaller and 32% lighter than below-barrier offspring. Using a novel analytical approach, we estimate that the mean size at which above-barrier fish switch between the resident and migrant tactic is 43% larger than below-barrier fish. As a result, above-barrier fish were 26% less likely to express the migratory tactic. Our results demonstrate how rapid and opposing changes in size-at-age and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution toward the resident life history on timescales relevant for conservation and management of conditionally migratory species. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Adaptive backstepping sliding mode control with fuzzy monitoring strategy for a kind of mechanical system.

PubMed

Song, Zhankui; Sun, Kaibiao

2014-01-01

A novel adaptive backstepping sliding mode control (ABSMC) law with fuzzy monitoring strategy is proposed for the tracking-control of a kind of nonlinear mechanical system. The proposed ABSMC scheme combining the sliding mode control and backstepping technique ensure that the occurrence of the sliding motion in finite-time and the trajectory of tracking-error converge to equilibrium point. To obtain a better perturbation rejection property, an adaptive control law is employed to compensate the lumped perturbation. Furthermore, we introduce fuzzy monitoring strategy to improve adaptive capacity and soften the control signal. The convergence and stability of the proposed control scheme are proved by using Lyaponov's method. Finally, numerical simulations demonstrate the effectiveness of the proposed control scheme. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity.

PubMed

Weng, Jing-Ke; Ye, Mingli; Li, Bin; Noel, Joseph P

2016-08-11

Classically, hormones elicit specific cellular responses by activating dedicated receptors. Nevertheless, the biosynthesis and turnover of many of these hormone molecules also produce chemically related metabolites. These molecules may also possess hormonal activities; therefore, one or more may contribute to the adaptive plasticity of signaling outcomes in host organisms. Here, we show that a catabolite of the plant hormone abscisic acid (ABA), namely phaseic acid (PA), likely emerged in seed plants as a signaling molecule that fine-tunes plant physiology, environmental adaptation, and development. This trait was facilitated by both the emergence-selection of a PA reductase that modulates PA concentrations and by the functional diversification of the ABA receptor family to perceive and respond to PA. Our results suggest that PA serves as a hormone in seed plants through activation of a subset of ABA receptors. This study demonstrates that the co-evolution of hormone metabolism and signaling networks can expand organismal resilience. Copyright © 2016 Elsevier Inc. All rights reserved.

Health co-benefits and risks of public health adaptation strategies to climate change: a review of current literature.

PubMed

Cheng, June J; Berry, Peter

2013-04-01

Many public health adaptation strategies have been identified in response to climate change. This report reviews current literature on health co-benefits and risks of these strategies to gain a better understanding of how they may affect health. A literature review was conducted electronically using English language literature from January 2000 to March 2012. Of 812 articles identified, 22 peer-reviewed articles that directly addressed health co-benefits or risks of adaptation were included in the review. The co-benefits and risks identified in the literature most commonly relate to improvements in health associated with adaptation actions that affect social capital and urban design. Health co-benefits of improvements in social capital have positive influences on mental health, independently of other determinants. Risks included reinforcing existing misconceptions regarding health. Health co-benefits of urban design strategies included reduced obesity, cardiovascular disease and improved mental health through increased physical activity, cooling spaces (e.g., shaded areas), and social connectivity. Risks included pollen allergies with increased urban green space, and adverse health effects from heat events through the use of air conditioning. Due to the current limited understanding of the full impacts of the wide range of existing climate change adaptation strategies, further research should focus on both unintended positive and negative consequences of public health adaptation.

Spatially heterogeneous stochasticity and the adaptive diversification of dormancy.

PubMed

Rajon, E; Venner, S; Menu, F

2009-10-01

Diversified bet-hedging, a strategy that leads several individuals with the same genotype to express distinct phenotypes in a given generation, is now well established as a common evolutionary response to environmental stochasticity. Life-history traits defined as diversified bet-hedging (e.g. germination or diapause strategies) display marked differences between populations in spatial proximity. In order to find out whether such differences can be explained by local adaptations to spatially heterogeneous environmental stochasticity, we explored the evolution of bet-hedging dormancy strategies in a metapopulation using a two-patch model with patch differences in stochastic juvenile survival. We found that spatial differences in the level of environmental stochasticity, restricted dispersal, increased fragmentation and intermediate survival during dormancy all favour the adaptive diversification of bet-hedging dormancy strategies. Density dependency also plays a major role in the diversification of dormancy strategies because: (i) it may interact locally with environmental stochasticity and amplify its effects; however, (ii) it can also generate chaotic population dynamics that may impede diversification. Our work proposes new hypotheses to explain the spatial patterns of bet-hedging strategies that we hope will encourage new empirical studies of this topic.

Evolution in an extreme environment: developmental biases and phenotypic integration in the adaptive radiation of antarctic notothenioids.

PubMed

Hu, Yinan; Ghigliotti, Laura; Vacchi, Marino; Pisano, Eva; Detrich, H William; Albertson, R Craig

2016-06-29

Over the past 40 million years water temperatures have dramatically dropped in the Southern Ocean, which has led to the local extinction of most nearshore fish lineages. The evolution of antifreeze glycoproteins in notothenioids, however, enabled these ancestrally benthic fishes to survive and adapt as temperatures reached the freezing point of seawater (-1.86 °C). Antarctic notothenioids now represent the primary teleost lineage in the Southern Ocean and are of fundamental importance to the local ecosystem. The radiation of notothenioids has been fostered by the evolution of "secondary pelagicism", the invasion of pelagic habitats, as the group diversified to fill newly available foraging niches in the water column. While elaborate craniofacial modifications have accompanied this adaptive radiation, little is known about how these morphological changes have contributed to the evolutionary success of notothenioids. We used a 3D-morphometrics approach to investigate patterns of morphological variation in the craniofacial skeleton among notothenioids, and show that variation in head shape is best explained by divergent selection with respect to foraging niche. We document further an accelerated rate of morphological evolution in the icefish family Channichthyidae, and show that their rapid diversification was accompanied by the evolution of relatively high levels of morphological integration. Whereas most studies suggest that extensive integration should constrain phenotypic evolution, icefish stand out as a rare example of increased integration possibly facilitating evolutionary potential. Finally, we show that the unique feeding apparatus in notothenioids in general, and icefish in particular, can be traced to shifts in early developmental patterning mechanisms and ongoing growth of the pharyngeal skeleton. Our work suggests that ecological opportunity is a major factor driving craniofacial variation in this group. Further, the observation that closely related

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

PubMed Central

Melo-Ferreira, José; Vilela, Joana; Fonseca, Miguel M.; da Fonseca, Rute R.; Boursot, Pierre; Alves, Paulo C.

2014-01-01

Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from 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. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive. PMID:24696399

Evolution of learning strategies in temporally and spatially variable environments: A review of theory

PubMed Central

Aoki, Kenichi; Feldman, Marcus W.

2013-01-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change – coevolutionary, two-timescale, and information decay – are compared and shown to sometimes yield contradictory results. The so-called Rogers’ paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers’ paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. PMID:24211681

Evolution of learning strategies in temporally and spatially variable environments: a review of theory.

PubMed

Aoki, Kenichi; Feldman, Marcus W

2014-02-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change--coevolutionary, two-timescale, and information decay--are compared and shown to sometimes yield contradictory results. The so-called Rogers' paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers' paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. Copyright © 2013 Elsevier Inc. All rights reserved.

The New Weather Radar for America's Space Program in Florida: A Temperature Profile Adaptive Scan Strategy

NASA Technical Reports Server (NTRS)

Carey, L. D.; Petersen, W. A.; Deierling, W.; Roeder, W. P.

2009-01-01

A new weather radar is being acquired for use in support of America s space program at Cape Canaveral Air Force Station, NASA Kennedy Space Center, and Patrick AFB on the east coast of central Florida. This new radar replaces the modified WSR-74C at Patrick AFB that has been in use since 1984. The new radar is a Radtec TDR 43-250, which has Doppler and dual polarization capability. A new fixed scan strategy was designed to best support the space program. The fixed scan strategy represents a complex compromise between many competing factors and relies on climatological heights of various temperatures that are important for improved lightning forecasting and evaluation of Lightning Launch Commit Criteria (LCC), which are the weather rules to avoid lightning strikes to in-flight rockets. The 0 C to -20 C layer is vital since most generation of electric charge occurs within it and so it is critical in evaluating Lightning LCC and in forecasting lightning. These are two of the most important duties of 45 WS. While the fixed scan strategy that covers most of the climatological variation of the 0 C to -20 C levels with high resolution ensures that these critical temperatures are well covered most of the time, it also means that on any particular day the radar is spending precious time scanning at angles covering less important heights. The goal of this project is to develop a user-friendly, Interactive Data Language (IDL) computer program that will automatically generate optimized radar scan strategies that adapt to user input of the temperature profile and other important parameters. By using only the required scan angles output by the temperature profile adaptive scan strategy program, faster update times for volume scans and/or collection of more samples per gate for better data quality is possible, while maintaining high resolution at the critical temperature levels. The temperature profile adaptive technique will also take into account earth curvature and refraction

Development of adaptive observation strategy using retrospective optimal interpolation

NASA Astrophysics Data System (ADS)

Noh, N.; Kim, S.; Song, H.; Lim, G.

2011-12-01

Retrospective optimal interpolation (ROI) is a method that is used to minimize cost functions with multiple minima without using adjoint models. Song and Lim (2011) perform the experiments to reduce the computational costs for implementing ROI by transforming the control variables into eigenvectors of background error covariance. We adapt the ROI algorithm to compute sensitivity estimates of severe weather events over the Korean peninsula. The eigenvectors of the ROI algorithm is modified every time the observations are assimilated. This implies that the modified eigenvectors shows the error distribution of control variables which are updated by assimilating observations. So, We can estimate the effects of the specific observations. In order to verify the adaptive observation strategy, High-impact weather over the Korean peninsula is simulated and interpreted using WRF modeling system and sensitive regions for each high-impact weather is calculated. The effects of assimilation for each observation type is discussed.

Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance.

PubMed

Miller, Corwin; Kong, Jiayi; Tran, Truc T; Arias, Cesar A; Saxer, Gerda; Shamoo, Yousif

2013-11-01

With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their clinical efficacy. While genomic studies have provided a wealth of information about the alleles associated with adaptation to antibiotics, they do not provide essential information about the relative importance of genomic changes, their order of appearance, or potential epistatic relationships between adaptive changes. Here we used quantitative experimental evolution of a single polymorphic population in continuous culture with whole-genome sequencing and allelic frequency measurements to study daptomycin (DAP) resistance in the vancomycin-resistant clinical pathogen Enterococcus faecalis S613. Importantly, we sustained both planktonic and nonplanktonic (i.e., biofilm) populations in coculture as the concentration of antibiotic was raised, facilitating the development of more ecological complexity than is typically observed in laboratory evolution. Quantitative experimental evolution revealed a clear order and hierarchy of genetic changes leading to resistance, the signaling and metabolic pathways responsible, and the relative importance of these mutations to the evolution of DAP resistance. Despite the relative simplicity of this ex vivo approach compared to the ecological complexity of the human body, we showed that experimental evolution allows for rapid identification of clinically relevant adaptive molecular pathways and new targets for drug design in pathogens.

Don't worry, be happy: The role of positive emotionality and adaptive emotion regulation strategies for youth depressive symptoms.

PubMed

Van Beveren, Marie-Lotte; Harding, Kaitlin; Beyers, Wim; Braet, Caroline

2018-03-01

Low positive emotionality (PE) represents a temperamental vulnerability to depression in youth. Until now, little research has examined the mechanisms linking PE to depressive symptoms. Starting from integrated cognitive-affective models of depression, we aimed to study adaptive emotion regulation (ER) as a key underlying mechanism in the temperament-depression relationship. This study investigated whether adaptive ER strategies mediate the association between PE and depressive symptoms in a large community-based sample of youth, using a cross-sectional design. Participants were 1,655 youth (54% girls; 7-16 years, M = 11.41, SD = 1.88) who filled out a set of questionnaires assessing temperament, adaptive ER strategies, and depressive symptoms. Results revealed that low PE was significantly related to higher depressive symptoms among youth and that a lack of total adaptive ER abilities mediated this relationship. More specifically, the infrequent use of problem-solving appeared to be of significant importance. Problems in positive refocusing and a deficient use of forgetting mediated the relationships between low PE and high negative emotionality (NE) in predicting depressive symptoms. Reappraisal and distraction were not significant mediators. Results highlight the need to account for temperamental PE and adaptive ER strategies when studying youth depression. The findings contribute to a more nuanced understanding on the differential role of temperamental risk factors for developing depressive symptoms at an early stage and advocate for greater attention to adaptive ER strategies. Clinical interventions for youth depression may be improved by incorporating adaptive emotion regulation (ER) strategies and enhancing positive emotions. Youth low in positive emotionality (PE) may especially benefit from learning adaptive ER skills. Clinical practitioners should focus on alleviating negative emotions and enhancing positive emotions, especially among youth low in PE

Anther evolution: pollen presentation strategies when pollinators differ.

PubMed

Castellanos, Maria Clara; Wilson, Paul; Keller, Sarah J; Wolfe, Andrea D; Thomson, James D

2006-02-01

Male-male competition in plants is thought to exert selection on flower morphology and on the temporal presentation of pollen. Theory suggests that a plant's pollen dosing strategy should evolve to match the abundance and pollen transfer efficiency of its pollinators. Simultaneous pollen presentation should be favored when pollinators are infrequent or efficient at delivering the pollen they remove, whereas gradual dosing should optimize delivery by frequent and wasteful pollinators. Among Penstemon and Keckiella species, anthers vary in ways that affect pollen release, and the morphology of dried anthers reliably indicates how they dispense pollen. In these genera, hummingbird pollination has evolved repeatedly from hymenopteran pollination. Pollen production does not change with evolutionary shifts between pollinators. We show that after we control for phylogeny, hymenopteran-adapted species present their pollen more gradually than hummingbird-adapted relatives. In a species pair that seemed to defy the pattern, the rhythm of anther maturation produced an equivalent dosing effect. These results accord with previous findings that hummingbirds can be more efficient than bees at delivering pollen.

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

PubMed

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

2017-03-01

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

Combined use of leaf size and economics traits allows direct comparison of hydrophyte and terrestrial herbaceous adaptive strategies.

PubMed

Pierce, Simon; Brusa, Guido; Sartori, Matteo; Cerabolini, Bruno E L

2012-04-01

Hydrophytes generally exhibit highly acquisitive leaf economics. However, a range of growth forms is evident, from small, free-floating and rapidly growing Lemniden to large, broad-leaved Nymphaeiden, denoting variability in adaptive strategies. Traits used to classify adaptive strategies in terrestrial species, such as canopy height, are not applicable to hydrophytes. We hypothesize that hydrophyte leaf size traits and economics exhibit sufficient overlap with terrestrial species to allow a common classification of plant functional types, sensu Grime's CSR theory. Leaf morpho-functional traits were measured for 61 species from 47 water bodies in lowland continental, sub-alpine and alpine bioclimatic zones in southern Europe and compared against the full leaf economics spectrum and leaf size range of terrestrial herbs, and between hydrophyte growth forms. Hydrophytes differed in the ranges and mean values of traits compared with herbs, but principal components analysis (PCA) demonstrated that both groups shared axes of trait variability: PCA1 encompassed size variation (area and mass), and PCA2 ranged from relatively dense, carbon-rich leaves to nitrogen-rich leaves of high specific leaf area (SLA). Most growth forms exhibited trait syndromes directly equivalent to herbs classified as R adapted, although Nymphaeiden ranged between C and SR adaptation. Our findings support the hypothesis that hydrophyte adaptive strategy variation reflects fundamental trade-offs in economics and size that govern all plants, and that hydrophyte adaptive strategies can be directly compared with terrestrial species by combining leaf economics and size traits.

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

PubMed Central

2009-01-01

Background Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. Results In the present study, we describe the genome sequencing of 11 endpoints of Escherichia coli that underwent 60-day laboratory adaptive evolution under growth rate selection pressure in lactate minimal media. Two to eight mutations were identified per endpoint. Generally, each endpoint acquired mutations to different genes. The most notable exception was an 82 base-pair deletion in the rph-pyrE operon that appeared in 7 of the 11 adapted strains. This mutation conferred an approximately 15% increase to the growth rate when experimentally introduced to the wild-type background and resulted in an approximately 30% increase to growth rate when introduced to a background already harboring two adaptive mutations. Additionally, most endpoints had a mutation in a regulatory gene (crp or relA, for example) or the RNA polymerase. Conclusions The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation. PMID:19849850

Convergent Evolution of the Osmoregulation System in Decapod Shrimps.

PubMed

Yuan, Jianbo; Zhang, Xiaojun; Liu, Chengzhang; Duan, Hu; Li, Fuhua; Xiang, Jianhai

2017-02-01

In adaptating to different aquatic environments, seawater (SW) and freshwater (FW) shrimps have exploited different adaptation strategies, which should generate clusters of genes with different adaptive features. However, little is known about the genetic basis of these physiological adaptations. Thus, in this study, we performed comparative transcriptomics and adaptive evolution analyses on SW and FW shrimps and found that convergent evolution may have happened on osmoregulation system of shrimps. We identified 275 and 234 positively selected genes in SW and FW shrimps, respectively, which enriched in the functions of ion-binding and membrane-bounded organelles. Among them, five (CaCC, BEST2, GPDH, NKA, and Integrin) and four (RasGAP, RhoGDI, CNK3, and ODC) osmoregulation-related genes were detected in SW and FW shrimps, respectively. All five genes in SW shrimps have been reported to have positive effects on ion transportation, whereas RasGAP and RhoGDI in FW shrimps are associated with negative control of ion transportation, and CNK3 and ODC play central roles in cation homeostasis. Besides, the phylogenetic tree reconstructed from the positively selected sites separated the SW and FW shrimps into two groups. Distinct subsets of parallel substitutions also have been found in these osmoregulation-related genes in SW and FW shrimps. Therefore, our results suggest that distinct convergent evolution may have occurred in the osmoregulation systems of SW and FW shrimps. Furthermore, positive selection of osmoregulation-related genes may be beneficial for the regulation of water and salt balance in decapod shrimps.

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

PubMed

Long, Christopher P; Gonzalez, Jacqueline E; Feist, Adam M; Palsson, Bernhard O; Antoniewicz, Maciek R

2017-11-01

Adaptive laboratory evolution (ALE) is a widely-used method for improving the fitness of microorganisms in selected environmental conditions. It has been applied previously to Escherichia coli K-12 MG1655 during aerobic exponential growth on glucose minimal media, a frequently used model organism and growth condition, to probe the limits of E. coli growth rate and gain insights into fast growth phenotypes. Previous studies have described up to 1.6-fold increases in growth rate following ALE, and have identified key causal genetic mutations and changes in transcriptional patterns. Here, we report for the first time intracellular metabolic fluxes for six such adaptively evolved strains, as determined by high-resolution 13 C-metabolic flux analysis. Interestingly, we found that intracellular metabolic pathway usage changed very little following adaptive evolution. Instead, at the level of central carbon metabolism the faster growth was facilitated by proportional increases in glucose uptake and all intracellular rates. Of the six evolved strains studied here, only one strain showed a small degree of flux rewiring, and this was also the strain with unique genetic mutations. A comparison of fluxes with two other wild-type (unevolved) E. coli strains, BW25113 and BL21, showed that inter-strain differences are greater than differences between the parental and evolved strains. Principal component analysis highlighted that nearly all flux differences (95%) between the nine strains were captured by only two principal components. The distance between measured and flux balance analysis predicted fluxes was also investigated. It suggested a relatively wide range of similar stoichiometric optima, which opens new questions about the path-dependency of adaptive evolution. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Adaptive evolution of voltage-gated sodium channels: The first 800 million years

PubMed Central

Zakon, Harold H.

2012-01-01

Voltage-gated Na+-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca2+ channels and were present in the common ancestor of choanoflagellates and animals, although this channel was likely permeable to both Na+ and Ca2+. Thus, like many other neuronal channels and receptors, Nav channels predated neurons. Invertebrates possess two Nav channels (Nav1 and Nav2), whereas vertebrate Nav channels are of the Nav1 family. Approximately 500 Mya in early chordates Nav channels evolved a motif that allowed them to cluster at axon initial segments, 50 million years later with the evolution of myelin, Nav channels “capitalized” on this property and clustered at nodes of Ranvier. The enhancement of conduction velocity along with the evolution of jaws likely made early gnathostomes fierce predators and the dominant vertebrates in the ocean. Later in vertebrate evolution, the Nav channel gene family expanded in parallel in tetrapods and teleosts (∼9 to 10 genes in amniotes, 8 in teleosts). This expansion occurred during or after the late Devonian extinction, when teleosts and tetrapods each diversified in their respective habitats, and coincided with an increase in the number of telencephalic nuclei in both groups. The expansion of Nav channels may have allowed for more sophisticated neural computation and tailoring of Nav channel kinetics with potassium channel kinetics to enhance energy savings. Nav channels show adaptive sequence evolution for increasing diversity in communication signals (electric fish), in protection against lethal Nav channel toxins (snakes, newts, pufferfish, insects), and in specialized habitats (naked mole rats). PMID:22723361

Implementing the Integrated Strategy for the Cultural Adaptation of Evidence-Based Interventions: An Illustration.

PubMed

Sidani, Souraya; Ibrahim, Sarah; Lok, Jana; Fan, Lifeng; Fox, Mary

2018-01-01

Background Persons' cultural beliefs about a health problem can affect their perceived acceptability of evidence-based interventions, undermining evidence-based interventions' adherence, and uptake to manage the problem. Cultural adaptation has the potential to enhance the acceptability, uptake, and adherence to evidence-based interventions. Purpose To illustrate the implementation of the first two phases of the integrated strategy for cultural adaptation by examining Chinese Canadians' perceptions of chronic insomnia and evidence-based behavioral therapies for insomnia. Methods Chinese Canadians ( n = 14) with chronic insomnia attended a group session during which they completed established instruments measuring beliefs about sleep and insomnia, and their perceptions of factors that contribute to chronic insomnia. Participants rated the acceptability of evidence-based behavioral therapies and discussed their cultural perspectives regarding chronic insomnia and its treatment. Results Participants actively engaged in the activities planned for the first two phases of the integrated strategy and identified the most significant factor contributing to chronic insomnia and the evidence-based intervention most acceptable for their cultural group. Conclusions The protocol for implementing the two phases of the integrated strategy for cultural adaptation of evidence-based interventions was feasible, acceptable, and useful in identifying culturally relevant evidence-based interventions.

Advance strategy for climate change adaptation and mitigation in cities

NASA Astrophysics Data System (ADS)

Varquez, A. C. G.; Kanda, M.; Darmanto, N. S.; Sueishi, T.; Kawano, N.

2017-12-01

An on-going 5-yr project financially supported by the Ministry of Environment, Japan, has been carried out to specifically address the issue of prescribing appropriate adaptation and mitigation measures to climate change in cities. Entitled "Case Study on Mitigation and Local Adaptation to Climate Change in an Asian Megacity, Jakarta", the project's relevant objectives is to develop a research framework that can consider both urbanization and climate change with the main advantage of being readily implementable for all cities around the world. The test location is the benchmark city, Jakarta, Indonesia, with the end focus of evaluating the benefits of various mitigation and adaptation strategies in Jakarta and other megacities. The framework was designed to improve representation of urban areas when conducting climate change investigations in cities; and to be able to quantify separately the impacts of urbanization and climate change to all cities globally. It is comprised of a sophisticated, top-down, multi-downscaling approach utilizing a regional model (numerical weather model) and a microscale model (energy balance model and CFD model), with global circulation models (GCM) as input. The models, except the GCM, were configured to reasonably consider land cover, urban morphology, and anthropogenic heating (AH). Equally as important, methodologies that can collect and estimate global distribution of urban parametric and AH datasets are continually being developed. Urban growth models, climate scenario matrices that match representative concentration pathways with shared socio-economic pathways, present distribution of socio-demographic indicators such as population and GDP, existing GIS datasets of urban parameters, are utilized. From these tools, future urbanization (urban morphological parameters and AH) can be introduced into the models. Sensitivity using various combinations of GCM and urbanization can be conducted. Furthermore, since the models utilize

Comparative genomics reveals insights into avian genome evolution and adaptation.

PubMed

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

2014-12-12

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. Copyright © 2014, American Association for the Advancement of Science.

Evolution with Reinforcement Learning in Negotiation

PubMed Central

Zou, Yi; Zhan, Wenjie; Shao, Yuan

2014-01-01

Adaptive behavior depends less on the details of the negotiation process and makes more robust predictions in the long term as compared to in the short term. However, the extant literature on population dynamics for behavior adjustment has only examined the current situation. To offset this limitation, we propose a synergy of evolutionary algorithm and reinforcement learning to investigate long-term collective performance and strategy evolution. The model adopts reinforcement learning with a tradeoff between historical and current information to make decisions when the strategies of agents evolve through repeated interactions. The results demonstrate that the strategies in populations converge to stable states, and the agents gradually form steady negotiation habits. Agents that adopt reinforcement learning perform better in payoff, fairness, and stableness than their counterparts using classic evolutionary algorithm. PMID:25048108

Evolution with reinforcement learning in negotiation.

PubMed

Zou, Yi; Zhan, Wenjie; Shao, Yuan

2014-01-01

Adaptive behavior depends less on the details of the negotiation process and makes more robust predictions in the long term as compared to in the short term. However, the extant literature on population dynamics for behavior adjustment has only examined the current situation. To offset this limitation, we propose a synergy of evolutionary algorithm and reinforcement learning to investigate long-term collective performance and strategy evolution. The model adopts reinforcement learning with a tradeoff between historical and current information to make decisions when the strategies of agents evolve through repeated interactions. The results demonstrate that the strategies in populations converge to stable states, and the agents gradually form steady negotiation habits. Agents that adopt reinforcement learning perform better in payoff, fairness, and stableness than their counterparts using classic evolutionary algorithm.

Adaptive control of dynamical synchronization on evolving networks with noise disturbances

NASA Astrophysics Data System (ADS)

Yuan, Wu-Jie; Zhou, Jian-Fang; Sendiña-Nadal, Irene; Boccaletti, Stefano; Wang, Zhen

2018-02-01

In real-world networked systems, the underlying structure is often affected by external and internal unforeseen factors, making its evolution typically inaccessible. An adaptive strategy was introduced for maintaining synchronization on unpredictably evolving networks [Sorrentino and Ott, Phys. Rev. Lett. 100, 114101 (2008), 10.1103/PhysRevLett.100.114101], which yet does not consider the noise disturbances widely existing in networks' environments. We provide here strategies to control dynamical synchronization on slowly and unpredictably evolving networks subjected to noise disturbances which are observed at the node and at the communication channel level. With our strategy, the nodes' coupling strength is adaptively adjusted with the aim of controlling synchronization, and according only to their received signal and noise disturbances. We first provide a theoretical analysis of the control scheme by introducing an error potential function to seek for the minimization of the synchronization error. Then, we show numerical experiments which verify our theoretical results. In particular, it is found that our adaptive strategy is effective even for the case in which the dynamics of the uncontrolled network would be explosive (i.e., the states of all the nodes would diverge to infinity).