The evolution within us

PubMed Central

Cobey, Sarah; Wilson, Patrick; Matsen, Frederick A.

2015-01-01

The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics. PMID:26194749

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions.

PubMed

Mongiardino Koch, N; Ceccarelli, F S; Ojanguren-Affilastro, A A; Ramírez, M J

2017-04-01

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character-taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time-calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an 'early burst' scenario whereas morphometric traits suggest species-specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

PubMed

Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

2014-11-11

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

A rich diversity of opercle bone shape among teleost fishes

PubMed Central

Small, Clayton M.; Knope, Matthew L.

2017-01-01

The opercle is a prominent craniofacial bone supporting the gill cover in all bony fish and has been the subject of morphological, developmental, and genetic investigation. We surveyed the shapes of this bone among 110 families spanning the teleost tree and examined its pattern of occupancy in a principal component-based morphospace. Contrasting with expectations from the literature that suggest the local morphospace would be only sparsely occupied, we find primarily dense, broad filling of the morphological landscape, indicating rich diversity. Phylomorphospace plots suggest that dynamic evolution underlies the observed spatial patterning. Evolutionary transits through the morphospaces are sometimes long, and occur in a variety of directions. The trajectories seem to represent both evolutionary divergences and convergences, the latter supported by convevol analysis. We suggest that that this pattern of occupancy reflects the various adaptations of different groups of fishes, seemingly paralleling their diverse marine and freshwater ecologies and life histories. Opercle shape evolution within the acanthomorphs, spiny ray-finned fishes, appears to have been especially dynamic. PMID:29281662

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

PubMed Central

Jiang, Zhi J; Castoe, Todd A; Austin, Christopher C; Burbrink, Frank T; Herron, Matthew D; McGuire, Jimmy A; Parkinson, Christopher L; Pollock, David D

2007-01-01

Background The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence. Results We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs. Conclusion Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria. PMID:17655768

Chaos and the (un)predictability of evolution in a changing environment.

PubMed

Rego-Costa, Artur; Débarre, Florence; Chevin, Luis-Miguel

2018-02-01

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior.

PubMed

Schrader, Lukas; Helanterä, Heikki; Oettler, Jan

2017-03-01

Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior-a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

Top predators induce the evolutionary diversification of intermediate predator species.

PubMed

Zu, Jian; Yuan, Bo; Du, Jianqiang

2015-12-21

We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Le Chatelier's principle in replicator dynamics

NASA Astrophysics Data System (ADS)

Allahverdyan, Armen E.; Galstyan, Aram

2011-10-01

The Le Chatelier principle states that physical equilibria are not only stable, but they also resist external perturbations via short-time negative-feedback mechanisms: a perturbation induces processes tending to diminish its results. The principle has deep roots, e.g., in thermodynamics it is closely related to the second law and the positivity of the entropy production. Here we study the applicability of the Le Chatelier principle to evolutionary game theory, i.e., to perturbations of a Nash equilibrium within the replicator dynamics. We show that the principle can be reformulated as a majorization relation. This defines a stability notion that generalizes the concept of evolutionary stability. We determine criteria for a Nash equilibrium to satisfy the Le Chatelier principle and relate them to mutualistic interactions (game-theoretical anticoordination) showing in which sense mutualistic replicators can be more stable than (say) competing ones. There are globally stable Nash equilibria, where the Le Chatelier principle is violated even locally: in contrast to the thermodynamic equilibrium a Nash equilibrium can amplify small perturbations, though both types of equilibria satisfy the detailed balance condition.

Le Chatelier's principle in replicator dynamics.

PubMed

Allahverdyan, Armen E; Galstyan, Aram

2011-10-01

The Le Chatelier principle states that physical equilibria are not only stable, but they also resist external perturbations via short-time negative-feedback mechanisms: a perturbation induces processes tending to diminish its results. The principle has deep roots, e.g., in thermodynamics it is closely related to the second law and the positivity of the entropy production. Here we study the applicability of the Le Chatelier principle to evolutionary game theory, i.e., to perturbations of a Nash equilibrium within the replicator dynamics. We show that the principle can be reformulated as a majorization relation. This defines a stability notion that generalizes the concept of evolutionary stability. We determine criteria for a Nash equilibrium to satisfy the Le Chatelier principle and relate them to mutualistic interactions (game-theoretical anticoordination) showing in which sense mutualistic replicators can be more stable than (say) competing ones. There are globally stable Nash equilibria, where the Le Chatelier principle is violated even locally: in contrast to the thermodynamic equilibrium a Nash equilibrium can amplify small perturbations, though both types of equilibria satisfy the detailed balance condition.

Effects of topology on network evolution

NASA Astrophysics Data System (ADS)

Oikonomou, Panos; Cluzel, Philippe

2006-08-01

The ubiquity of scale-free topology in nature raises the question of whether this particular network design confers an evolutionary advantage. A series of studies has identified key principles controlling the growth and the dynamics of scale-free networks. Here, we use neuron-based networks of boolean components as a framework for modelling a large class of dynamical behaviours in both natural and artificial systems. Applying a training algorithm, we characterize how networks with distinct topologies evolve towards a pre-established target function through a process of random mutations and selection. We find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. Whereas homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously. Remarkably, this latter property is robust to variations of the degree exponent. In contrast, homogeneous random networks require a specific tuning of their connectivity to optimize their ability to evolve. These results highlight an organizing principle that governs the evolution of complex networks and that can improve the design of engineered systems.

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

PubMed

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

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels.

PubMed

McLean, Bryan S; Helgen, Kristofer M; Goodwin, H Thomas; Cook, Joseph A

2018-03-01

Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Using four ecologically relevant trait datasets (body size, cranial, mandibular, and molariform tooth shape), we compared and contrasted variation, covariation, and disparity patterns in a new phylogenetic framework. Strong correlations existed between body size and two skull traits (allometry) and among skull traits themselves (integration). Inferred evolutionary modes were also concordant across traits (Ornstein-Uhlenbeck with two adaptive regimes). However, despite these broad similarities, we found divergent dynamics on the macroevolutionary landscape, with phenotypic disparity being differentially shaped by convergence and conservatism. Such among-trait heterogeneity in process (but not always pattern) reiterates the mosaic nature of morphological evolution, and suggests ground squirrel evolution is poorly captured by single process descriptors. Our results also highlight how use of single traits can bias macroevolutionary inference, affirming the importance of broader trait-bases in understanding phenotypic evolutionary dynamics. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Big Bang Tumor Growth and Clonal Evolution.

PubMed

Sun, Ruping; Hu, Zheng; Curtis, Christina

2018-05-01

The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks.

PubMed

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks

NASA Astrophysics Data System (ADS)

Iyer, Swami; Killingback, Timothy

2014-10-01

The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

PubMed Central

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L

2017-05-01

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The Evolutionary Basis of Risky Adolescent Behavior: Implications for Science, Policy, and Practice

ERIC Educational Resources Information Center

Ellis, Bruce J.; Del Giudice, Marco; Dishion, Thomas J.; Figueredo, Aurelio Jose; Gray, Peter; Griskevicius, Vladas; Hawley, Patricia H.; Jacobs, W. Jake; James, Jenee; Volk, Anthony A.; Wilson, David Sloan

2012-01-01

This article proposes an evolutionary model of risky behavior in adolescence and contrasts it with the prevailing developmental psychopathology model. The evolutionary model contends that understanding the evolutionary functions of adolescence is critical to explaining why adolescents engage in risky behavior and that successful intervention…

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes.

PubMed

Mank, Judith E

2012-01-01

Although sex chromosomes have been the focus of a great deal of scientific scrutiny, most interest has centred on understanding the evolution and relative importance of X and Z chromosomes. By contrast, the sex-limited W and Y chromosomes have received far less attention, both because of their generally degenerate nature and the difficulty in studying non-recombining and often highly heterochromatic genomic regions. However, recent theory and empirical evidence suggest that the W and Y chromosomes play a far more important role in sex-specific fitness traits than would be expected based on their size alone, and this importance may explain the persistence of some Y and W chromosomes in the face of powerful degradative forces. In addition to their role in fertility and fecundity, the sex-limited nature of these genomic regions results in unique evolutionary forces acting on Y and W chromosomes, implicating them as potentially major contributors to sexual selection and speciation. Recent empirical studies have borne out these predictions and revealed that some W and Y chromosomes play a vital role in key sex-specific evolutionary processes.

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes

PubMed Central

2012-01-01

Although sex chromosomes have been the focus of a great deal of scientific scrutiny, most interest has centred on understanding the evolution and relative importance of X and Z chromosomes. By contrast, the sex-limited W and Y chromosomes have received far less attention, both because of their generally degenerate nature and the difficulty in studying non-recombining and often highly heterochromatic genomic regions. However, recent theory and empirical evidence suggest that the W and Y chromosomes play a far more important role in sex-specific fitness traits than would be expected based on their size alone, and this importance may explain the persistence of some Y and W chromosomes in the face of powerful degradative forces. In addition to their role in fertility and fecundity, the sex-limited nature of these genomic regions results in unique evolutionary forces acting on Y and W chromosomes, implicating them as potentially major contributors to sexual selection and speciation. Recent empirical studies have borne out these predictions and revealed that some W and Y chromosomes play a vital role in key sex-specific evolutionary processes. PMID:22038285

Contrasting effects of intralocus sexual conflict on sexually antagonistic coevolution

PubMed Central

Pennell, Tanya M.; de Haas, Freek J. H.; Morrow, Edward H.; van Doorn, G. Sander

2016-01-01

Evolutionary conflict between the sexes can induce arms races in which males evolve traits that are detrimental to the fitness of their female partners, and vice versa. This interlocus sexual conflict (IRSC) has been proposed as a cause of perpetual intersexual antagonistic coevolution with wide-ranging evolutionary consequences. However, theory suggests that the scope for perpetual coevolution is limited, if traits involved in IRSC are subject to pleiotropic constraints. Here, we consider a biologically plausible form of pleiotropy that has hitherto been ignored in treatments of IRSC and arrive at drastically different conclusions. Our analysis is based on a quantitative genetic model of sexual conflict, in which genes controlling IRSC traits have side effects in the other sex, due to incompletely sex-limited gene expression. As a result, the genes are exposed to intralocus sexual conflict (IASC), a tug-of-war between opposing male- and female-specific selection pressures. We find that the interaction between the two forms of sexual conflict has contrasting effects on antagonistic coevolution: Pleiotropic constraints stabilize the dynamics of arms races if the mating traits are close to evolutionary equilibrium but can prevent populations from ever reaching such a state. Instead, the sexes are drawn into a continuous cycle of arms races, causing the buildup of IASC, alternated by phases of IASC resolution that trigger the next arms race. These results encourage an integrative perspective on the biology of sexual conflict and generally caution against relying exclusively on equilibrium stability analysis. PMID:26755609

Modelling and strategy optimisation for a kind of networked evolutionary games with memories under the bankruptcy mechanism

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

This paper investigates the evolutionary dynamic and strategy optimisation for a kind of networked evolutionary games whose strategy updating rules incorporate 'bankruptcy' mechanism, and the situation that each player's bankruptcy is due to the previous continuous low profits gaining from the game is considered. First, by using semi-tensor product of matrices method, the evolutionary dynamic of this kind of games is expressed as a higher order logical dynamic system and then converted into its algebraic form, based on which, the evolutionary dynamic of the given games can be discussed. Second, the strategy optimisation problem is investigated, and some free-type control sequences are designed to maximise the total payoff of the whole game. Finally, an illustrative example is given to show that our new results are very effective.

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 evolutionary processes and ecological costs and benefits of different plant growth strategies.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity.

PubMed

Frickel, Jens; Theodosiou, Loukas; Becks, Lutz

2017-10-17

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host-virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host-virus coevolution in the complex system and that the virus' effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

PubMed

Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

2017-07-01

Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Eco-evolutionary dynamics in a coevolving host-virus system.

PubMed

Frickel, Jens; Sieber, Michael; Becks, Lutz

2016-04-01

Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.

Apollo and the geology of the moon /Twenty-eighth William Smith Lecture/

NASA Technical Reports Server (NTRS)

Schmitt, H. H.

1975-01-01

Lunar geology evidence is examined for clues to the origin and evolution of the moon and earth. Seven evolutionary episodes, the last covering three billion years to the present day, are constructed for the moon. Parallel episodes in the earth's evolution are masked by the dynamic continuing evolution of the earth over a 4.5 billion year span, in contrast to the moon's quiescence and inability to retain fluids. Comparisons are drawn between the geochemistry and tectonics of the lunar basaltic maria and the earth's ocean basins. Lunar maria rocks differ strikingly in chemical composition from meteoritic matter and solar material. Inundation of frontside lunar maria basins by vast oceans of dark basalt mark the last of the major internally generated evolutionary episodes, and is attributed to consequences of meltdown of the lunar mantle and crust by radioisotope decay from below. Data are drawn primarily from Apollo missions 11-17, supplemented by other sources.

On the evolution of specialization with a mechanistic underpinning in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2008-03-01

We analyze the evolution of specialization in resource utilization in a discrete-time metapopulation model using the adaptive dynamics approach. The local dynamics in the metapopulation are based on the Beverton-Holt model with mechanistic underpinnings. The consumer faces a trade-off in the abilities to consume two resources that are spatially heterogeneously distributed to patches that are prone to local catastrophes. We explore the factors favoring the spread of generalist or specialist strategies. Increasing fecundity or decreasing catastrophe probability favors the spread of the generalist strategy and increasing environmental heterogeneity enlarges the parameter domain where the evolutionary branching is possible. When there are no catastrophes, increasing emigration diminishes the parameter domain where the evolutionary branching may occur. Otherwise, the effect of emigration on evolutionary dynamics is non-monotonous: both small and large values of emigration probability favor the spread of the specialist strategies whereas the parameter domain where evolutionary branching may occur is largest when the emigration probability has intermediate values. We compare how different forms of spatial heterogeneity and different models of local growth affect the evolutionary dynamics. We show that even small changes in the resource dynamics may have outstanding evolutionary effects to the consumers.

The mass function and dynamical mass of young star clusters: why their initial crossing-time matters crucially

NASA Astrophysics Data System (ADS)

Parmentier, Geneviève; Baumgardt, Holger

2012-12-01

We highlight the impact of cluster-mass-dependent evolutionary rates upon the evolution of the cluster mass function during violent relaxation, that is, while clusters dynamically respond to the expulsion of their residual star-forming gas. Mass-dependent evolutionary rates arise when the mean volume density of cluster-forming regions is mass-dependent. In that case, even if the initial conditions are such that the cluster mass function at the end of violent relaxation has the same shape as the embedded-cluster mass function (i.e. infant weight-loss is mass-independent), the shape of the cluster mass function does change transiently during violent relaxation. In contrast, for cluster-forming regions of constant mean volume density, the cluster mass function shape is preserved all through violent relaxation since all clusters then evolve at the same mass-independent rate. On the scale of individual clusters, we model the evolution of the ratio of the dynamical mass to luminous mass of a cluster after gas expulsion. Specifically, we map the radial dependence of the time-scale for a star cluster to return to equilibrium. We stress that fields of view a few pc in size only, typical of compact clusters with rapid evolutionary rates, are likely to reveal cluster regions which have returned to equilibrium even if the cluster experienced a major gas expulsion episode a few Myr earlier. We provide models with the aperture and time expressed in units of the initial half-mass radius and initial crossing-time, respectively, so that our results can be applied to clusters with initial densities, sizes, and apertures different from ours.

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.

PubMed

Vrancken, Bram; Suchard, Marc A; Lemey, Philippe

2017-07-01

Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology , 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.

Falsification of matching theory and confirmation of an evolutionary theory of behavior dynamics in a critical experiment.

PubMed

McDowell, J J; Calvin, Olivia L; Hackett, Ryan; Klapes, Bryan

2017-07-01

Two competing predictions of matching theory and an evolutionary theory of behavior dynamics, and one additional prediction of the evolutionary theory, were tested in a critical experiment in which human participants worked on concurrent schedules for money (Dallery et al., 2005). The three predictions concerned the descriptive adequacy of matching theory equations, and of equations describing emergent equilibria of the evolutionary theory. Tests of the predictions falsified matching theory and supported the evolutionary theory. Copyright © 2017 Elsevier B.V. All rights reserved.

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

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

Maljkovic-berry, Irina; Athreya, Gayathri; Daniels, Marcus

Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changedmore » over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.« less

Improving the Adaptability of Simulated Evolutionary Swarm Robots in Dynamically Changing Environments

PubMed Central

Yao, Yao; Marchal, Kathleen; Van de Peer, Yves

2014-01-01

One of the important challenges in the field of evolutionary robotics is the development of systems that can adapt to a changing environment. However, the ability to adapt to unknown and fluctuating environments is not straightforward. Here, we explore the adaptive potential of simulated swarm robots that contain a genomic encoding of a bio-inspired gene regulatory network (GRN). An artificial genome is combined with a flexible agent-based system, representing the activated part of the regulatory network that transduces environmental cues into phenotypic behaviour. Using an artificial life simulation framework that mimics a dynamically changing environment, we show that separating the static from the conditionally active part of the network contributes to a better adaptive behaviour. Furthermore, in contrast with most hitherto developed ANN-based systems that need to re-optimize their complete controller network from scratch each time they are subjected to novel conditions, our system uses its genome to store GRNs whose performance was optimized under a particular environmental condition for a sufficiently long time. When subjected to a new environment, the previous condition-specific GRN might become inactivated, but remains present. This ability to store ‘good behaviour’ and to disconnect it from the novel rewiring that is essential under a new condition allows faster re-adaptation if any of the previously observed environmental conditions is reencountered. As we show here, applying these evolutionary-based principles leads to accelerated and improved adaptive evolution in a non-stable environment. PMID:24599485

Detecting reciprocity at a global scale

PubMed Central

Frank, Morgan R.; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L.; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other’s cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation. PMID:29326983

Detecting reciprocity at a global scale.

PubMed

Frank, Morgan R; Obradovich, Nick; Sun, Lijun; Woon, Wei Lee; LeVeck, Brad L; Rahwan, Iyad

2018-01-01

Reciprocity stabilizes cooperation from the level of microbes all the way up to humans interacting in small groups, but does reciprocity also underlie stable cooperation between larger human agglomerations, such as nation states? Famously, evolutionary models show that reciprocity could emerge as a widespread strategy for achieving international cooperation. However, existing studies have only detected reciprocity-driven cooperation in a small number of country pairs. We apply a new method for detecting mutual influence in dynamical systems to a new large-scale data set that records state interactions with high temporal resolution. Doing so, we detect reciprocity between many country pairs in the international system and find that these reciprocating country pairs exhibit qualitatively different cooperative dynamics when compared to nonreciprocating pairs. Consistent with evolutionary theories of cooperation, reciprocating country pairs exhibit higher levels of stable cooperation and are more likely to punish instances of noncooperation. However, countries in reciprocity-based relationships are also quicker to forgive single acts of noncooperation by eventually returning to previous levels of mutual cooperation. By contrast, nonreciprocating pairs are more likely to exploit each other's cooperation via higher rates of defection. Together, these findings provide the strongest evidence to date that reciprocity is a widespread mechanism for achieving international cooperation.

An evolutionary game approach for determination of the structural conflicts in signed networks

PubMed Central

Tan, Shaolin; Lü, Jinhu

2016-01-01

Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks. PMID:26915581

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. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity

PubMed Central

Frickel, Jens; Theodosiou, Loukas

2017-01-01

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species. PMID:28973943

J.A. Schumpeter and T.B. Veblen on economic evolution: the dichotomy between statics and dynamics

PubMed Central

Schütz, Marlies; Rainer, Andreas

2016-01-01

Abstract At present, the discussion on the dichotomy between statics and dynamics is resolved by concentrating on its mathematical meaning. Yet, a simple formalisation masks the underlying methodological discussion. Overcoming this limitation, the paper discusses Schumpeter's and Veblen's viewpoint on dynamic economic systems as systems generating change from within. It contributes to an understanding on their ideas of how economics could become an evolutionary science and on their contributions to elaborate an evolutionary economics. It confronts Schumpeter's with Veblen's perspective on evolutionary economics and provides insight into their evolutionary economic theorising by discussing their ideas on the evolution of capitalism. PMID:28057981

Evolutionary dynamics from a variational principle.

PubMed

Klimek, Peter; Thurner, Stefan; Hanel, Rudolf

2010-07-01

We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of some evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. These novel entities change the conditions for already existing species. Even Darwin's Demon, a hypothetical entity with exact knowledge of the abundance of all species and their fitness functions at a given time, could not prestate the impact of these novelties on established populations. We argue that fitness is always a posteriori knowledge--it measures but does not explain why a species has reproductive success or not. To overcome these conceptual limitations, a variational principle is proposed in a spin-model-like setup of evolutionary systems. We derive a functional which is minimized under the most general evolutionary formulation of a dynamical system, i.e., evolutionary trajectories causally emerge as a minimization of a functional. This functional allows the derivation of analytic solutions of the asymptotic diversity for stochastic evolutionary systems within a mean-field approximation. We test these approximations by numerical simulations of the corresponding model and find good agreement in the position of phase transitions in diversity curves. The model is further able to reproduce stylized facts of timeseries from several man-made and natural evolutionary systems. Light will be thrown on how species and their fitness landscapes dynamically coevolve.

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.

Competition-Colonization Trade-Offs, Competitive Uncertainty, and the Evolutionary Assembly of Species

PubMed Central

Pillai, Pradeep; Guichard, Frédéric

2012-01-01

We utilize a standard competition-colonization metapopulation model in order to study the evolutionary assembly of species. Based on earlier work showing how models assuming strict competitive hierarchies will likely lead to runaway evolution and self-extinction for all species, we adopt a continuous competition function that allows for levels of uncertainty in the outcome of competition. We then, by extending the standard patch-dynamic metapopulation model in order to include evolutionary dynamics, allow for the coevolution of species into stable communities composed of species with distinct limiting similarities. Runaway evolution towards stochastic extinction then becomes a limiting case controlled by the level of competitive uncertainty. We demonstrate how intermediate competitive uncertainty maximizes the equilibrium species richness as well as maximizes the adaptive radiation and self-assembly of species under adaptive dynamics with mutations of non-negligible size. By reconciling competition-colonization tradeoff theory with co-evolutionary dynamics, our results reveal the importance of intermediate levels of competitive uncertainty for the evolutionary assembly of species. PMID:22448253

Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics

NASA Astrophysics Data System (ADS)

Zhou, Da; Qian, Hong

2011-09-01

Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical “device” that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.

Pedagogy as influencing nursing students' essentialized understanding of culture.

PubMed

Gregory, David; Harrowing, Jean; Lee, Bonnie; Doolittle, Lisa; O'Sullivan, Patrick S

2010-01-01

In this qualitative study, we explored how students understood "culture." Participants defined culture and wrote narratives regarding specific cultural encounters. The sample comprised both nursing (n=14) and non-nursing (n=8) students to allow for comparison groups. Content analysis of the narratives revealed two broad paradigms of cultural understanding: essentialist and constructivist. Essentialist narratives comprised four themes: determinism (culture defied individual resistance); relativism (the possibility of making value judgments disappeared); Othering (culture was equated to exotica, and emphasized difference); and, reductionism (personhood was eclipsed by culture). In contrast, the constructivist narratives were characterized by influence (non-determinism), dynamism (culture was dynamic and evolutionary); and, relationship-building. The unintended negative consequences of essentialist notions of culture were revealed in the nursing students' narratives. Pedagogy is implicated in nursing students' essentialized understanding of culture.

Imitation versus payoff: Duality of the decision-making process demonstrates criticality and consensus formation

NASA Astrophysics Data System (ADS)

Turalska, M.; West, B. J.

2014-11-01

We consider a dual model of decision making, in which an individual forms its opinion based on contrasting mechanisms of imitation and rational calculation. The decision-making model (DMM) implements imitating behavior by means of a network of coupled two-state master equations that undergoes a phase transition at a critical value of a control parameter. The evolutionary spatial game, being a generalization of the prisoner's dilemma game, is used to determine in objective fashion the cooperative or anticooperative strategy adopted by individuals. Interactions between two sources of dynamics increases the domain of initial states attracted to phase transition dynamics beyond that of the DMM network in isolation. Additionally, on average the influence of the DMM on the game increases the final observed fraction of cooperators in the system.

Evolutionary genetics of maternal effects

PubMed Central

Wolf, Jason B.; Wade, Michael J.

2016-01-01

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

Population delimitation across contrasting evolutionary clines in deer mice (Peromyscus maniculatus)

PubMed Central

Yang, D-S; Kenagy, G

2011-01-01

Despite current interest in population genetics, a concrete definition of a “population” remains elusive. Multiple ecologically and evolutionarily based definitions of population are in current use, which focus, respectively, on demographic and genetic interactions. Accurate population delimitation is crucial for not only evolutionary and ecological population biology, but also for conservation of threatened populations. Along the Pacific Coast of North America, two contrasting patterns of geographic variation in deer mice (Peromyscus maniculatus) converge within the state of Oregon. Populations of these mice diverge morphologically across an east–west axis, and they diverge in mitochondrial DNA haplotypes across a north–south axis. In this study, we investigate these geographically contrasting patterns of differentiation in the context of ecological and evolutionary definitions (paradigms) of populations. We investigate these patterns using a new and geographically expansive sample that integrates data on morphology, mitochondrial DNA, and nuclear DNA. We found no evidence of nuclear genetic differentiation between the morphologically and mitochondrially distinct populations, thus indicating the occurrence of gene flow across Oregon. Under the evolutionary paradigm, Oregon populations can be considered a single population, whereas morphological and mitochondrial differentiations do not indicate distinct populations. In contrast, under the ecological paradigm morphological differentiation indicates distinct populations based on the low likelihood of demographic interactions between geographically distant individuals. The two sympatric but mitochondrially distinct haplogroups form a single population under the ecological paradigm. Hence, we find that the difference between evolutionary and ecological paradigms is the time-scale of interest, and we believe that the more chronologically inclusive evolutionary paradigm may be preferable except in cases where only a single generation is of interest. PMID:22393480

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence

PubMed Central

McLeish, Tom C. B.

2015-01-01

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity—the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity—essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution. PMID:26640648

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence.

PubMed

McLeish, Tom C B

2015-12-06

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity-the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity-essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution.

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

PubMed Central

Sanchez, Alvaro; Gore, Jeff

2013-01-01

The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of those species that rely on cooperation for their survival. PMID:23637571

Individual heterogeneity in life histories and eco-evolutionary dynamics

PubMed Central

Vindenes, Yngvild; Langangen, Øystein

2015-01-01

Individual heterogeneity in life history shapes eco-evolutionary processes, and unobserved heterogeneity can affect demographic outputs characterising life history and population dynamical properties. Demographic frameworks like matrix models or integral projection models represent powerful approaches to disentangle mechanisms linking individual life histories and population-level processes. Recent developments have provided important steps towards their application to study eco-evolutionary dynamics, but so far individual heterogeneity has largely been ignored. Here, we present a general demographic framework that incorporates individual heterogeneity in a flexible way, by separating static and dynamic traits (discrete or continuous). First, we apply the framework to derive the consequences of ignoring heterogeneity for a range of widely used demographic outputs. A general conclusion is that besides the long-term growth rate lambda, all parameters can be affected. Second, we discuss how the framework can help advance current demographic models of eco-evolutionary dynamics, by incorporating individual heterogeneity. For both applications numerical examples are provided, including an empirical example for pike. For instance, we demonstrate that predicted demographic responses to climate warming can be reversed by increased heritability. We discuss how applications of this demographic framework incorporating individual heterogeneity can help answer key biological questions that require a detailed understanding of eco-evolutionary dynamics. PMID:25807980

Unexpected Nongenetic Individual Heterogeneity and Trait Covariance in Daphnia and Its Consequences for Ecological and Evolutionary Dynamics.

PubMed

Cressler, Clayton E; Bengtson, Stefan; Nelson, William A

2017-07-01

Individual differences in genetics, age, or environment can cause tremendous differences in individual life-history traits. This individual heterogeneity generates demographic heterogeneity at the population level, which is predicted to have a strong impact on both ecological and evolutionary dynamics. However, we know surprisingly little about the sources of individual heterogeneity for particular taxa or how different sources scale up to impact ecological and evolutionary dynamics. Here we experimentally study the individual heterogeneity that emerges from both genetic and nongenetic sources in a species of freshwater zooplankton across a large gradient of food quality. Despite the tight control of environment, we still find that the variation from nongenetic sources is greater than that from genetic sources over a wide range of food quality and that this variation has strong positive covariance between growth and reproduction. We evaluate the general consequences of genetic and nongenetic covariance for ecological and evolutionary dynamics theoretically and find that increasing nongenetic variation slows evolution independent of the correlation in heritable life-history traits but that the impact on ecological dynamics depends on both nongenetic and genetic covariance. Our results demonstrate that variation in the relative magnitude of nongenetic versus genetic sources of variation impacts the predicted ecological and evolutionary dynamics.

Evolution of specialization under non-equilibrium population dynamics.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2013-03-21

We analyze the evolution of specialization in resource utilization in a mechanistically underpinned discrete-time model using the adaptive dynamics approach. We assume two nutritionally equivalent resources that in the absence of consumers grow sigmoidally towards a resource-specific carrying capacity. The consumers use resources according to the law of mass-action with rates involving trade-off. The resulting discrete-time model for the consumer population has over-compensatory dynamics. We illuminate the way non-equilibrium population dynamics affect the evolutionary dynamics of the resource consumption rates, and show that evolution to the trimorphic coexistence of a generalist and two specialists is possible due to asynchronous non-equilibrium population dynamics of the specialists. In addition, various forms of cyclic evolutionary dynamics are possible. Furthermore, evolutionary suicide may occur even without Allee effects and demographic stochasticity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evolutionary models of interstellar chemistry

NASA Technical Reports Server (NTRS)

Prasad, Sheo S.

1987-01-01

The goal of evolutionary models of interstellar chemistry is to understand how interstellar clouds came to be the way they are, how they will change with time, and to place them in an evolutionary sequence with other celestial objects such as stars. An improved Mark II version of an earlier model of chemistry in dynamically evolving clouds is presented. The Mark II model suggests that the conventional elemental C/O ratio less than one can explain the observed abundances of CI and the nondetection of O2 in dense clouds. Coupled chemical-dynamical models seem to have the potential to generate many observable discriminators of the evolutionary tracks. This is exciting, because, in general, purely dynamical models do not yield enough verifiable discriminators of the predicted tracks.

Evolutionary dynamics of group interactions on structured populations: a review

PubMed Central

Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

2013-01-01

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. PMID:23303223

Evolutionary Dynamics of the W Chromosome in Caenophidian Snakes

PubMed Central

Augstenová, Barbora; Rovatsos, Michail

2017-01-01

The caenophidian (assigned also as “advanced”) snakes are traditionally viewed as a group of reptiles with a limited karyotypic variation and stable ZZ/ZW sex chromosomes. The W chromosomes of the caenophidian snakes are heterochromatic, and pioneering studies demonstrated that they are rich in repetitive elements. However, a comparative study of the evolutionary dynamics of the repetitive content of the W chromosome across the whole lineage is missing. Using molecular-cytogenetic techniques, we explored the distribution of four repetitive motifs (microsatellites GATA, GACA, AG and telomeric-like sequences), which are frequently accumulated in differentiated sex chromosomes in vertebrates, in the genomes of 13 species of the caenophidian snakes covering a wide phylogenetic spectrum of the lineage. The results demonstrate a striking variability in the morphology and the repetitive content of the W chromosomes even between closely-related species, which is in contrast to the homology and long-term stability of the gene content of the caenophidian Z chromosome. We uncovered that the tested microsatellite motifs are accumulated on the degenerated, heterochromatic W chromosomes in all tested species of the caenophidian snakes with the exception of the Javan file snake representing a basal clade. On the other hand, the presence of the accumulation of the telomeric-like sequences on the caenophidian W chromosome is evolutionary much less stable. Moreover, we demonstrated that large accumulations of telomeric-like motifs on the W chromosome contribute to sexual differences in the number of copies of the telomeric and telomeric-like repeats estimated by quantitative PCR, which might be confusing and incorrectly interpreted as sexual differences in telomere length. PMID:29283388

Jumping genes: Genomic ballast or powerhouse of biological diversification.

PubMed

Choudhury, Rimjhim Roy; Parisod, Christian

2017-09-01

Studying hybridization has the potential to elucidate challenging questions in evolutionary biology such as the nature of adaptive genetic variation and reproductive isolation. A growing body of work highlights that the merging of divergent genomes goes beyond the reshuffling of standing variation from related species and promotes mutations (Abbott et al., ). However, to what extent such genome instability generates evolutionary significant variation remains largely elusive. In this issue of Molecular Ecology, Dennenmoser et al. () report considerable dynamics of transposable elements (TEs) in a recent invasive fish species of hybrid origin (Cottus; Figure ). It adds to the recent examples from plants to support TE-specific genome variation following hybridization. Insights from early, as well as established, hybrids are largely coherent with increased TE activity, and this fish system thus represents an inspiring opportunity to further address the possible association between genome dynamics and "rapid evolution of hybrid species." This work based on genome (re)sequencing contrasts with prior transcriptomics or PCR-based studies of TEs and illustrates how unprecedented amount of information promises a better understanding of the multiple patterns of variation across eukaryotic genomes; provided that we get the better of methodological advances. As discussed here, unbiased assessment of TE variation from genome surveys indeed remains a challenge precluding firm conclusions to be reached about the evolutionary significance of TEs. Despite methodological and conceptual developments that appear necessary to unambiguously uncover the unexplored iceberg below the known tip, the role of coding genes vs. TEs in promoting adaptation and speciation might be clarified in a not so remote future. © 2017 John Wiley & Sons Ltd.

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

PubMed Central

Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

2014-01-01

Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420

New method for predicting estrogen receptor status utilizing breast MRI texture kinetic analysis

NASA Astrophysics Data System (ADS)

Chaudhury, Baishali; Hall, Lawrence O.; Goldgof, Dmitry B.; Gatenby, Robert A.; Gillies, Robert; Drukteinis, Jennifer S.

2014-03-01

Magnetic Resonance Imaging (MRI) of breast cancer typically shows that tumors are heterogeneous with spatial variations in blood flow and cell density. Here, we examine the potential link between clinical tumor imaging and the underlying evolutionary dynamics behind heterogeneity in the cellular expression of estrogen receptors (ER) in breast cancer. We assume, in an evolutionary environment, that ER expression will only occur in the presence of significant concentrations of estrogen, which is delivered via the blood stream. Thus, we hypothesize, the expression of ER in breast cancer cells will correlate with blood flow on gadolinium enhanced breast MRI. To test this hypothesis, we performed quantitative analysis of blood flow on dynamic contrast enhanced MRI (DCE-MRI) and correlated it with the ER status of the tumor. Here we present our analytic methods, which utilize a novel algorithm to analyze 20 volumetric DCE-MRI breast cancer tumors. The algorithm generates post initial enhancement (PIE) maps from DCE-MRI and then performs texture features extraction from the PIE map, feature selection, and finally classification of tumors into ER positive and ER negative status. The combined gray level co-occurrence matrices, gray level run length matrices and local binary pattern histogram features allow quantification of breast tumor heterogeneity. The algorithm predicted ER expression with an accuracy of 85% using a Naive Bayes classifier in leave-one-out cross-validation. Hence, we conclude that our data supports the hypothesis that imaging characteristics can, through application of evolutionary principles, provide insights into the cellular and molecular properties of cancer cells.

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.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

PubMed

Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas

2016-05-20

The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.

Precise Ages for the Benchmark Brown Dwarfs HD 19467 B and HD 4747 B

NASA Astrophysics Data System (ADS)

Wood, Charlotte; Boyajian, Tabetha; Crepp, Justin; von Braun, Kaspar; Brewer, John; Schaefer, Gail; Adams, Arthur; White, Tim

2018-01-01

Large uncertainty in the age of brown dwarfs, stemming from a mass-age degeneracy, makes it difficult to constrain substellar evolutionary models. To break the degeneracy, we need ''benchmark" brown dwarfs (found in binary systems) whose ages can be determined independent of their masses. HD~19467~B and HD~4747~B are two benchmark brown dwarfs detected through the TRENDS (TaRgeting bENchmark objects with Doppler Spectroscopy) high-contrast imaging program for which we have dynamical mass measurements. To constrain their ages independently through isochronal analysis, we measured the radii of the host stars with interferometry using the Center for High Angular Resolution Astronomy (CHARA) Array. Assuming the brown dwarfs have the same ages as their host stars, we use these results to distinguish between several substellar evolutionary models. In this poster, we present new age estimates for HD~19467 and HD~4747 that are more accurate and precise and show our preliminary comparisons to cooling models.

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs.

PubMed

Stollmeier, Frank; Nagler, Jan

2018-02-02

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair," meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the prisoner's dilemma, and an unexpected selection reversal in the hawk-dove game.

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs

NASA Astrophysics Data System (ADS)

Stollmeier, Frank; Nagler, Jan

2018-02-01

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair," meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the prisoner's dilemma, and an unexpected selection reversal in the hawk-dove game.

Metapopulation dynamics and the evolution of dispersal

NASA Astrophysics Data System (ADS)

Parvinen, Kalle

A metapopulation consists of local populations living in habitat patches. In this chapter metapopulation dynamics and the evolution of dispersal is studied in two metapopulation models defined in discrete time. In the first model there are finitely many patches, and in the other one there are infinitely many patches, which allows to incorporate catastrophes into the model. In the first model, cyclic local population dynamics can be either synchronized or not, and increasing dispersal both synchronizes and stabilizes metapopulation dynamics. On the other hand, the type of dynamics has a strong effect on the evolution of dispersal. In case of non-synchronized metapopulation dynamics, dispersal is much more beneficial than in the case of synchronized metapopulation dynamics. Local dynamics has a substantial effect also on the possibility of evolutionary branching in both models. Furthermore, with an Allee effect in the local dynamics of the second model, even evolutionary suicide can occur. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist.

A theory for the evolution of other-regard integrating proximate and ultimate perspectives.

PubMed

Akçay, Erol; Van Cleve, Jeremy; Feldman, Marcus W; Roughgarden, Joan

2009-11-10

Although much previous work describes evolutionary mechanisms that promote or stabilize different social behaviors, we still have little understanding of the factors that drive animal behavior proximately. Here we present a modeling approach to answer this question. Our model rests on motivations to achieve objectives as the proximate determinants of behavior. We develop a two-tiered framework by first modeling the dynamics of a social interaction at the behavioral time scale and then find the evolutionarily stable objectives that result from the outcomes these dynamics produce. We use this framework to ask whether "other-regarding" motivations, which result from a kind of nonselfish objective, can evolve when individuals are engaged in a social interaction that entails a conflict between their material payoffs. We find that, at the evolutionarily stable state, individuals can be other-regarding in that they are motivated to increase their partners' payoff as well as their own. In contrast to previous theories, we find that such motivations can evolve because of their direct effect on fitness and do not require kin selection or a special group structure. We also derive general conditions for the evolutionary stability of other-regarding motivations. Our conditions indicate that other-regarding motivations are more likely to evolve when social interactions and behavioral objectives are both synergistic.

Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system.

PubMed

Hiltunen, Teppo; Ayan, Gökçe B; Becks, Lutz

2015-06-07

Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria-ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2017-11-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2018-07-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Genome chaos: survival strategy during crisis.

PubMed

Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

2014-01-01

Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life

PubMed Central

Ivancevic, Atma M.; Kortschak, R. Daniel; Bertozzi, Terry; Adelson, David L.

2016-01-01

LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to ‘jump’ around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6–8 kb sequences containing a 5′-UTR, two open reading frames working harmoniously in cis, and a 3′-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional ‘hyperactivity’ far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes. PMID:27702814

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 generally, the approach provides insights into both evolutionary processes and ecological costs and benefits of different plant growth strategies. PMID:24651371

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

PubMed

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The coevolutionary dynamics of obligate ant social parasite systems--between prudence and antagonism.

PubMed

Brandt, Miriam; Foitzik, Susanne; Fischer-Blass, Birgit; Heinze, Jürgen

2005-05-01

In this synthesis we apply coevolutionary models to the interactions between socially parasitic ants and their hosts. Obligate social parasite systems are ideal models for coevolution, because the close phylogenetic relationship between these parasites and their hosts results in similar evolutionary potentials, thus making mutual adaptations in a stepwise fashion especially likely to occur. The evolutionary dynamics of host-parasite interactions are influenced by a number of parameters, for example the parasite's transmission mode and rate, the genetic structure of host and parasite populations, the antagonists' migration rates, and the degree of mutual specialisation. For the three types of obligate ant social parasites, queen-tolerant and queen-intolerant inquilines and slavemakers, several of these parameters, and thus the evolutionary trajectory, are likely to differ. Because of the fundamental differences in lifestyle between these social parasite systems, coevolution should further select for different traits in the parasites and their hosts. Queen-tolerant inquilines are true parasites that exert a low selection pressure on their host, because of their rarity and the fact that they do not conduct slave raids to replenish their labour force. Due to their high degree of specialisation and the potential for vertical transmission, coevolutionary theory would predict interactions between these workerless parasites and their hosts to become even more benign over time. Queen-intolerant inquilines that kill the host queen during colony take-over are best described as parasitoids, and their reproductive success is limited by the existing worker force of the invaded host nest. These parasites should therefore evolve strategies to best exploit this fixed resource. Slavemaking ants, by contrast, act as parasites only during colony foundation, while their frequent slave raids follow a predator prey dynamic. They often exploit a number of host species at a given site, and theory predicts that their associations are best described in terms of a highly antagonistic coevolutionary arms race.

The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa.

PubMed

Davis, P L; Rambaut, A; Bourhy, H; Holmes, E C

2007-01-01

Two variants of rabies virus (RABV) currently circulate in southern Africa: canid RABV, mainly associated with dogs, jackals, and bat-eared foxes, and mongoose RABV. To investigate the evolutionary dynamics of these variants, we performed coalescent-based analyses of the G-L inter-genic region, allowing for rate variation among viral lineages through the use of a relaxed molecular clock. This revealed that mongoose RABV is evolving more slowly than canid RABV, with mean evolutionary rates of 0.826 and 1.676 x 10(-3) nucleotide substitutions per site, per year, respectively. Additionally, mongoose RABV exhibits older genetic diversity than canid RABV, with common ancestors dating to 73 and 30 years, respectively, and while mongoose RABV has experienced exponential population growth over its evolutionary history in Africa, populations of canid RABV have maintained a constant size. Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology.

Asynchronous spatial evolutionary games.

PubMed

Newth, David; Cornforth, David

2009-02-01

Over the past 50 years, much attention has been given to the Prisoner's Dilemma as a metaphor for problems surrounding the evolution and maintenance of cooperative and altruistic behavior. The bulk of this work has dealt with the successfulness and robustness of various strategies. Nowak and May (1992) considered an alternative approach to studying evolutionary games. They assumed that players were distributed across a two-dimensional (2D) lattice, interactions between players occurred locally, rather than at long range as in the well mixed situation. The resulting spatial evolutionary games display dynamics not seen in their well-mixed counterparts. An assumption underlying much of the work on spatial evolutionary games is that the state of all players is updated in unison or in synchrony. Using the framework outlined in Nowak and May (1992), we examine the effect of various asynchronous updating schemes on the dynamics of spatial evolutionary games. There are potential implications for the dynamics of a wide variety of spatially extended systems in biology, physics and chemistry.

A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming.

PubMed

Cotto, Olivier; Wessely, Johannes; Georges, Damien; Klonner, Günther; Schmid, Max; Dullinger, Stefan; Thuiller, Wilfried; Guillaume, Frédéric

2017-05-05

Withstanding extinction while facing rapid climate change depends on a species' ability to track its ecological niche or to evolve a new one. Current methods that predict climate-driven species' range shifts use ecological modelling without eco-evolutionary dynamics. Here we present an eco-evolutionary forecasting framework that combines niche modelling with individual-based demographic and genetic simulations. Applying our approach to four endemic perennial plant species of the Austrian Alps, we show that accounting for eco-evolutionary dynamics when predicting species' responses to climate change is crucial. Perennial species persist in unsuitable habitats longer than predicted by niche modelling, causing delayed range losses; however, their evolutionary responses are constrained because long-lived adults produce increasingly maladapted offspring. Decreasing population size due to maladaptation occurs faster than the contraction of the species range, especially for the most abundant species. Monitoring of species' local abundance rather than their range may likely better inform on species' extinction risks under climate change.

Cancer Evolution: Mathematical Models and Computational Inference

PubMed Central

Beerenwinkel, Niko; Schwarz, Roland F.; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. PMID:25293804

Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades

NASA Astrophysics Data System (ADS)

Hansen, Sabine; Krishna, Sandeep; Semsey, Szabolcs; Lo Svenningsen, Sine

2015-07-01

Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.

The evolutionary dynamics of language.

PubMed

Steels, Luc; Szathmáry, Eörs

2018-02-01

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, and points to open problems. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evolutionary Dynamics and Diversity in Microbial Populations

NASA Astrophysics Data System (ADS)

Thompson, Joel; Fisher, Daniel

2013-03-01

Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

Reconstructing Networks from Profit Sequences in Evolutionary Games via a Multiobjective Optimization Approach with Lasso Initialization

PubMed Central

Wu, Kai; Liu, Jing; Wang, Shuai

2016-01-01

Evolutionary games (EG) model a common type of interactions in various complex, networked, natural and social systems. Given such a system with only profit sequences being available, reconstructing the interacting structure of EG networks is fundamental to understand and control its collective dynamics. Existing approaches used to handle this problem, such as the lasso, a convex optimization method, need a user-defined constant to control the tradeoff between the natural sparsity of networks and measurement error (the difference between observed data and simulated data). However, a shortcoming of these approaches is that it is not easy to determine these key parameters which can maximize the performance. In contrast to these approaches, we first model the EG network reconstruction problem as a multiobjective optimization problem (MOP), and then develop a framework which involves multiobjective evolutionary algorithm (MOEA), followed by solution selection based on knee regions, termed as MOEANet, to solve this MOP. We also design an effective initialization operator based on the lasso for MOEA. We apply the proposed method to reconstruct various types of synthetic and real-world networks, and the results show that our approach is effective to avoid the above parameter selecting problem and can reconstruct EG networks with high accuracy. PMID:27886244

Reconstructing Networks from Profit Sequences in Evolutionary Games via a Multiobjective Optimization Approach with Lasso Initialization

NASA Astrophysics Data System (ADS)

Wu, Kai; Liu, Jing; Wang, Shuai

2016-11-01

Evolutionary games (EG) model a common type of interactions in various complex, networked, natural and social systems. Given such a system with only profit sequences being available, reconstructing the interacting structure of EG networks is fundamental to understand and control its collective dynamics. Existing approaches used to handle this problem, such as the lasso, a convex optimization method, need a user-defined constant to control the tradeoff between the natural sparsity of networks and measurement error (the difference between observed data and simulated data). However, a shortcoming of these approaches is that it is not easy to determine these key parameters which can maximize the performance. In contrast to these approaches, we first model the EG network reconstruction problem as a multiobjective optimization problem (MOP), and then develop a framework which involves multiobjective evolutionary algorithm (MOEA), followed by solution selection based on knee regions, termed as MOEANet, to solve this MOP. We also design an effective initialization operator based on the lasso for MOEA. We apply the proposed method to reconstruct various types of synthetic and real-world networks, and the results show that our approach is effective to avoid the above parameter selecting problem and can reconstruct EG networks with high accuracy.

Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes

PubMed Central

Chugunov, Anton O.; Volynsky, Pavel E.; Krylov, Nikolay A.; Boldyrev, Ivan A.; Efremov, Roman G.

2014-01-01

Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0–100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and “branched” hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems. PMID:25501042

Aspiration dynamics of multi-player games in finite populations

PubMed Central

Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

2014-01-01

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

Aspiration dynamics of multi-player games in finite populations.

PubMed

Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

The proper treatment of language acquisition and change in a population setting.

PubMed

Niyogi, Partha; Berwick, Robert C

2009-06-23

Language acquisition maps linguistic experience, primary linguistic data (PLD), onto linguistic knowledge, a grammar. Classically, computational models of language acquisition assume a single target grammar and one PLD source, the central question being whether the target grammar can be acquired from the PLD. However, real-world learners confront populations with variation, i.e., multiple target grammars and PLDs. Removing this idealization has inspired a new class of population-based language acquisition models. This paper contrasts 2 such models. In the first, iterated learning (IL), each learner receives PLD from one target grammar but different learners can have different targets. In the second, social learning (SL), each learner receives PLD from possibly multiple targets, e.g., from 2 parents. We demonstrate that these 2 models have radically different evolutionary consequences. The IL model is dynamically deficient in 2 key respects. First, the IL model admits only linear dynamics and so cannot describe phase transitions, attested rapid changes in languages over time. Second, the IL model cannot properly describe the stability of languages over time. In contrast, the SL model leads to nonlinear dynamics, bifurcations, and possibly multiple equilibria and so suffices to model both the case of stable language populations, mixtures of more than 1 language, as well as rapid language change. The 2 models also make distinct, empirically testable predictions about language change. Using historical data, we show that the SL model more faithfully replicates the dynamics of the evolution of Middle English.

A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

NASA Astrophysics Data System (ADS)

Lin, XuXun; Yuan, PengCheng

2018-01-01

In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

The evolution of colour pattern complexity: selection for conspicuousness favours contrasting within-body colour combinations in lizards.

PubMed

Pérez I de Lanuza, G; Font, E

2016-05-01

Many animals display complex colour patterns that comprise several adjacent, often contrasting colour patches. Combining patches of complementary colours increases the overall conspicuousness of the complex pattern, enhancing signal detection. Therefore, selection for conspicuousness may act not only on the design of single colour patches, but also on their combination. Contrasting long- and short-wavelength colour patches are located on the ventral and lateral surfaces of many lacertid lizards. As the combination of long- and short-wavelength-based colours generates local chromatic contrast, we hypothesized that selection may favour the co-occurrence of lateral and ventral contrasting patches, resulting in complex colour patterns that maximize the overall conspicuousness of the signal. To test this hypothesis, we performed a comparative phylogenetic study using a categorical colour classification based on spectral data and descriptive information on lacertid coloration collected from the literature. Our results demonstrate that conspicuous ventral (long-wavelength-based) and lateral (short-wavelength-based) colour patches co-occur throughout the lacertid phylogeny more often than expected by chance, especially in the subfamily Lacertini. These results suggest that selection promotes the evolution of the complex pattern rather than the acquisition of a single conspicuous colour patch, possibly due to the increased conspicuousness caused by the combination of colours with contrasting spectral properties. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Dynamic species classification of microorganisms across time, abiotic and biotic environments—A sliding window approach

PubMed Central

Griffiths, Jason I.; Fronhofer, Emanuel A.; Garnier, Aurélie; Seymour, Mathew; Altermatt, Florian; Petchey, Owen L.

2017-01-01

The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learning (ML) algorithms into meaningful ecological information. ML uses user defined classes (e.g. species), derived from a subset (i.e. training data) of video-observed quantitative features (e.g. phenotypic variation), to infer classes in subsequent observations. However, phenotypic variation often changes due to environmental conditions, which may lead to poor classification, if environmentally induced variation in phenotypes is not accounted for. Here we describe a framework for classifying species under changing environmental conditions based on the random forest classification. A sliding window approach was developed that restricts temporal and environmentally conditions to improve the classification. We tested our approach by applying the classification framework to experimental data. The experiment used a set of six ciliate species to monitor changes in community structure and behavior over hundreds of generations, in dozens of species combinations and across a temperature gradient. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, as phenotypic differences driven by environmental change, could be captured by the classifier. Importantly, classification using the random forest algorithm showed comparable success when validated against traditional, slower, manual identification. Our framework allows for reliable classification in dynamic environments, and may help to improve strategies for long-term monitoring of species in changing environments. Our classification pipeline can be applied in fields assessing species community dynamics, such as eco-toxicology, ecology and evolutionary ecology. PMID:28472193

Bridging Developmental Systems Theory and Evolutionary Psychology Using Dynamic Optimization

ERIC Educational Resources Information Center

Frankenhuis, Willem E.; Panchanathan, Karthik; Clark Barrett, H.

2013-01-01

Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic…

Evolutionary Dynamics of Digitized Organizational Routines

ERIC Educational Resources Information Center

Liu, Peng

2013-01-01

This dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of…

Ecological and evolutionary approaches to managing honeybee disease.

PubMed

Brosi, Berry J; Delaplane, Keith S; Boots, Michael; de Roode, Jacobus C

2017-09-01

Honeybee declines are a serious threat to global agricultural security and productivity. Although multiple factors contribute to these declines, parasites are a key driver. Disease problems in honeybees have intensified in recent years, despite increasing attention to addressing them. Here we argue that we must focus on the principles of disease ecology and evolution to understand disease dynamics, assess the severity of disease threats, and control these threats via honeybee management. We cover the ecological context of honeybee disease, including both host and parasite factors driving current transmission dynamics, and then discuss evolutionary dynamics including how beekeeping management practices may drive selection for more virulent parasites. We then outline how ecological and evolutionary principles can guide disease mitigation in honeybees, including several practical management suggestions for addressing short- and long-term disease dynamics and consequences.

Laboratory evolution of protein conformational dynamics.

PubMed

Campbell, Eleanor C; Correy, Galen J; Mabbitt, Peter D; Buckle, Ashley M; Tokuriki, Nobuhiko; Jackson, Colin J

2017-11-08

This review focuses on recent work that has begun to establish specific functional roles for protein conformational dynamics, specifically how the conformational landscapes that proteins can sample can evolve under laboratory based evolutionary selection. We discuss recent technical advances in computational and biophysical chemistry, which have provided us with new ways to dissect evolutionary processes. Finally, we offer some perspectives on the emerging view of conformational dynamics and evolution, and the challenges that we face in rationally engineering conformational dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Price Equation, Gradient Dynamics, and Continuous Trait Game Theory.

PubMed

Lehtonen, Jussi

2018-01-01

A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts. Using Taylor polynomials and the Price equation, I derive a dynamic measure of evolutionary change, a condition for singular points, the convergence stability criterion, and an alternative interpretation of evolutionary stability. Furthermore, by applying the Price equation to a multivariable Taylor polynomial, the direct fitness approach to kin selection emerges. Finally, I compare these results to the mean gradient equation of quantitative genetics and the canonical equation of adaptive dynamics.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. Copyright © 2016 Elsevier Ltd. All rights reserved.

Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

PubMed Central

Mannakee, Brian K.; Gutenkunst, Ryan N.

2016-01-01

The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265

The one-third law of evolutionary dynamics.

PubMed

Ohtsuki, Hisashi; Bordalo, Pedro; Nowak, Martin A

2007-11-21

Evolutionary game dynamics in finite populations provide a new framework for studying selection of traits with frequency-dependent fitness. Recently, a "one-third law" of evolutionary dynamics has been described, which states that strategy A fixates in a B-population with selective advantage if the fitness of A is greater than that of B when A has a frequency 13. This relationship holds for all evolutionary processes examined so far, from the Moran process to games on graphs. However, the origin of the "number"13 is not understood. In this paper we provide an intuitive explanation by studying the underlying stochastic processes. We find that in one invasion attempt, an individual interacts on average with B-players twice as often as with A-players, which yields the one-third law. We also show that the one-third law implies that the average Malthusian fitness of A is positive.

Progenitor cell dynamics in the Newt Telencephalon during homeostasis and neuronal regeneration.

PubMed

Kirkham, Matthew; Hameed, L Shahul; Berg, Daniel A; Wang, Heng; Simon, András

2014-04-08

The adult newt brain has a marked neurogenic potential and is highly regenerative. Ventricular, radial glia-like ependymoglia cells give rise to neurons both during normal homeostasis and after injury, but subpopulations among ependymoglia cells have not been defined. We show here that a substantial portion of GFAP(+) ependymoglia cells in the proliferative hot spots of the telencephalon has transit-amplifying characteristics. In contrast, proliferating ependymoglia cells, which are scattered along the ventricular wall, have stem cell features in terms of label retention and insensitivity to AraC treatment. Ablation of neurons remodels the proliferation dynamics and leads to de novo formation of regions displaying features of neurogenic niches, such as the appearance of cells with transit-amplifying features and proliferating neuroblasts. The results have implication both for our understanding of the evolutionary diversification of radial glia cells as well as the processes regulating neurogenesis and regeneration in the adult vertebrate brain.

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

PubMed

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

2011-11-01

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

Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks

PubMed Central

Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

2015-01-01

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint. PMID:26306175

On Reciprocal Causation in the Evolutionary Process.

PubMed

Svensson, Erik I

2018-01-01

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach might have been underestimated by critics of contemporary evolutionary biology.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

Treesearch

Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

2012-01-01

Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Life history determines genetic structure and evolutionary potential of host–parasite interactions

PubMed Central

Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

2009-01-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

Life history determines genetic structure and evolutionary potential of host-parasite interactions.

PubMed

Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

2008-12-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

Cancer evolution: mathematical models and computational inference.

PubMed

Beerenwinkel, Niko; Schwarz, Roland F; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Recent social and biogeophysical changes in the Ganges-Brahmaputra-Meghna, Mekong, and Amazon deltas as inputs into evolutionary policy-making.

NASA Astrophysics Data System (ADS)

de Araujo Barbosa, C. C.; Hossain, S.; Szabo, S.; Matthews, Z.; Heard, S.; Dearing, J.

2014-12-01

Policy-making in social-ecological systems increasingly looks to iterative, evolutionary approaches that can address the inherent complexity of interactions between human wellbeing, agricultural and aquacultural production, and ecosystem services. Here we show how an analysis of available time-series in delta regions over past decades can provide important insight into the social-ecological system dynamics that result from the complexity. The presentation summarises the recent changes for major elements of each social-ecological system, for example demography, economy, health, climate, food, and water. Time-series data from official statistics, monitoring programmes and sequential satellite imagery are analysed to define the range of trends, the presence of change points, slow and fast variables, and the significant drivers of change. For example, in the Bangladesh delta zone, increasing gross domestic product and per capita income levels since the 1980s mirror rising levels of food and inland fish production. In contrast, non-food ecosystem services such as water availability, water quality and land stability have deteriorated. As a result, poverty alleviation is associated with environmental degradation. Trends in indicators of human wellbeing and ecosystem services point to widespread non-stationary dynamics governed by slowly changing variables with increased probability of systemic threshold changes/tipping points in the near future. We conclude by examining how the findings could feed into new management tools, such as system dynamic models and assessments of safe operating spaces. Such tools have the potential to help create policies that deliver alternative and sustainable paths for land management while accommodating social and environmental change.

Individual Development and Evolution: Experiential Canalization of Self-Regulation

ERIC Educational Resources Information Center

Blair, Clancy; Raver, C. Cybele

2012-01-01

In this article, we contrast evolutionary and psychobiological models of individual development to address the idea that individual development occurring in prototypically risky and unsupportive environments can be understood as adaptation. We question traditional evolutionary explanations of individual development, calling on the principle of…

Ecological and evolutionary approaches to managing honey bee disease

PubMed Central

Brosi, Berry J.; Delaplane, Keith S.; Boots, Michael; de Roode, Jacobus C.

2017-01-01

Honey bee declines are a serious threat to global agricultural security and productivity. While multiple factors contribute to these declines, parasites are a key driver. Disease problems in honey bees have intensified in recent years, despite increasing attention to addressing them. Here we argue that we must focus on the principles of disease ecology and evolution to understand disease dynamics, assess the severity of disease threats, and manage these threats via honey bee management. We cover the ecological context of honey bee disease, including both host and parasite factors driving current transmission dynamics, and then discuss evolutionary dynamics including how beekeeping management practices may drive selection for more virulent parasites. We then outline how ecological and evolutionary principles can guide disease mitigation in honey bees, including several practical management suggestions for addressing short- and long-term disease dynamics and consequences. PMID:29046562

Evolution and social epidemiology.

PubMed

Nishi, Akihiro

2015-11-01

Evolutionary biology, which aims to explain the dynamic process of shaping the diversity of life, has not yet significantly affected thinking in social epidemiology. Current challenges in social epidemiology include understanding how social exposures can affect our biology, explaining the dynamics of society and health, and designing better interventions that are mindful of the impact of exposures during critical periods. I review how evolutionary concepts and tools, such as fitness gradient in cultural evolution, evolutionary game theory, and contemporary evolution in cancer, can provide helpful insights regarding social epidemiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ecological and Evolutionary Effects of Dispersal on Freshwater Zooplankton

ERIC Educational Resources Information Center

Allen, Michael R.

2009-01-01

A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate ecology with evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species…

When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin.

PubMed

Faucher, Leslie; Hénocq, Laura; Vanappelghem, Cédric; Rondel, Stéphanie; Quevillart, Robin; Gallina, Sophie; Godé, Cécile; Jaquiéry, Julie; Arnaud, Jean-François

2017-09-01

Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries. © 2017 John Wiley & Sons Ltd.

The evolutionary origins of Lévy walk foraging

PubMed Central

Wosniack, Marina E.

2017-01-01

We study through a reaction-diffusion algorithm the influence of landscape diversity on the efficiency of search dynamics. Remarkably, the identical optimal search strategy arises in a wide variety of environments, provided the target density is sparse and the searcher’s information is restricted to its close vicinity. Our results strongly impact the current debate on the emergentist vs. evolutionary origins of animal foraging. The inherent character of the optimal solution (i.e., independent on the landscape for the broad scenarios assumed here) suggests an interpretation favoring the evolutionary view, as originally implied by the Lévy flight foraging hypothesis. The latter states that, under conditions of scarcity of information and sparse resources, some organisms must have evolved to exploit optimal strategies characterized by heavy-tailed truncated power-law distributions of move lengths. These results strongly suggest that Lévy strategies—and hence the selection pressure for the relevant adaptations—are robust with respect to large changes in habitat. In contrast, the usual emergentist explanation seems not able to explain how very similar Lévy walks can emerge from all the distinct non-Lévy foraging strategies that are needed for the observed large variety of specific environments. We also report that deviations from Lévy can take place in plentiful ecosystems, where locomotion truncation is very frequent due to high encounter rates. So, in this case normal diffusion strategies—performing as effectively as the optimal one—can naturally emerge from Lévy. Our results constitute the strongest theoretical evidence to date supporting the evolutionary origins of experimentally observed Lévy walks. PMID:28972973

The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird.

PubMed

Bertrand, J A M; Delahaie, B; Bourgeois, Y X C; Duval, T; García-Jiménez, R; Cornuault, J; Pujol, B; Thébaud, C; Milá, B

2016-04-01

Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST ) and phenotypic differentiation (PST ) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection

PubMed Central

Soularue, J-P; Kremer, A

2014-01-01

The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations. PMID:24924591

A formal theory of the selfish gene.

PubMed

Gardner, A; Welch, J J

2011-08-01

Adaptation is conventionally regarded as occurring at the level of the individual organism. In contrast, the theory of the selfish gene proposes that it is more correct to view adaptation as occurring at the level of the gene. This view has received much popular attention, yet has enjoyed only limited uptake in the primary research literature. Indeed, the idea of ascribing goals and strategies to genes has been highly controversial. Here, we develop a formal theory of the selfish gene, using optimization theory to capture the analogy of 'gene as fitness-maximizing agent' in mathematical terms. We provide formal justification for this view of adaptation by deriving mathematical correspondences that translate the optimization formalism into dynamical population genetics. We show that in the context of social interactions between genes, it is the gene's inclusive fitness that provides the appropriate maximand. Hence, genic selection can drive the evolution of altruistic genes. Finally, we use the formalism to assess the various criticisms that have been levelled at the theory of the selfish gene, dispelling some and strengthening others. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens.

PubMed

Wininger, Kerry; Rank, Nathan

2017-11-01

Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research. © 2017 New York Academy of Sciences.

Dynamic Adaptive Neural Network Arrays: A Neuromorphic Architecture

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

Disney, Adam; Reynolds, John

2015-01-01

Dynamic Adaptive Neural Network Array (DANNA) is a neuromorphic hardware implementation. It differs from most other neuromorphic projects in that it allows for programmability of structure, and it is trained or designed using evolutionary optimization. This paper describes the DANNA structure, how DANNA is trained using evolutionary optimization, and an application of DANNA to a very simple classification task.

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

PubMed

Argasinski, Krzysztof

2006-07-01

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

A piecewise smooth model of evolutionary game for residential mobility and segregation

NASA Astrophysics Data System (ADS)

Radi, D.; Gardini, L.

2018-05-01

The paper proposes an evolutionary version of a Schelling-type dynamic system to model the patterns of residential segregation when two groups of people are involved. The payoff functions of agents are the individual preferences for integration which are empirically grounded. Differently from Schelling's model, where the limited levels of tolerance are the driving force of segregation, in the current setup agents benefit from integration. Despite the differences, the evolutionary model shows a dynamics of segregation that is qualitatively similar to the one of the classical Schelling's model: segregation is always a stable equilibrium, while equilibria of integration exist only for peculiar configurations of the payoff functions and their asymptotic stability is highly sensitive to parameter variations. Moreover, a rich variety of integrated dynamic behaviors can be observed. In particular, the dynamics of the evolutionary game is regulated by a one-dimensional piecewise smooth map with two kink points that is rigorously analyzed using techniques recently developed for piecewise smooth dynamical systems. The investigation reveals that when a stable internal equilibrium exists, the bimodal shape of the map leads to several different kinds of bifurcations, smooth, and border collision, in a complicated interplay. Our global analysis can give intuitions to be used by a social planner to maximize integration through social policies that manipulate people's preferences for integration.

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

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

Evolutionary game based control for biological systems with applications in drug delivery.

PubMed

Li, Xiaobo; Lenaghan, Scott C; Zhang, Mingjun

2013-06-07

Control engineering and analysis of biological systems have become increasingly important for systems and synthetic biology. Unfortunately, no widely accepted control framework is currently available for these systems, especially at the cell and molecular levels. This is partially due to the lack of appropriate mathematical models to describe the unique dynamics of biological systems, and the lack of implementation techniques, such as ultra-fast and ultra-small devices and corresponding control algorithms. This paper proposes a control framework for biological systems subject to dynamics that exhibit adaptive behavior under evolutionary pressures. The control framework was formulated based on evolutionary game based modeling, which integrates both the internal dynamics and the population dynamics. In the proposed control framework, the adaptive behavior was characterized as an internal dynamic, and the external environment was regarded as an external control input. The proposed open-interface control framework can be integrated with additional control algorithms for control of biological systems. To demonstrate the effectiveness of the proposed framework, an optimal control strategy was developed and validated for drug delivery using the pathogen Giardia lamblia as a test case. In principle, the proposed control framework can be applied to any biological system exhibiting adaptive behavior under evolutionary pressures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolutionary dynamics of a smoothed war of attrition game.

PubMed

Iyer, Swami; Killingback, Timothy

2016-05-07

In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Unto Others: Illustrating the Human Capacity for Cooperation

ERIC Educational Resources Information Center

Morris, J. Andrew; Urbanski, John; Hunt, Jason

2011-01-01

Research in both evolutionary economics and evolutionary psychology provides strong evidence that human behavior can be, and is, a complex mix of hedonism and altruism with a strong inclination toward cooperation under certain conditions. In this article, behavioral assumptions made in mainstream business theory are compared and contrasted with…

A new bio-inspired, population-level approach to the socioeconomic evolution of dynamic spectrum access services

NASA Astrophysics Data System (ADS)

Horvath, Denis; Gazda, Juraj; Brutovsky, Branislav

Evolutionary species and quasispecies models provide the universal and flexible basis for a large-scale description of the dynamics of evolutionary systems, which can be built conceived as a constraint satisfaction dynamics. It represents a general framework to design and study many novel, technologically contemporary models and their variants. Here, we apply the classical quasispecies concept to model the emerging dynamic spectrum access (DSA) markets. The theory describes the mechanisms of mimetic transfer, competitive interactions between socioeconomic strata of the end-users, their perception of the utility and inter-operator switching in the variable technological environments of the operators offering the wireless spectrum services. The algorithmization and numerical modeling demonstrate the long-term evolutionary socioeconomic changes which reflect the end-user preferences and results of the majorization of their irrational decisions in the same manner as the prevailing tendencies which are embodied in the efficient market hypothesis.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Evolution of intrinsic disorder in eukaryotic proteins.

PubMed

Ahrens, Joseph B; Nunez-Castilla, Janelle; Siltberg-Liberles, Jessica

2017-09-01

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.

Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

PubMed Central

Brodersen, Jakob; Seehausen, Ole

2014-01-01

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061

Eco-evolutionary effects on population recovery following catastrophic disturbance

PubMed Central

Weese, Dylan J; Schwartz, Amy K; Bentzen, Paul; Hendry, Andrew P; Kinnison, Michael T

2011-01-01

Fine-scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco-evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco-evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double-edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco-evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation. PMID:25567978

An Improved Co-evolutionary Particle Swarm Optimization for Wireless Sensor Networks with Dynamic Deployment

PubMed Central

Wang, Xue; Wang, Sheng; Ma, Jun-Jie

2007-01-01

The effectiveness of wireless sensor networks (WSNs) depends on the coverage and target detection probability provided by dynamic deployment, which is usually supported by the virtual force (VF) algorithm. However, in the VF algorithm, the virtual force exerted by stationary sensor nodes will hinder the movement of mobile sensor nodes. Particle swarm optimization (PSO) is introduced as another dynamic deployment algorithm, but in this case the computation time required is the big bottleneck. This paper proposes a dynamic deployment algorithm which is named “virtual force directed co-evolutionary particle swarm optimization” (VFCPSO), since this algorithm combines the co-evolutionary particle swarm optimization (CPSO) with the VF algorithm, whereby the CPSO uses multiple swarms to optimize different components of the solution vectors for dynamic deployment cooperatively and the velocity of each particle is updated according to not only the historical local and global optimal solutions, but also the virtual forces of sensor nodes. Simulation results demonstrate that the proposed VFCPSO is competent for dynamic deployment in WSNs and has better performance with respect to computation time and effectiveness than the VF, PSO and VFPSO algorithms.

Evolutionary dynamics of fearfulness and boldness.

PubMed

Ji, Ting; Zhang, Boyu; Sun, Yuehua; Tao, Yi

2009-02-21

A negative relationship between reproductive effort and survival is consistent with life-history. Evolutionary dynamics and evolutionarily stable strategy (ESS) for the trade-off between survival and reproduction are investigated using a simple model with two phenotypes, fearfulness and boldness. The dynamical stability of the pure strategy model and analysis of ESS conditions reveal that: (i) the simple coexistence of fearfulness and boldness is impossible; (ii) a small population size is favorable to fearfulness, but a large population size is favorable to boldness, i.e., neither fearfulness, nor boldness is always favored by natural selection; and (iii) the dynamics of population density is crucial for a proper understanding of the strategy dynamics.

Genetics of dispersal.

PubMed

Saastamoinen, Marjo; Bocedi, Greta; Cote, Julien; Legrand, Delphine; Guillaume, Frédéric; Wheat, Christopher W; Fronhofer, Emanuel A; Garcia, Cristina; Henry, Roslyn; Husby, Arild; Baguette, Michel; Bonte, Dries; Coulon, Aurélie; Kokko, Hanna; Matthysen, Erik; Niitepõld, Kristjan; Nonaka, Etsuko; Stevens, Virginie M; Travis, Justin M J; Donohue, Kathleen; Bullock, James M; Del Mar Delgado, Maria

2018-02-01

Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Genetics of dispersal

PubMed Central

Bocedi, Greta; Cote, Julien; Legrand, Delphine; Guillaume, Frédéric; Wheat, Christopher W.; Fronhofer, Emanuel A.; Garcia, Cristina; Henry, Roslyn; Husby, Arild; Baguette, Michel; Bonte, Dries; Coulon, Aurélie; Kokko, Hanna; Matthysen, Erik; Niitepõld, Kristjan; Nonaka, Etsuko; Stevens, Virginie M.; Travis, Justin M. J.; Donohue, Kathleen; Bullock, James M.; del Mar Delgado, Maria

2017-01-01

ABSTRACT Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits. PMID:28776950

Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach

NASA Astrophysics Data System (ADS)

Pizzolato, Nicola; Valenti, Davide; Adorno, Dominique Persano; Spagnolo, Bernardo

2009-09-01

The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic behavior of cell reproduction and death in a population of blood cells which can experience genetic mutations. In CML front line therapy is represented by the tyrosine kinase inhibitor imatinib which strongly affects the reproduction of leukemic cells only. In this work, we analyze the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. Several scenarios of the evolutionary dynamics of imatinib-treated leukemic cells are described as a consequence of the efficacy of the different modelled therapies. We show how the patient response to the therapy changes when a high value of the mutation rate from healthy to cancerous cells is present. Our results are in agreement with clinical observations. Unfortunately, development of resistance to imatinib is observed in a fraction of patients, whose blood cells are characterized by an increasing number of genetic alterations. We find that the occurrence of resistance to the therapy can be related to a progressive increase of deleterious mutations.

Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat.

PubMed

Senerchia, Natacha; Wicker, Thomas; Felber, François; Parisod, Christian

2013-01-01

Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.

Antibiotic resistance in the wild: an eco-evolutionary perspective.

PubMed

Hiltunen, Teppo; Virta, Marko; Laine, Anna-Liisa

2017-01-19

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Authors.

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.

Antibiotic resistance in the wild: an eco-evolutionary perspective

PubMed Central

Virta, Marko

2017-01-01

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'. PMID:27920384

Large fluctuations in anti-coordination games on scale-free graphs

NASA Astrophysics Data System (ADS)

Sabsovich, Daniel; Mobilia, Mauro; Assaf, Michael

2017-05-01

We study the influence of the complex topology of scale-free graphs on the dynamics of anti-coordination games (e.g. snowdrift games). These reference models are characterized by the coexistence (evolutionary stable mixed strategy) of two competing species, say ‘cooperators’ and ‘defectors’, and, in finite systems, by metastability and large-fluctuation-driven fixation. In this work, we use extensive computer simulations and an effective diffusion approximation (in the weak selection limit) to determine under which circumstances, depending on the individual-based update rules, the topology drastically affects the long-time behavior of anti-coordination games. In particular, we compute the variance of the number of cooperators in the metastable state and the mean fixation time when the dynamics is implemented according to the voter model (death-first/birth-second process) and the link dynamics (birth/death or death/birth at random). For the voter update rule, we show that the scale-free topology effectively renormalizes the population size and as a result the statistics of observables depend on the network’s degree distribution. In contrast, such a renormalization does not occur with the link dynamics update rule and we recover the same behavior as on complete graphs.

Character convergence under competition for nutritionally essential resources.

PubMed

Fox, Jeremy W; Vasseur, David A

2008-11-01

Resource competition is thought to drive divergence in resource use traits (character displacement) by generating selection favoring individuals able to use resources unavailable to others. However, this picture assumes nutritionally substitutable resources (e.g., different prey species). When species compete for nutritionally essential resources (e.g., different nutrients), theory predicts that selection drives character convergence. We used models of two species competing for two essential resources to address several issues not considered by existing theory. The models incorporated either slow evolutionary change in resource use traits or fast physiological or behavioral change. We report four major results. First, competition always generates character convergence, but differences in resource requirements prevent competitors from evolving identical resource use traits. Second, character convergence promotes coexistence. Competing species always attain resource use traits that allow coexistence, and adaptive trait change stabilizes the ecological equilibrium. In contrast, adaptation in allopatry never preadapts species to coexist in sympatry. Third, feedbacks between ecological dynamics and trait dynamics lead to surprising dynamical trajectories such as transient divergence in resource use traits followed by subsequent convergence. Fourth, under sufficiently slow trait change, ecological dynamics often drive one of the competitors to near extinction, which would prevent realization of long-term character convergence in practice.

Host-pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies.

PubMed

Streicker, Daniel G; Winternitz, Jamie C; Satterfield, Dara A; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andrés; Altizer, Sonia; Valderrama, William

2016-09-27

Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared completely isolated. In contrast, greater population connectivity in biparentally inherited nuclear microsatellites explained the historical limits of invasions, suggesting that dispersing male bats spread VBRV between genetically isolated female populations. Host nuclear DNA further indicated unanticipated gene flow through the Andes mountains connecting the VBRV-free Pacific coast to the VBRV-endemic Amazon rainforest. By combining Bayesian phylogeography with landscape resistance models, we projected invasion routes through northern Peru that were validated by real-time livestock rabies mortality data. The first outbreaks of VBRV on the Pacific coast of South America could occur by June 2020, which would have serious implications for agriculture, wildlife conservation, and human health. Our results show that combining host and pathogen genetic data can identify sex biases in pathogen spatial spread, which may be a widespread but underappreciated phenomenon, and demonstrate that genetic forecasting can aid preparedness for impending viral invasions.

Host–pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

PubMed Central

Streicker, Daniel G.; Winternitz, Jamie C.; Satterfield, Dara A.; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andrés; Altizer, Sonia; Valderrama, William

2016-01-01

Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared completely isolated. In contrast, greater population connectivity in biparentally inherited nuclear microsatellites explained the historical limits of invasions, suggesting that dispersing male bats spread VBRV between genetically isolated female populations. Host nuclear DNA further indicated unanticipated gene flow through the Andes mountains connecting the VBRV-free Pacific coast to the VBRV-endemic Amazon rainforest. By combining Bayesian phylogeography with landscape resistance models, we projected invasion routes through northern Peru that were validated by real-time livestock rabies mortality data. The first outbreaks of VBRV on the Pacific coast of South America could occur by June 2020, which would have serious implications for agriculture, wildlife conservation, and human health. Our results show that combining host and pathogen genetic data can identify sex biases in pathogen spatial spread, which may be a widespread but underappreciated phenomenon, and demonstrate that genetic forecasting can aid preparedness for impending viral invasions. PMID:27621441

Controlled recovery of phylogenetic communities from an evolutionary model using a network approach

NASA Astrophysics Data System (ADS)

Sousa, Arthur M. Y. R.; Vieira, André P.; Prado, Carmen P. C.; Andrade, Roberto F. S.

2016-04-01

This works reports the use of a complex network approach to produce a phylogenetic classification tree of a simple evolutionary model. This approach has already been used to treat proteomic data of actual extant organisms, but an investigation of its reliability to retrieve a traceable evolutionary history is missing. The used evolutionary model includes key ingredients for the emergence of groups of related organisms by differentiation through random mutations and population growth, but purposefully omits other realistic ingredients that are not strictly necessary to originate an evolutionary history. This choice causes the model to depend only on a small set of parameters, controlling the mutation probability and the population of different species. Our results indicate that for a set of parameter values, the phylogenetic classification produced by the used framework reproduces the actual evolutionary history with a very high average degree of accuracy. This includes parameter values where the species originated by the evolutionary dynamics have modular structures. In the more general context of community identification in complex networks, our model offers a simple setting for evaluating the effects, on the efficiency of community formation and identification, of the underlying dynamics generating the network itself.

Understanding rapid evolution in predator‐prey interactions using the theory of fast‐slow dynamical systems.

PubMed

Cortez, Michael H; Ellner, Stephen P

2010-11-01

The accumulation of evidence that ecologically important traits often evolve at the same time and rate as ecological dynamics (e.g., changes in species' abundances or spatial distributions) has outpaced theory describing the interplay between ecological and evolutionary processes with comparable timescales. The disparity between experiment and theory is partially due to the high dimensionality of models that include both evolutionary and ecological dynamics. Here we show how the theory of fast-slow dynamical systems can be used to reduce model dimension, and we use that body of theory to study a general predator-prey system exhibiting fast evolution in either the predator or the prey. Our approach yields graphical methods with predictive power about when new and unique dynamics (e.g., completely out-of-phase oscillations and cryptic dynamics) can arise in ecological systems exhibiting fast evolution. In addition, we derive analytical expressions for determining when such behavior arises and how evolution affects qualitative properties of the ecological dynamics. Finally, while the theory requires a separation of timescales between the ecological and evolutionary processes, our approach yields insight into systems where the rates of those processes are comparable and thus is a step toward creating a general ecoevolutionary theory.

Deontic Reasoning with Emotional Content: Evolutionary Psychology or Decision Theory?

ERIC Educational Resources Information Center

Perham, Nick; Oaksford, Mike

2005-01-01

Three experiments investigated the contrasting predictions of the evolutionary and decision-theoretic approaches to deontic reasoning. Two experiments embedded a hazard management (HM) rule in a social contract scenario that should lead to competition between innate modules. A 3rd experiment used a pure HM task. Threatening material was also…

Testability of evolutionary game dynamics based on experimental economics data

NASA Astrophysics Data System (ADS)

Wang, Yijia; Chen, Xiaojie; Wang, Zhijian

2017-11-01

Understanding the dynamic processes of a real game system requires an appropriate dynamics model, and rigorously testing a dynamics model is nontrivial. In our methodological research, we develop an approach to testing the validity of game dynamics models that considers the dynamic patterns of angular momentum and speed as measurement variables. Using Rock-Paper-Scissors (RPS) games as an example, we illustrate the geometric patterns in the experiment data. We then derive the related theoretical patterns from a series of typical dynamics models. By testing the goodness-of-fit between the experimental and theoretical patterns, we show that the validity of these models can be evaluated quantitatively. Our approach establishes a link between dynamics models and experimental systems, which is, to the best of our knowledge, the most effective and rigorous strategy for ascertaining the testability of evolutionary game dynamics models.

The Role of Time-Scales in Socio-hydrology

NASA Astrophysics Data System (ADS)

Blöschl, Günter; Sivapalan, Murugesu

2016-04-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time scale interactions and the coevolution of humans and water. Water Resour. Res., 51, 6988-7022, doi:10.1002/2015WR017896.

Multiscale Modeling of Human-Water Interactions: The Role of Time-Scales

NASA Astrophysics Data System (ADS)

Bloeschl, G.; Sivapalan, M.

2015-12-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time Scale Interactions and the Co-evolution of Humans and Water. Water Resour. Res., 51, in press.

Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: Many losses of photosynthesis and complex patterns of rate variation

PubMed Central

dePamphilis, Claude W.; Young, Nelson D.; Wolfe, Andrea D.

1997-01-01

The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism. PMID:9207097

Evolutionary biosemiotics and multilevel construction networks.

PubMed

Sharov, Alexei A

2016-12-01

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition . Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents.

Evolutionary biosemiotics and multilevel construction networks

PubMed Central

Sharov, Alexei A.

2016-01-01

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents. PMID:28163801

Evolutionary suicide through a non-catastrophic bifurcation: adaptive dynamics of pathogens with frequency-dependent transmission.

PubMed

Boldin, Barbara; Kisdi, Éva

2016-03-01

Evolutionary suicide is a riveting phenomenon in which adaptive evolution drives a viable population to extinction. Gyllenberg and Parvinen (Bull Math Biol 63(5):981-993, 2001) showed that, in a wide class of deterministic population models, a discontinuous transition to extinction is a necessary condition for evolutionary suicide. An implicit assumption of their proof is that the invasion fitness of a rare strategy is well-defined also in the extinction state of the population. Epidemic models with frequency-dependent incidence, which are often used to model the spread of sexually transmitted infections or the dynamics of infectious diseases within herds, violate this assumption. In these models, evolutionary suicide can occur through a non-catastrophic bifurcation whereby pathogen adaptation leads to a continuous decline of host (and consequently pathogen) population size to zero. Evolutionary suicide of pathogens with frequency-dependent transmission can occur in two ways, with pathogen strains evolving either higher or lower virulence.

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Construction of multiple trade-offs to obtain arbitrary singularities of adaptive dynamics.

PubMed

Kisdi, Éva

2015-04-01

Evolutionary singularities are central to the adaptive dynamics of evolving traits. The evolutionary singularities are strongly affected by the shape of any trade-off functions a model assumes, yet the trade-off functions are often chosen in an ad hoc manner, which may unjustifiably constrain the evolutionary dynamics exhibited by the model. To avoid this problem, critical function analysis has been used to find a trade-off function that yields a certain evolutionary singularity such as an evolutionary branching point. Here I extend this method to multiple trade-offs parameterized with a scalar strategy. I show that the trade-off functions can be chosen such that an arbitrary point in the viability domain of the trait space is a singularity of an arbitrary type, provided (next to certain non-degeneracy conditions) that the model has at least two environmental feedback variables and at least as many trade-offs as feedback variables. The proof is constructive, i.e., it provides an algorithm to find trade-off functions that yield the desired singularity. I illustrate the construction of trade-offs with an example where the virulence of a pathogen evolves in a small ecosystem of a host, its pathogen, a predator that attacks the host and an alternative prey of the predator.

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

NASA Astrophysics Data System (ADS)

Huizhong, Dong; Hongli, Song

An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

Evolutionary Dynamic Multiobjective Optimization Via Kalman Filter Prediction.

PubMed

Muruganantham, Arrchana; Tan, Kay Chen; Vadakkepat, Prahlad

2016-12-01

Evolutionary algorithms are effective in solving static multiobjective optimization problems resulting in the emergence of a number of state-of-the-art multiobjective evolutionary algorithms (MOEAs). Nevertheless, the interest in applying them to solve dynamic multiobjective optimization problems has only been tepid. Benchmark problems, appropriate performance metrics, as well as efficient algorithms are required to further the research in this field. One or more objectives may change with time in dynamic optimization problems. The optimization algorithm must be able to track the moving optima efficiently. A prediction model can learn the patterns from past experience and predict future changes. In this paper, a new dynamic MOEA using Kalman filter (KF) predictions in decision space is proposed to solve the aforementioned problems. The predictions help to guide the search toward the changed optima, thereby accelerating convergence. A scoring scheme is devised to hybridize the KF prediction with a random reinitialization method. Experimental results and performance comparisons with other state-of-the-art algorithms demonstrate that the proposed algorithm is capable of significantly improving the dynamic optimization performance.

Towards a physics of evolution: Critical diversity dynamics at the edges of collapse and bursts of diversification

NASA Astrophysics Data System (ADS)

Hanel, Rudolf; Kauffman, Stuart A.; Thurner, Stefan

2007-09-01

Systems governed by the standard mechanisms of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find an analogy with classical thermodynamic systems. In particular, we can demonstrate the existence of several distinct phases of evolutionary dynamics: a phase of fast growing diversity, one of stationary, finite diversity, and one of rapidly decaying diversity. While the first two phases have been subject to previous work, here we focus on the destructive aspects—in particular the phase diagram—of evolutionary dynamics. The main message is that within a critical region, massive loss of diversity can be triggered by very small external fluctuations. We further propose a dynamical model of diversity which captures spontaneous creation and destruction processes fully respecting the phase diagrams of evolutionary systems. The emergent time series show rich diversity dynamics, including power laws as observed in actual economical data, e.g., firm bankruptcy data. We believe the present model presents a possibility to cast the famous qualitative picture of Schumpeterian economic evolution, into a quantifiable and testable framework.

Application of stochastic processes in random growth and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Oikonomou, Panagiotis

We study the effect of power-law distributed randomness on the dynamical behavior of processes such as stochastic growth patterns and evolution. First, we examine the geometrical properties of random shapes produced by a generalized stochastic Loewner Evolution driven by a superposition of a Brownian motion and a stable Levy process. The situation is defined by the usual stochastic Loewner Evolution parameter, kappa, as well as alpha which defines the power-law tail of the stable Levy distribution. We show that the properties of these patterns change qualitatively and singularly at critical values of kappa and alpha. It is reasonable to call such changes "phase transitions". These transitions occur as kappa passes through four and as alpha passes through one. Numerical simulations are used to explore the global scaling behavior of these patterns in each "phase". We show both analytically and numerically that the growth continues indefinitely in the vertical direction for alpha greater than 1, goes as logarithmically with time for alpha equals to 1, and saturates for alpha smaller than 1. The probability density has two different scales corresponding to directions along and perpendicular to the boundary. Scaling functions for the probability density are given for various limiting cases. Second, we study the effect of the architecture of biological networks on their evolutionary dynamics. In recent years, studies of the architecture of large networks have unveiled a common topology, called scale-free, in which a majority of the elements are poorly connected except for a small fraction of highly connected components. We ask how networks with distinct topologies can evolve towards a pre-established target phenotype through a process of random mutations and selection. We use networks of Boolean components as a framework to model a large class of phenotypes. Within this approach, we find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. While homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously towards the target phenotype. Moreover, we show that scale-free networks always evolve faster than homogeneous random networks; remarkably, this property does not depend on the precise value of the topological parameter. By contrast, homogeneous random networks require a specific tuning of their topological parameter in order to optimize their fitness. This model suggests that the evolutionary paths of biological networks, punctuated or continuous, may solely be determined by the network topology.

Cycle frequency in standard Rock-Paper-Scissors games: Evidence from experimental economics

NASA Astrophysics Data System (ADS)

Xu, Bin; Zhou, Hai-Jun; Wang, Zhijian

2013-10-01

The Rock-Paper-Scissors (RPS) game is a widely used model system in game theory. Evolutionary game theory predicts the existence of persistent cycles in the evolutionary trajectories of the RPS game, but experimental evidence has remained to be rather weak. In this work, we performed laboratory experiments on the RPS game and analyzed the social-state evolutionary trajectories of twelve populations of N=6 players. We found strong evidence supporting the existence of persistent cycles. The mean cycling frequency was measured to be 0.029±0.009 period per experimental round. Our experimental observations can be quantitatively explained by a simple non-equilibrium model, namely the discrete-time logit dynamical process with a noise parameter. Our work therefore favors the evolutionary game theory over the classical game theory for describing the dynamical behavior of the RPS game.

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night.

PubMed

Liow, Lee Hsiang; Reitan, Trond; Harnik, Paul G

2015-10-01

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution. © 2015 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

The amazing evolutionary dynamics of non-linear optical systems with feedback

NASA Astrophysics Data System (ADS)

Yaroslavsky, Leonid

2013-09-01

Optical systems with feedback are, generally, non-linear dynamic systems. As such, they exhibit evolutionary behavior. In the paper we present results of experimental investigation of evolutionary dynamics of several models of such systems. The models are modifications of the famous mathematical "Game of Life". The modifications are two-fold: "Game of Life" rules are made stochastic and mutual influence of cells is made spatially non-uniform. A number of new phenomena in the evolutionary dynamics of the models are revealed: - "Ordering of chaos". Formation, from seed patterns, of stable maze-like patterns with chaotic "dislocations" that resemble natural patterns, such as skin patterns of some animals and fishes, see shell, fingerprints, magnetic domain patterns and alike, which one can frequently find in the nature. These patterns and their fragments exhibit a remarkable capability of unlimited growth. - "Self-controlled growth" of chaotic "live" formations into "communities" bounded, depending on the model, by a square, hexagon or octagon, until they reach a certain critical size, after which the growth stops. - "Eternal life in a bounded space" of "communities" after reaching a certain size and shape. - "Coherent shrinkage" of "mature", after reaching a certain size, "communities" into one of stable or oscillating patterns preserving in this process isomorphism of their bounding shapes until the very end.

Applying evolutionary concepts to wildlife disease ecology and management

PubMed Central

Vander Wal, Eric; Garant, Dany; Calmé, Sophie; Chapman, Colin A; Festa-Bianchet, Marco; Millien, Virginie; Rioux-Paquette, Sébastien; Pelletier, Fanie

2014-01-01

Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host–pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment–disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management. PMID:25469163

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

Applying evolutionary concepts to wildlife disease ecology and management.

PubMed

Vander Wal, Eric; Garant, Dany; Calmé, Sophie; Chapman, Colin A; Festa-Bianchet, Marco; Millien, Virginie; Rioux-Paquette, Sébastien; Pelletier, Fanie

2014-08-01

Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host-pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment-disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management.

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

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

McDonald, Bradon R.; Currie, Cameron R.

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. For this paper, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genusStreptomyces. Using a molecular clock, we estimate that theStreptomycesbacteria are ~380 million years old, indicating that this bacterial genus is as ancient as landmore » vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span,Streptomycesaccumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genusStreptomyces, with merely one gene acquired inStreptomyceslineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.« less

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

DOE PAGES

McDonald, Bradon R.; Currie, Cameron R.

2017-06-06

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. For this paper, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genusStreptomyces. Using a molecular clock, we estimate that theStreptomycesbacteria are ~380 million years old, indicating that this bacterial genus is as ancient as landmore » vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span,Streptomycesaccumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genusStreptomyces, with merely one gene acquired inStreptomyceslineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.« less

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces.

PubMed

McDonald, Bradon R; Currie, Cameron R

2017-06-06

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces , with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial. Copyright © 2017 McDonald and Currie.

Evolutionary advantage via common action of recombination and neutrality

NASA Astrophysics Data System (ADS)

Saakian, David B.; Hu, Chin-Kun

2013-11-01

We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.

Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

NASA Astrophysics Data System (ADS)

Ma, Zhanshan (Sam)

In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three categories of population dynamics models: deterministic modeling with Logistic chaos map as an example, stochastic modeling with spatial distribution patterns as an example, as well as survival analysis and extended evolutionary game theory (EEGT) modeling. Sample experiment results with Genetic algorithms (GA) are presented to demonstrate the applications of these models. The proposed EC population dynamics approach also makes survival selection largely unnecessary or much simplified since the individuals are naturally selected (controlled) by the mathematical models for EC population dynamics.

The evolutionary development of plant-feeding insects and their nutritional endosymbionts.

PubMed

Skidmore, Isabel H; Hansen, Allison K

2017-12-01

Herbivorous insects have evolved diverse mechanisms enabling them to feed on plants with suboptimal nutrient availability. Low nutrient availability negatively impacts insect herbivore development and fitness. To overcome this obstacle numerous insect lineages have evolved intimate associations with nutritional endosymbionts. This is especially true for insects that specialize on nitrogen-poor substrates, as these insects are highly dependent on intracellular symbionts to provide nitrogen lacking in their insect host's diet. Emerging evidence in these systems suggest that the symbiont's and/or the insect's biosynthetic pathways are dynamically regulated throughout the insect's development to potentially cope with the insect's changing nutritional demands. In this review, we evaluate the evolutionary development of symbiotic insect cells (bacteriocytes) by comparing and contrasting genes and mechanisms involved in maintaining and regulating the nutritional symbiosis throughout insect development in a diversity of insect herbivore-endosymbiont associations. With new advances in genome sequencing and functional genomics, we evaluate to what extent nutritional symbioses are shaped by (i) the regulation of symbiont titer, (ii) the regulation of insect symbiosis genes, and (iii) the regulation of symbiont genes. We discuss how important these mechanisms are for the biosynthesis of essential amino acids and vitamins across insect life stages in divergent insect-symbiont systems. We conclude by suggesting future directions of research to further elucidate the evolutionary development of bacteriocytes and the impact of these nutritional symbioses on insect-plant interactions. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

NASA Astrophysics Data System (ADS)

Cucchi, T.; Mohaseb, A.; Peigné, S.; Debue, K.; Orlando, L.; Mashkour, M.

2017-04-01

The Plio-Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys.

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

PubMed Central

Mohaseb, A.; Peigné, S.; Debue, K.; Orlando, L.; Mashkour, M.

2017-01-01

The Plio–Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys. PMID:28484618

Selection on skewed characters and the paradox of stasis

PubMed Central

Bonamour, Suzanne; Teplitsky, Céline; Charmantier, Anne; Crochet, Pierre-André; Chevin, Luis-Miguel

2018-01-01

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modelling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold’s (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson-Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate samples size. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date – repeatedly described as more evolutionarily stable than expected –, so this skewness should be accounted for when investigating evolutionary dynamics in the wild. PMID:28921508

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

A key, yet often neglected, component of digital evolution and evolutionary models is the ‘selection method’ which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations’ average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics. PMID:24152811

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy.

PubMed

Bank, Claudia; Renzette, Nicholas; Liu, Ping; Matuszewski, Sebastian; Shim, Hyunjin; Foll, Matthieu; Bolon, Daniel N A; Zeldovich, Konstantin B; Kowalik, Timothy F; Finberg, Robert W; Wang, Jennifer P; Jensen, Jeffrey D

2016-11-01

The rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. Here, we evaluate a novel antiviral drug therapy, favipiravir, for which the mechanism of action in IAV involves an interaction with the viral RNA-dependent RNA polymerase resulting in an effective increase in the viral mutation rate. We used an experimental evolution framework, combined with novel population genetic method development for inference from time-sampled data, to evaluate the effectiveness of favipiravir against IAV. Evaluating whole genome polymorphism data across 15 time points under multiple drug concentrations and in controls, we present the first evidence for the ability of IAV populations to effectively adapt to low concentrations of favipiravir. In contrast, under high concentrations, we observe population extinction, indicative of mutational meltdown. We discuss the observed dynamics with respect to the evolutionary forces at play and emphasize the utility of evolutionary theory to inform drug development. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Persistent social isolation reflects identity and social context but not maternal effects or early environment.

PubMed

Brent, L J N; Ruiz-Lambides, A; Platt, M L

2017-12-19

Individuals who are well integrated into society have greater access to resources and tend to live longer. Why some individuals are socially isolated and others are not is therefore puzzling from an evolutionary perspective. Answering this question requires establishing the mix of intrinsic and contextual factors that contribute to social isolation. Using social network data spanning up to half of the median adult lifespan in a gregarious primate, we found that some measures of social isolation were modestly repeatable within individuals, consistent with a trait. By contrast, social isolation was not explained by the identity of an animal's mother or the group into which it was born. Nevertheless, age, sex and social status each played a role, as did kin dynamics and familiarity. Females with fewer close relatives were more isolated, and the more time males spent in a new group the less isolated they became, independent of their social status. These results show that social isolation results from a combination of intrinsic and environmental factors. From an evolutionary perspective, these findings suggest that social isolation could be adaptive in some contexts and partly maintained by selection.

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game

PubMed Central

Sasaki, Tatsuya; Okada, Isamu

2015-01-01

It is well known that in contrast to the Prisoner’s Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. PMID:25868940

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game.

PubMed

Sasaki, Tatsuya; Okada, Isamu

2015-05-01

It is well known that in contrast to the Prisoner's Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Natural selection. IV. The Price equation.

PubMed

Frank, S A

2012-06-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation's greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

PubMed

Wise, Michael J

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

Mean Protein Evolutionary Distance: A Method for Comparative Protein Evolution and Its Application

PubMed Central

Wise, Michael J.

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins’ roles. Different species’ proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz. PMID:23613826

Ornament size and colour as alternative strategies for effective communication in gliding lizards.

PubMed

Klomp, D A; Ord, T J; Das, I; Diesmos, A; Ahmad, N; Stuart-Fox, D

2016-09-01

Sexual ornamentation needs to be conspicuous to be effective in attracting potential mates and defending territories and indeed, a multitude of ways exists to achieve this. Two principal mechanisms for increasing conspicuousness are to increase the ornament's colour or brightness contrast against the background and to increase the size of the ornament. We assessed the relationship between the colour and size of the dewlap, a large extendible throat-fan, across a range of species of gliding lizards (Agamidae; genus Draco) from Malaysia and the Philippines. We found a negative relationship across species between colour contrast against the background and dewlap size in males, but not in females, suggesting that males of different species use increasing colour contrast and dewlap size as alternative strategies for effective communication. Male dewlap size also increases with increasing sexual size dimorphism, and dewlap colour and brightness contrast increase with increasing sexual dichromatism in colour and brightness, respectively, suggesting that sexual selection may act on both dewlap size and colour. We further found evidence that relative predation intensity, as measured from predator attacks on models placed in the field, may play a role in the choice of strategy (high chromatic contrast or large dewlap area) a species employs. More broadly, these results highlight that each component in a signal (such as colour or size) may be influenced by different selection pressures and that by assessing components individually, we can gain a greater understanding of the evolution of signal diversity. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Individual-based modeling of ecological and evolutionary processes

USGS Publications Warehouse

DeAngelis, Donald L.; Mooij, Wolf M.

2005-01-01

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

Incorporating evolutionary processes into population viability models.

PubMed

Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

2015-06-01

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

Landscape community genomics: understanding eco-evolutionary processes in complex environments

USGS Publications Warehouse

Hand, Brian K.; Lowe, Winsor H.; Kovach, Ryan P.; Muhlfeld, Clint C.; Luikart, Gordon

2015-01-01

Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

Towards a mechanistic foundation of evolutionary theory.

PubMed

Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

2017-02-15

Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

PubMed Central

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

PubMed Central

Fournier-Level, Alexandre; Perry, Emily O.; Wang, Jonathan A.; Braun, Peter T.; Migneault, Andrew; Cooper, Martha D.; Metcalf, C. Jessica E.; Schmitt, Johanna

2016-01-01

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation. PMID:27140640

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana.

PubMed

Fournier-Level, Alexandre; Perry, Emily O; Wang, Jonathan A; Braun, Peter T; Migneault, Andrew; Cooper, Martha D; Metcalf, C Jessica E; Schmitt, Johanna

2016-05-17

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.

Simple versus complex models of trait evolution and stasis as a response to environmental change

NASA Astrophysics Data System (ADS)

Hunt, Gene; Hopkins, Melanie J.; Lidgard, Scott

2015-04-01

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Characterization and evolutionary analysis of tributyltin-binding protein and pufferfish saxitoxin and tetrodotoxin-binding protein genes in toxic and nontoxic pufferfishes.

PubMed

Hashiguchi, Y; Lee, J M; Shiraishi, M; Komatsu, S; Miki, S; Shimasaki, Y; Mochioka, N; Kusakabe, T; Oshima, Y

2015-05-01

Understanding the evolutionary mechanisms of toxin accumulation in pufferfishes has been long-standing problem in toxicology and evolutionary biology. Pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) is involved in the transport and accumulation of tetrodotoxin and is one of the most intriguing proteins related to the toxicity of pufferfishes. PSTBPs are fusion proteins consisting of two tandem repeated tributyltin-binding protein type 2 (TBT-bp2) domains. In this study, we examined the evolutionary dynamics of TBT-bp2 and PSTBP genes to understand the evolution of toxin accumulation in pufferfishes. Database searches and/or PCR-based cDNA cloning in nine pufferfish species (6 toxic and 3 nontoxic) revealed that all species possessed one or more TBT-bp2 genes, but PSTBP genes were found only in 5 toxic species belonging to genus Takifugu. These toxic Takifugu species possessed two or three copies of PSTBP genes. Phylogenetic analysis of TBT-bp2 and PSTBP genes suggested that PSTBPs evolved in the common ancestor of Takifugu species by repeated duplications and fusions of TBT-bp2 genes. In addition, a detailed comparison of Takifugu TBT-bp2 and PSTBP gene sequences detected a signature of positive selection under the pressure of gene conversion. The complicated evolutionary dynamics of TBT-bp2 and PSTBP genes may reflect the diversity of toxicity in pufferfishes. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

In Vitro "Evolutionary Arms-Races" Between Hosts and Parasites in an Artificial RNA Replication System

NASA Astrophysics Data System (ADS)

Furubayashi, T.; Bansho, Y.; Motooka, D.; Nakamura, S.; Ichihashi, N.

2017-07-01

We performed coevolution of artificial RNA self-replicators and parasitic replicators in microdroplets. We observed evolutionary arms-races with oscillating population dynamics and faster evolution of self-replicators caused by parasitic replicators.

Stochastic dynamics and stable equilibrium of evolutionary optional public goods game in finite populations

NASA Astrophysics Data System (ADS)

Quan, Ji; Liu, Wei; Chu, Yuqing; Wang, Xianjia

2018-07-01

Continuous noise caused by mutation is widely present in evolutionary systems. Considering the noise effects and under the optional participation mechanism, a stochastic model for evolutionary public goods game in a finite size population is established. The evolutionary process of strategies in the population is described as a multidimensional ergodic and continuous time Markov process. The stochastic stable state of the system is analyzed by the limit distribution of the stochastic process. By numerical experiments, the influences of the fixed income coefficient for non-participants and the investment income coefficient of the public goods on the stochastic stable equilibrium of the system are analyzed. Through the numerical calculation results, we found that the optional participation mechanism can change the evolutionary dynamics and the equilibrium of the public goods game, and there is a range of parameters which can effectively promote the evolution of cooperation. Further, we obtain the accurate quantitative relationship between the parameters and the probabilities for the system to choose different stable equilibriums, which can be used to realize the control of cooperation.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions.

PubMed

Zenni, Rafael Dudeque; Dickie, Ian A; Wingfield, Michael J; Hirsch, Heidi; Crous, Casparus J; Meyerson, Laura A; Burgess, Treena I; Zimmermann, Thalita G; Klock, Metha M; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J

2016-12-30

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics, and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand, and manage biological invasions. Published by Oxford University Press on behalf of the Annals of Botany Company.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions

PubMed Central

Dickie, Ian A.; Wingfield, Michael J.; Hirsch, Heidi; Crous, Casparus J.; Meyerson, Laura A.; Burgess, Treena I.; Zimmermann, Thalita G.; Klock, Metha M.; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J.

2017-01-01

Abstract Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand and manage biological invasions. PMID:28039118

Extinction rates in tumour public goods games.

PubMed

Gerlee, Philip; Altrock, Philipp M

2017-09-01

Cancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumour cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here show that this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the time scales, in particular, in coevolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell-type-specific rates have to be accounted for explicitly. © 2017 The Authors.

Research traditions and evolutionary explanations in medicine.

PubMed

Méthot, Pierre-Olivier

2011-02-01

In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

PubMed

Feng, Jiangyan; Shukla, Diwakar

2018-01-25

Understanding of protein conformational dynamics is essential for elucidating molecular origins of protein structure-function relationship. Traditionally, reaction coordinates, i.e., some functions of protein atom positions and velocities have been used to interpret the complex dynamics of proteins obtained from experimental and computational approaches such as molecular dynamics simulations. However, it is nontrivial to identify the reaction coordinates a priori even for small proteins. Here, we evaluate the power of evolutionary couplings (ECs) to capture protein dynamics by exploring their use as reaction coordinates, which can efficiently guide the sampling of a conformational free energy landscape. We have analyzed 10 diverse proteins and shown that a few ECs are sufficient to characterize complex conformational dynamics of proteins involved in folding and conformational change processes. With the rapid strides in sequencing technology, we expect that ECs could help identify reaction coordinates a priori and enhance the sampling of the slow dynamical process associated with protein folding and conformational change.

Origin and Evolution of the Kiwifruit Canker Pandemic

PubMed Central

Li, Li; Liu, Yifei; Li, Dawei; Pan, Hui; Zhong, Caihong; Rikkerink, Erik H.A.; Templeton, Matthew D.; Straub, Christina; Colombi, Elena

2017-01-01

Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose. PMID:28369338

Spatial competition and price formation

NASA Astrophysics Data System (ADS)

Nagel, Kai; Shubik, Martin; Paczuski, Maya; Bak, Per

2000-12-01

We look at price formation in a retail setting, that is, companies set prices, and consumers either accept prices or go someplace else. In contrast to most other models in this context, we use a two-dimensional spatial structure for information transmission, that is, consumers can only learn from nearest neighbors. Many aspects of this can be understood in terms of generalized evolutionary dynamics. In consequence, we first look at spatial competition and cluster formation without price. This leads to establishement size distributions, which we compare to reality. After some theoretical considerations, which at least heuristically explain our simulation results, we finally return to price formation, where we demonstrate that our simple model with nearly no organized planning or rationality on the part of any of the agents indeed leads to an economically plausible price.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

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

EPA Science Inventory

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

Incorporating Eco-Evolutionary Processes into Population Models:Design and Applications

EPA Science Inventory

Eco-evolutionary population models are powerful new tools for exploring howevolutionary processes influence plant and animal population dynamics andvice-versa. The need to manage for climate change and other dynamicdisturbance regimes is creating a demand for the incorporation of...

NexGen PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

EPA Science Inventory

We examine how the integration of evolutionary and ecological processes in population dynamics – an emerging framework in ecology – could be incorporated into population viability analysis (PVA). Driven by parallel, complementary advances in population genomics and computational ...

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Evolutionary Games with Randomly Changing Payoff Matrices

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun

2015-06-01

Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.

Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history.

PubMed

Coulson, Tim; MacNulty, Daniel R; Stahler, Daniel R; vonHoldt, Bridgett; Wayne, Robert K; Smith, Douglas W

2011-12-02

Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected to generate eco-evolutionary change, that changes in the average environment will affect wolves to a greater extent than changes in how variable it is, and that accurate prediction of the consequences of environmental change will probably prove elusive.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses.

PubMed

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-11-26

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model.

PubMed

Martins, José; Pinto, Alberto

2017-04-01

We use the reinfection SIRI epidemiological model to analyze the impact of education programs and vaccine scares on individuals decisions to vaccinate or not. The presence of the reinfection provokes the novelty of the existence of three Nash equilibria for the same level of the morbidity relative risk instead of a single Nash equilibrium as occurs in the SIR model studied by Bauch and Earn (PNAS 101:13391-13394, 2004). The existence of three Nash equilibria, with two of them being evolutionary stable, introduces two scenarios with relevant and opposite features for the same level of the morbidity relative risk: the low-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a low probability; and the high-vaccination scenario corresponding to the evolutionary stable vaccination strategy, where individuals will vaccinate with a high probability. We introduce the evolutionary vaccination dynamics for the SIRI model and we prove that it is bistable. The bistability of the evolutionary dynamics indicates that the damage provoked by false scares on the vaccination perceived morbidity risks can be much higher and much more persistent than in the SIR model. Furthermore, the vaccination education programs to be efficient they need to implement a mechanism to suddenly increase the vaccination coverage level.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

PubMed Central

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-01-01

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics. PMID:27898037

Why the null matters: statistical tests, random walks and evolution.

PubMed

Sheets, H D; Mitchell, C E

2001-01-01

A number of statistical tests have been developed to determine what type of dynamics underlie observed changes in morphology in evolutionary time series, based on the pattern of change within the time series. The theory of the 'scaled maximum', the 'log-rate-interval' (LRI) method, and the Hurst exponent all operate on the same principle of comparing the maximum change, or rate of change, in the observed dataset to the maximum change expected of a random walk. Less change in a dataset than expected of a random walk has been interpreted as indicating stabilizing selection, while more change implies directional selection. The 'runs test' in contrast, operates on the sequencing of steps, rather than on excursion. Applications of these tests to computer generated, simulated time series of known dynamical form and various levels of additive noise indicate that there is a fundamental asymmetry in the rate of type II errors of the tests based on excursion: they are all highly sensitive to noise in models of directional selection that result in a linear trend within a time series, but are largely noise immune in the case of a simple model of stabilizing selection. Additionally, the LRI method has a lower sensitivity than originally claimed, due to the large range of LRI rates produced by random walks. Examination of the published results of these tests show that they have seldom produced a conclusion that an observed evolutionary time series was due to directional selection, a result which needs closer examination in light of the asymmetric response of these tests.

Genomics of Adaptation Depends on the Rate of Environmental Change in Experimental Yeast Populations.

PubMed

Gorter, Florien A; Derks, Martijn F L; van den Heuvel, Joost; Aarts, Mark G M; Zwaan, Bas J; de Ridder, Dick; de Visser, J Arjan G M

2017-10-01

The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae populations for 500 generations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium, nickel, and zinc. Here, we investigate how each of these treatments affected genomic evolution. Whole-genome sequencing of evolved clones revealed that adaptation occurred via a combination of SNPs, small indels, and whole-genome duplications and other large-scale structural changes. In contrast to some theoretical predictions, gradual and abrupt environmental change caused similar numbers of genomic changes. For cadmium, which is toxic already at comparatively low concentrations, mutations in the same genes were used for adaptation to both gradual and abrupt increase in concentration. Conversely, for nickel and zinc, which are toxic at high concentrations only, mutations in different genes were used for adaptation depending on the rate of change. Moreover, evolution was more repeatable following a sudden change in the environment, particularly for nickel and zinc. Our results show that the rate of environmental change and the nature of the selection pressure are important drivers of evolutionary dynamics and outcomes, which has implications for a better understanding of societal problems such as climate change and pollution. © 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.

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

A Systematic Bayesian Integration of Epidemiological and Genetic Data

PubMed Central

Lau, Max S. Y.; Marion, Glenn; Streftaris, George; Gibson, Gavin

2015-01-01

Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process. PMID:26599399

Informations in Models of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Rivoire, Olivier

2016-03-01

Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.

Evolutionary Game Theory in Growing Populations

NASA Astrophysics Data System (ADS)

Melbinger, Anna; Cremer, Jonas; Frey, Erwin

2010-10-01

Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We present here a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show that genuinely stochastic events can ease the dilemma by leading to a transient but robust increase in cooperation.

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

PubMed

O'Malley, Maureen A

2018-06-01

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates.

PubMed

Murrell, Ben; Vollbrecht, Thomas; Guatelli, John; Wertheim, Joel O

2016-09-15

Molecular evolutionary arms races between viruses and their hosts are important drivers of adaptation. These Red Queen dynamics have been frequently observed in primate retroviruses and their antagonists, host restriction factor genes, such as APOBEC3F/G, TRIM5-α, SAMHD1, and BST-2. Host restriction factors have experienced some of the most intense and pervasive adaptive evolution documented in primates. Recently, two novel host factors, SERINC3 and SERINC5, were identified as the targets of HIV-1 Nef, a protein crucial for the optimal infectivity of virus particles. Here, we compared the evolutionary fingerprints of SERINC3 and SERINC5 to those of other primate restriction factors and to a set of other genes with diverse functions. SERINC genes evolved in a manner distinct from the canonical arms race dynamics seen in the other restriction factors. Despite their antiviral activity against HIV-1 and other retroviruses, SERINC3 and SERINC5 have a relatively uneventful evolutionary history in primates. Restriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominate the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes, SERINC3 and SERINC5, were recently identified as targets of an HIV-1 accessory protein important for viral infectivity. Unexpectedly, we found that these SERINC genes, unlike other host restriction factor genes, show no evidence of a recent evolutionary arms race with viral pathogens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Howling about Trophic Cascades

ERIC Educational Resources Information Center

Kowalewski, David

2012-01-01

Following evolutionary theory and an agriculture model, ecosystem research has stressed bottom-up dynamics, implying that top wild predators are epiphenomenal effects of more basic causes. As such, they are assumed expendable. A more modern co-evolutionary and wilderness approach--trophic cascades--instead suggests that top predators, whose…

Kramers problem in evolutionary strategies

NASA Astrophysics Data System (ADS)

Dunkel, J.; Ebeling, W.; Schimansky-Geier, L.; Hänggi, P.

2003-06-01

We calculate the escape rates of different dynamical processes for the case of a one-dimensional symmetric double-well potential. In particular, we compare the escape rates of a Smoluchowski process, i.e., a corresponding overdamped Brownian motion dynamics in a metastable potential landscape, with the escape rates obtained for a biologically motivated model known as the Fisher-Eigen process. The main difference between the two models is that the dynamics of the Smoluchowski process is determined by local quantities, whereas the Fisher-Eigen process is based on a global coupling (nonlocal interaction). If considered in the context of numerical optimization algorithms, both processes can be interpreted as archetypes of physically or biologically inspired evolutionary strategies. In this sense, the results discussed in this work are utile in order to evaluate the efficiency of such strategies with regard to the problem of surmounting various barriers. We find that a combination of both scenarios, starting with the Fisher-Eigen strategy, provides a most effective evolutionary strategy.

Dynamics of dental evolution in ornithopod dinosaurs.

PubMed

Strickson, Edward; Prieto-Márquez, Albert; Benton, Michael J; Stubbs, Thomas L

2016-07-14

Ornithopods were key herbivorous dinosaurs in Mesozoic terrestrial ecosystems, with a variety of tooth morphologies. Several clades, especially the 'duck-billed' hadrosaurids, became hugely diverse and abundant almost worldwide. Yet their evolutionary dynamics have been disputed, particularly whether they diversified in response to events in plant evolution. Here we focus on their remarkable dietary adaptations, using tooth and jaw characters to examine changes in dental disparity and evolutionary rate. Ornithopods explored different areas of dental morphospace throughout their evolution, showing a long-term expansion. There were four major evolutionary rate increases, the first among basal iguanodontians in the Middle-Late Jurassic, and the three others among the Hadrosauridae, above and below the split of their two major clades, in the middle of the Late Cretaceous. These evolutionary bursts do not correspond to times of plant diversification, including the radiation of the flowering plants, and suggest that dental innovation rather than coevolution with major plant clades was a major driver in ornithopod evolution.

Stationary stability for evolutionary dynamics in finite populations

DOE PAGES

Harper, Marc; Fryer, Dashiell

2016-08-25

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISSmore » candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.« less

Effect of the spatial autocorrelation of empty sites on the evolution of cooperation

NASA Astrophysics Data System (ADS)

Zhang, Hui; Wang, Li; Hou, Dongshuang

2016-02-01

An evolutionary game model is constructed to investigate the spatial autocorrelation of empty sites on the evolution of cooperation. Each individual is assumed to imitate the strategy of the one who scores the highest in its neighborhood including itself. Simulation results illustrate that the evolutionary dynamics based on the Prisoner's Dilemma game (PD) depends severely on the initial conditions, while the Snowdrift game (SD) is hardly affected by that. A high degree of autocorrelation of empty sites is beneficial for the evolution of cooperation in the PD, whereas it shows diversification effects depending on the parameter of temptation to defect in the SD. Moreover, for the repeated game with three strategies, 'always defect' (ALLD), 'tit-for-tat' (TFT), and 'always cooperate' (ALLC), simulations reveal that an amazing evolutionary diversity appears for varying of parameters of the temptation to defect and the probability of playing in the next round of the game. The spatial autocorrelation of empty sites can have profound effects on evolutionary dynamics (equilibrium and oscillation) and spatial distribution.

Dynamics of dental evolution in ornithopod dinosaurs

NASA Astrophysics Data System (ADS)

Strickson, Edward; Prieto-Márquez, Albert; Benton, Michael J.; Stubbs, Thomas L.

2016-07-01

Ornithopods were key herbivorous dinosaurs in Mesozoic terrestrial ecosystems, with a variety of tooth morphologies. Several clades, especially the ‘duck-billed’ hadrosaurids, became hugely diverse and abundant almost worldwide. Yet their evolutionary dynamics have been disputed, particularly whether they diversified in response to events in plant evolution. Here we focus on their remarkable dietary adaptations, using tooth and jaw characters to examine changes in dental disparity and evolutionary rate. Ornithopods explored different areas of dental morphospace throughout their evolution, showing a long-term expansion. There were four major evolutionary rate increases, the first among basal iguanodontians in the Middle-Late Jurassic, and the three others among the Hadrosauridae, above and below the split of their two major clades, in the middle of the Late Cretaceous. These evolutionary bursts do not correspond to times of plant diversification, including the radiation of the flowering plants, and suggest that dental innovation rather than coevolution with major plant clades was a major driver in ornithopod evolution.

Consumer co-evolution as an important component of the eco-evolutionary feedback.

PubMed

Hiltunen, Teppo; Becks, Lutz

2014-10-22

Rapid evolution in ecologically relevant traits has recently been recognized to significantly alter the interaction between consumers and their resources, a key interaction in all ecological communities. While these eco-evolutionary dynamics have been shown to occur when prey populations are evolving, little is known about the role of predator evolution and co-evolution between predator and prey in this context. Here, we investigate the role of consumer co-evolution for eco-evolutionary feedback in bacteria-ciliate microcosm experiments by manipulating the initial trait variation in the predator populations. With co-evolved predators, prey evolve anti-predatory defences faster, trait values are more variable, and predator and prey population sizes are larger at the end of the experiment compared with the non-co-evolved predators. Most importantly, differences in predator traits results in a shift from evolution driving ecology, to ecology driving evolution. Thus we demonstrate that predator co-evolution has important effects on eco-evolutionary dynamics.

OF TRYPANOSOMATIDS. ENDOTRANSFORMATIONS AND ABERRATIONS].

PubMed

Frolov, A O; Malysheva, M N; Kostygov, A Yu

2016-01-01

Endotransformations and aberrations of the life cycle in the evolutionary history of trypanosomatids (Kinetoplastea: Trypanosomatidae) are analyzed. We treat the term "endotransformations" as evolutionarily fixed changes of phases and/or developmental stages of parasites. By contrast, we treat aberrations as evolutionary unstable, periodically arising deformations of developmental phases of trypanosomatids, never leading to life cycle changes. Various examples of life cycle endotransformations and aberrations in representatives of the family Trypanosomatidae are discussed.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

Evolution of an ancient venom: recognition of a novel family of cnidarian toxins and the common evolutionary origin of sodium and potassium neurotoxins in sea anemone.

PubMed

Jouiaei, Mahdokht; Sunagar, Kartik; Federman Gross, Aya; Scheib, Holger; Alewood, Paul F; Moran, Yehu; Fry, Bryan G

2015-06-01

Despite Cnidaria (sea anemones, corals, jellyfish, and hydroids) being the oldest venomous animal lineage, structure-function relationships, phyletic distributions, and the molecular evolutionary regimes of toxins encoded by these intriguing animals are poorly understood. Hence, we have comprehensively elucidated the phylogenetic and molecular evolutionary histories of pharmacologically characterized cnidarian toxin families, including peptide neurotoxins (voltage-gated Na(+) and K(+) channel-targeting toxins: NaTxs and KTxs, respectively), pore-forming toxins (actinoporins, aerolysin-related toxins, and jellyfish toxins), and the newly discovered small cysteine-rich peptides (SCRiPs). We show that despite long evolutionary histories, most cnidarian toxins remain conserved under the strong influence of negative selection-a finding that is in striking contrast to the rapid evolution of toxin families in evolutionarily younger lineages, such as cone snails and advanced snakes. In contrast to the previous suggestions that implicated SCRiPs in the biomineralization process in corals, we demonstrate that they are potent neurotoxins that are likely involved in the envenoming function, and thus represent the first family of neurotoxins from corals. We also demonstrate the common evolutionary origin of type III KTxs and NaTxs in sea anemones. We show that type III KTxs have evolved from NaTxs under the regime of positive selection, and likely represent a unique evolutionary innovation of the Actinioidea lineage. We report a correlation between the accumulation of episodically adaptive sites and the emergence of novel pharmacological activities in this rapidly evolving neurotoxic clade. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Divergent and convergent evolution in metastases suggest treatment strategies based on specific metastatic sites

PubMed Central

Cunningham, Jessica J.; Brown, Joel S.; Vincent, Thomas L.

2015-01-01

Background and objective: Systemic therapy for metastatic cancer is currently determined exclusively by the site of tumor origin. Yet, there is increasing evidence that the molecular characteristics of metastases significantly differ from the primary tumor. We define the evolutionary dynamics of metastases that govern this molecular divergence and examine their potential contribution to variations in response to targeted therapies. Methodology: Darwinian interactions of transformed cells with the tissue microenvironments at primary and metastatic sites are analyzed using evolutionary game theory. Computational models simulate responses to targeted therapies in different organs within the same patient. Results: Tumor cells, although maximally fit at their primary site, typically have lower fitness on the adaptive landscapes offered by the metastatic sites due to organ-specific variations in mesenchymal properties and signaling pathways. Clinically evident metastases usually exhibit time-dependent divergence from the phenotypic mean of the primary population as the tumor cells evolve and adapt to their new circumstances. In contrast, tumors from different primary sites evolving on identical metastatic adaptive landscapes exhibit phenotypic convergence. Thus, metastases in the liver from different primary tumors and even in different hosts will evolve toward similar adaptive phenotypes. The combination of evolutionary divergence from the primary cancer phenotype and convergence towards similar adaptive strategies in the same tissue cause significant variations in treatment responses particularly for highly targeted therapies. Conclusion and implications: The results suggest that optimal therapies for disseminated cancer must take into account the site(s) of metastatic growth as well as the primary organ. PMID:25794501

Introduction to the special issue: Tree invasions: towards a better understanding of their complex evolutionary dynamics.

PubMed

Hirsch, Heidi; Richardson, David M; Le Roux, Johannes J

2017-05-01

Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees. The main outcome of this workshop is this Special Issue of AoB PLANTS . The collection of papers in this issue has helped to identify and assess the evolutionary mechanisms that are likely to influence tree invasions. It also facilitated expansion of the unified framework for biological invasions to incorporate key evolutionary processes. The papers cover a wide range of evolutionary mechanisms in tree genomes (adaptation), epigenomes (phenotypic plasticity) and their second genomes (mutualists), and show how such mechanisms can impact tree invasion processes and management. The special issue provides a comprehensive overview of the factors that promote and mitigate the invasive success of tree species in many parts of the world. It also shows that incorporating evolutionary concepts is crucial for understanding the complex drivers of tree invasions and has much potential to improve management. The contributions of the special issue also highlight many priorities for further work in the face of ever-increasing tree invasions; the complexity of this research needs calls for expanded interdisciplinary research collaborations.

How much can history constrain adaptive evolution? A real-time evolutionary approach of inversion polymorphisms in Drosophila subobscura.

PubMed

Fragata, I; Lopes-Cunha, M; Bárbaro, M; Kellen, B; Lima, M; Santos, M A; Faria, G S; Santos, M; Matos, M; Simões, P

2014-12-01

Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Dynamic and scalable audio classification by collective network of binary classifiers framework: an evolutionary approach.

PubMed

Kiranyaz, Serkan; Mäkinen, Toni; Gabbouj, Moncef

2012-10-01

In this paper, we propose a novel framework based on a collective network of evolutionary binary classifiers (CNBC) to address the problems of feature and class scalability. The main goal of the proposed framework is to achieve a high classification performance over dynamic audio and video repositories. The proposed framework adopts a "Divide and Conquer" approach in which an individual network of binary classifiers (NBC) is allocated to discriminate each audio class. An evolutionary search is applied to find the best binary classifier in each NBC with respect to a given criterion. Through the incremental evolution sessions, the CNBC framework can dynamically adapt to each new incoming class or feature set without resorting to a full-scale re-training or re-configuration. Therefore, the CNBC framework is particularly designed for dynamically varying databases where no conventional static classifiers can adapt to such changes. In short, it is entirely a novel topology, an unprecedented approach for dynamic, content/data adaptive and scalable audio classification. A large set of audio features can be effectively used in the framework, where the CNBCs make appropriate selections and combinations so as to achieve the highest discrimination among individual audio classes. Experiments demonstrate a high classification accuracy (above 90%) and efficiency of the proposed framework over large and dynamic audio databases. Copyright © 2012 Elsevier Ltd. All rights reserved.

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India.

PubMed

Lewnard, Joseph A; Townsend, Jeffrey P

2016-12-20

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference.

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India

PubMed Central

Lewnard, Joseph A.

2016-01-01

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference. PMID:27791071

Hybrid zone formation and contrasting outcomes of secondary contact over transects in common toads.

PubMed

Arntzen, Jan W; de Vries, Wouter; Canestrelli, Daniele; Martínez-Solano, Iñigo

2017-10-01

Much progress in speciation research stems from documenting patterns of morphological and genetic variation in hybrid zones. Contrasting patterns of marker introgression in different sections of the contact can provide valuable insights on the relative importance of various evolutionary mechanisms maintaining species differences in the face of hybridization and gene flow and on hybrid zone temporal and spatial dynamics. We studied species interactions in the common toads Bufo bufo and B. spinosus in France and northwestern Italy using morphological and molecular data from the mitochondrial and nuclear genomes in an extensive survey, including two independent transects west and east of the Alps. At both, we found sharp, coincident and concordant nuclear genetic transitions. However, morphological clines were wider or absent and mtDNA introgression was asymmetric. We discuss alternative, nonexclusive hypotheses about evolutionary processes generating these patterns, including drift, selection, long-distance dispersal and spatial shifts in hybrid zone location and structure. The distribution of intraspecific mtDNA lineages supports a scenario in which B. bufo held a local refugium during the last glacial maximum. Present-day genetic profiles are best explained by an advance of B. spinosus from a nearby Iberian refugium, largely superseding the local B. bufo population, followed by an advance of B. bufo from the Balkans, with prongs north and south of the Alps, driving B. spinosus southwards. A pendulum moving hybrid zone, first northwards and then southwards, explains the wide areas of introgression at either side of the current position of the contact zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Adaptive dynamics on an environmental gradient that changes over a geological time-scale.

PubMed

Fortelius, Mikael; Geritz, Stefan; Gyllenberg, Mats; Toivonen, Jaakko

2015-07-07

The standard adaptive dynamics framework assumes two timescales, i.e. fast population dynamics and slow evolutionary dynamics. We further assume a third timescale, which is even slower than the evolutionary timescale. We call this the geological timescale and we assume that slow climatic change occurs within this timescale. We study the evolution of our model population over this very slow geological timescale with bifurcation plots of the standard adaptive dynamics framework. The bifurcation parameter being varied describes the abiotic environment that changes over the geological timescale. We construct evolutionary trees over the geological timescale and observe both gradual phenotypic evolution and punctuated branching events. We concur with the established notion that branching of a monomorphic population on an environmental gradient only happens when the gradient is not too shallow and not too steep. However, we show that evolution within the habitat can produce polymorphic populations that inhabit steep gradients. What is necessary is that the environmental gradient at some point in time is such that the initial branching of the monomorphic population can occur. We also find that phenotypes adapted to environments in the middle of the existing environmental range are more likely to branch than phenotypes adapted to extreme environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

PubMed

Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

2016-05-01

Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

PubMed Central

Solé, Ricard V; Montoya, José M; Erwin, Douglas H

2002-01-01

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems. PMID:12079530

Emergence and dynamics of self-producing information niches as a step towards pre-evolutionary organization

PubMed Central

Carter, Richard J.; Wiesner, Karoline

2018-01-01

As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches. In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions. By determining the information required to generate each niche, we show that niche transitions are only allowed if accompanied by an equal or increased level of information production that arises internally or via environmental perturbations that serve as an exogenous source of population diversification. Overall, our simulations show how proto-autopoietic networks of basic information processors form and compete, and under what conditions they persist over time or go extinct. These findings may be relevant to understanding how inanimate systems such as chemically communicating protocells can initiate the transition to living matter prior to the onset of contemporary evolutionary and genetic mechanisms. PMID:29343630

The σ law of evolutionary dynamics in community-structured population.

PubMed

Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

2012-08-07

Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

Hybrid zone studies: An interdisciplinary approach for the analysis of evolutionary processes

USGS Publications Warehouse

Scribner, Kim T.

1994-01-01

There has been considerable debate in the ecological and evolutionary literature over the relative importance and rate by which microevolutionary processes operating at the population level result in separation and differentiation of lineages and populations, and ultimately in speciation. Our understanding of evolutionary processes have need greatly enhances through the study of hybridization and hybrid zones. Indeed, hybrid zones have been described as “natural laboratories” (Barton, N. H., and G .M. Hewitt, 189. Adaptation, speciation, and hybrid zones. Nature 341:497-503) or as “windows on the evolutionary processes” (Harrison, R. G. 1990. Hybrid zones: windows on the evolutionary process. Oxford Surveys in Evolutionary Biology 7:69-128). Hybrid zones greatly facilitate analyses of evolutionary dynamics because differences in factors such as mating preference, fertility, and viability are likely to be magnified, making the consequences easier to document over short periods of time.

Comparison of multiobjective evolutionary algorithms: empirical results.

PubMed

Zitzler, E; Deb, K; Thiele, L

2000-01-01

In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly in converging to the Pareto-optimal front (e.g., multimodality and deception). By investigating these different problem features separately, it is possible to predict the kind of problems to which a certain technique is or is not well suited. However, in contrast to what was suspected beforehand, the experimental results indicate a hierarchy of the algorithms under consideration. Furthermore, the emerging effects are evidence that the suggested test functions provide sufficient complexity to compare multiobjective optimizers. Finally, elitism is shown to be an important factor for improving evolutionary multiobjective search.

Host–parasite fluctuating selection in the absence of specificity

PubMed Central

Ashby, Ben; White, Andy; Bowers, Roger; Buckling, Angus; Koskella, Britt

2017-01-01

Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time, to our knowledge, that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection. PMID:29093222

Genetic drift and selection in many-allele range expansions.

PubMed

Weinstein, Bryan T; Lavrentovich, Maxim O; Möbius, Wolfram; Murray, Andrew W; Nelson, David R

2017-12-01

We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony's curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.

Public goods games in populations with fluctuating size.

PubMed

McAvoy, Alex; Fraiman, Nicolas; Hauert, Christoph; Wakeley, John; Nowak, Martin A

2018-05-01

Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is possible that the entire population becomes extinct. Survival of the population may depend on which strategy prevails in the game dynamics. Studying cooperative dilemmas, it is a natural feature of such a model that cooperators enable survival, while defectors drive extinction. Although defectors are favored for any mixed population, random drift could lead to their elimination and the resulting pure-cooperator population could survive. On the other hand, if the defectors remain, then the population will quickly go extinct because the frequency of cooperators steadily declines and defectors alone cannot survive. In a mutation-selection model, we find that (i) a steady supply of cooperators can enable long-term population survival, provided selection is sufficiently strong, and (ii) selection can increase the abundance of cooperators but reduce their relative frequency. Thus, evolutionary game dynamics in populations with variable size generate a multifaceted notion of what constitutes a trait's long-term success. Copyright © 2018 Elsevier Inc. All rights reserved.

Selection on skewed characters and the paradox of stasis.

PubMed

Bonamour, Suzanne; Teplitsky, Céline; Charmantier, Anne; Crochet, Pierre-André; Chevin, Luis-Miguel

2017-11-01

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modeling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold's (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson-Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate sample sizes. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date - repeatedly described as more evolutionarily stable than expected - so this skewness should be accounted for when investigating evolutionary dynamics in the wild. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Inbreeding depression in an insect with maternal care: influences of family interactions, life stage and offspring sex.

PubMed

Meunier, J; Kölliker, M

2013-10-01

Although inbreeding is commonly known to depress individual fitness, the severity of inbreeding depression varies considerably across species. Among the factors contributing to this variation, family interactions, life stage and sex of offspring have been proposed, but their joint influence on inbreeding depression remains poorly understood. Here, we demonstrate that these three factors jointly shape inbreeding depression in the European earwig, Forficula auricularia. Using a series of cross-breeding, split-clutch and brood size manipulation experiments conducted over two generations, we first showed that sib mating (leading to inbred offspring) did not influence the reproductive success of earwig parents. Second, the presence of tending mothers and the strength of sibling competition (i.e. brood size) did not influence the expression of inbreeding depression in the inbred offspring. By contrast, our results revealed that inbreeding dramatically depressed the reproductive success of inbred adult male offspring, but only had little effect on the reproductive success of inbred adult female offspring. Overall, this study demonstrates limited effects of family interactions on inbreeding depression in this species and emphasizes the importance of disentangling effects of sib mating early and late during development to better understand the evolution of mating systems and population dynamics. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

The contrasting phylodynamics of human influenza B viruses.

PubMed

Vijaykrishna, Dhanasekaran; Holmes, Edward C; Joseph, Udayan; Fourment, Mathieu; Su, Yvonne C F; Halpin, Rebecca; Lee, Raphael T C; Deng, Yi-Mo; Gunalan, Vithiagaran; Lin, Xudong; Stockwell, Timothy B; Fedorova, Nadia B; Zhou, Bin; Spirason, Natalie; Kühnert, Denise; Bošková, Veronika; Stadler, Tanja; Costa, Anna-Maria; Dwyer, Dominic E; Huang, Q Sue; Jennings, Lance C; Rawlinson, William; Sullivan, Sheena G; Hurt, Aeron C; Maurer-Stroh, Sebastian; Wentworth, David E; Smith, Gavin J D; Barr, Ian G

2015-01-16

A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.

Multiple tolerances dilute the second order cooperative dilemma

NASA Astrophysics Data System (ADS)

Sui, Xiukai; Wu, Bin; Wang, Long

2017-12-01

A peer punisher directly imposes fines upon defectors at a cost to himself. It is one of the mechanisms promoting cooperation, which is ubiquitous in nature. Typically, it is assumed that a peer punisher punishes provided that there is one defector in the group. The threshold that triggers punishment, however, is not necessarily one. The larger the threshold is, the more tolerant the peer punisher is. We study the evolutionary dynamics of those diverse tolerant peer punishment strategies in public goods game. We find that, i) less tolerant punishers prevail over tolerant ones; ii) large group size could enhance punishment, in contrast with the case in the first-order cooperative dilemma. Our analytical results are based on weak selection limit and large population size, which are verified by simulations. Our work sheds light on how punishment of diverse tolerance evolves.

Modes of Brachiopod Body Size Evolution throughout the Phanerozoic Eon

NASA Astrophysics Data System (ADS)

Zhang, Z.; Payne, J.

2012-12-01

Body size correlates with numerous physiological and behavioral traits and is therefore one of the most important influences on the survival prospects of individuals and species. Patterns of body size evolution across taxa can therefore complement taxonomic diversity and geochemical proxy data in quantifying controls on long-term trends in the history of life. In contrast to widely available and synoptic taxonomic diversity data for fossil animal families and genera, however, no comprehensive size dataset exists, even for a single fossil animal phylum. For this study, we compiled a comprehensive, genus-level dataset of body sizes spanning the entire Phanerozoic for the phylum Brachiopoda. We use this dataset to examine statistical support for several possible modes of size evolution, in addition to environmental covariates: CO2, O2, and sea level. Brachiopod body size in the Phanerozoic followed two evolutionary modes: directional trend in the Early Paleozoic (Cambrian - Mississippian), and unbiased random walk from the Mississippian to the modern. We find no convincing correlation between trends in any single environmental parameter and brachiopod body size over time. The Paleozoic size increase follows Cope's Rule, and has been documented in many other marine invertebrates, while the Mesozoic size plateau has not been. This interval of size stability correlates with increased competition for resources from bivalves beginning during the Mesozoic Marine Revolution, and may be causally linked. The Late Mesozoic decline in size is an artifact of the improved sampling of smaller genera, many of which are less abundant than their Paleozoic ancestors. The Cenozoic brachiopod dataset is similarly incomplete. Biodiversity is decoupled from size dynamics even within the Paleozoic when brachiopods are on average becoming larger and more abundant, suggesting the presence of different controls. Our findings reveal that the dynamics of body size evolution changed over time in brachiopods, indicating that no single, simple model is likely to capture the true complexity of their evolutionary dynamics.

On the need for widespread horizontal gene transfers under genome size constraint.

PubMed

Isambert, Hervé; Stein, Richard R

2009-08-25

While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes. This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.

Automated design of spacecraft systems power subsystems

NASA Technical Reports Server (NTRS)

Terrile, Richard J.; Kordon, Mark; Mandutianu, Dan; Salcedo, Jose; Wood, Eric; Hashemi, Mona

2006-01-01

This paper discusses the application of evolutionary computing to a dynamic space vehicle power subsystem resource and performance simulation in a parallel processing environment. Our objective is to demonstrate the feasibility, application and advantage of using evolutionary computation techniques for the early design search and optimization of space systems.

A Coevolutionary Arms Race: Understanding Plant-Herbivore Interactions

ERIC Educational Resources Information Center

Becklin, Katie M.

2008-01-01

Plants and insects share a long evolutionary history characterized by relationships that affect individual, population, and community dynamics. Plant-herbivore interactions are a prominent feature of this evolutionary history; it is by plant-herbivore interactions that energy is transferred from primary producers to the rest of the food web. Not…

Relevance of East African Drill Cores to Human Evolution: the Case of the Olorgesailie Drilling Project

NASA Astrophysics Data System (ADS)

Potts, R.

2016-12-01

Drill cores reaching the local basement of the East African Rift were obtained in 2012 south of the Olorgesailie Basin, Kenya, 20 km from excavations that document key benchmarks in the origin of Homo sapiens. Sediments totaling 216 m were obtained from two drilling locations representing the past 1 million years. The cores were acquired to build a detailed environmental record spatially associated with the transition from Acheulean to Middle Stone Age technology and extensive turnover in mammalian species. The project seeks precise tests of how climate dynamics and tectonic events were linked with these transitions. Core lithology (A.K. Behrensmeyer), geochronology (A. Deino), diatoms (R.B. Owen), phytoliths (R. Kinyanjui), geochemistry (N. Rabideaux, D. Deocampo), among other indicators, show evidence of strong environmental variability in agreement with predicted high-eccentricity modulation of climate during the evolutionary transitions. Increase in hominin mobility, elaboration of symbolic behavior, and concurrent turnover in mammalian species indicating heightened adaptability to unpredictable ecosystems, point to a direct link between the evolutionary transitions and the landscape dynamics reflected in the Olorgesailie drill cores. For paleoanthropologists and Earth scientists, any link between evolutionary transitions and environmental dynamics requires robust evolutionary datasets pertinent to how selection, extinction, population divergence, and other evolutionary processes were impacted by the dynamics uncovered in drill core studies. Fossil and archeological data offer a rich source of data and of robust environment-evolution explanations that must be integrated into efforts by Earth scientists who seek to examine high-resolution climate records of human evolution. Paleoanthropological examples will illustrate the opportunities that exist for connecting evolutionary benchmarks to the data obtained from drilled African muds. Project members: R. Potts, A.K. Behrensmeyer, E. Beverly, K. Brady, J. Bright, E. Brown, J. Clark, A. Cohen, A. Deino, P. deMenocal, D. Deocampo, R. Dommain, J.T. Faith, J. King, R. Kinyanjui, N. Levin, J. Moerman, V. Muiruri, A. Noren, R.B. Owen, N. Rabideaux, R. Renaut, S. Rucina, J. Russell, J. Scott, M. Stockhecke, K. Uno

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents.

PubMed

Gilbert, Scott F; Bosch, Thomas C G; Ledón-Rettig, Cristina

2015-10-01

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

Contrasting evolutionary patterns in two reef-corals and their possible relationship to life history traits

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

Foster, A.B.

1985-01-01

Multivariate statistical analyses have been used to redefine species within two genera of reef-corals (Porites and Montastraea) and to trace their evolutionary patterns through a continuous sequence from late Miocene to early Pliocene time. The material studied consists of populations sampled at regular intervals through four stratigraphic sections in the northern Dominican Republic. The results show that species in the first genus (Porites) have relatively short durations, morphologic stability, and narrow spatial distributions. Their overall evolutionary history is characterized by short periods of radiation and widespread extinction, separated by longer periods of stasis. In contrast, species in the second genusmore » (Montastraea) exhibit various different durations and distributions and directional morphologic trends. These differences in patterns may be related to the dissimilar life histories of the two genera. Patterns in the first genus appear more common in organisms having high larval recruitment, high mortality, high genetic variation, and less morphologic distance between species. Patterns in the second genus occur more frequently in slower growing, phenotypically plastic organisms experiencing less recruitment and mortality and showing more morphologic distance between species.« less

STUDYING THE PHYSICAL DIVERSITY OF LATE-M DWARFS WITH DYNAMICAL MASSES

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

Dupuy, Trent J.; Liu, Michael C.; Bowler, Brendan P.

2010-10-01

We present a systematic study of the physical properties of late-M dwarfs based on high-quality dynamical mass measurements and near-infrared (NIR) spectroscopy. We use astrometry from Keck natural and laser guide star adaptive optics imaging to determine orbits for the late-M binaries LP 349 - 25AB (M7.5+M8), LHS 1901AB (M6.5+M6.5), and Gl 569Bab (M8.5+M9). We find that LP 349 - 25AB (M{sub tot} = 0.120{sup +0.008}{sub -0.007} M{sub sun}) is a pair of young brown dwarfs for which Lyon and Tucson evolutionary models jointly predict an age of 140 {+-} 30 Myr, consistent with the age of the Pleiades. However,more » at least the primary component seems to defy the empirical Pleiades lithium depletion boundary, implying that the system is in fact older (if the parallax is correct) and that evolutionary models under-predict the component luminosities for this magnetically active binary. We find that LHS 1901AB is a pair of very low-mass stars (M{sub tot} = 0.194{sup +0.025}{sub -0.021} M{sub sun}) with evolutionary model-derived ages consistent with the old age (>6 Gyr) implied by its lack of activity. Our improved orbit for Gl 569Bab results in a higher mass for this binary (M{sub tot} = 0.140{sup +0.009}{sub -0.008} M{sub sun}) compared to previous work (0.125 {+-} 0.007 M{sub sun}). We use these mass measurements along with our published results for 2MASS J2206 - 2047AB (M8+M8) to test four sets of ultracool model atmospheres currently in use. Fitting these models to our NIR integrated-light spectra provides temperature estimates warmer by {approx}250 K than those derived independently from Dusty evolutionary models given the measured masses and luminosities. We propose that model atmospheres are more likely to be the source of this discrepancy, as it would be difficult to explain a uniform temperature offset over such a wide range of masses, ages, and activity levels in the context of evolutionary models. This contrasts with the conclusion of Konopacky et al. that model-predicted masses (given input T{sub eff} and L{sub bol}) are at fault for differences between theory and observations. In addition, we find an opposite (and smaller) mass discrepancy from what they report when we adopt their model-testing approach: masses are too high rather than too low because our T{sub eff} estimates derived from fitting NIR spectra are {approx}650 K higher than their values from fitting broadband photometry alone.« less

Mean-Potential Law in Evolutionary Games

NASA Astrophysics Data System (ADS)

Nałecz-Jawecki, Paweł; Miekisz, Jacek

2018-01-01

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Evolutionary principles and their practical application

PubMed Central

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

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

Evolutionary principles and their practical application.

PubMed

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

2011-03-01

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

Women, behavior, and evolution: understanding the debate between feminist evolutionists and evolutionary psychologists.

PubMed

Liesen, Laurette T

2007-03-01

Often since the early 1990s, feminist evolutionists have criticized evolutionary psychologists, finding fault in their analyses of human male and female reproductive behavior. Feminist evolutionists have criticized various evolutionary psychologists for perpetuating gender stereotypes, using questionable methodology, and exhibiting a chill toward feminism. Though these criticisms have been raised many times, the conflict itself has not been fully analyzed. Therefore, I reconsider this conflict, both in its origins and its implications. I find that the approaches and perspectives of feminist evolutionists and evolutionary psychologists are distinctly different, leading many of the former to work in behavioral ecology, primatology, and evolutionary biology. Invitingly to feminist evolutionists, these three fields emphasize social behavior and the influences of environmental variables; in contrast, evolutionary psychology has come to rely on assumptions deemphasizing the pliability of psychological mechanisms and the flexibility of human behavior. In behavioral ecology, primatology, and evolutionary biology, feminist evolutionists have found old biases easy to correct and new hypotheses practical to test, offering new insights into male and female behavior, explaining the emergence and persistence of patriarchy, and potentially bringing closer a prime feminist goal, sexual equality.

Modelling the influence of parental effects on gene-network evolution.

PubMed

Odorico, Andreas; Rünneburger, Estelle; Le Rouzic, Arnaud

2018-05-01

Understanding the importance of nongenetic heredity in the evolutionary process is a major topic in modern evolutionary biology. We modified a classical gene-network model by allowing parental transmission of gene expression and studied its evolutionary properties through individual-based simulations. We identified ontogenetic time (i.e. the time gene networks have to stabilize before being submitted to natural selection) as a crucial factor in determining the evolutionary impact of this phenotypic inheritance. Indeed, fast-developing organisms display enhanced adaptation and greater robustness to mutations when evolving in presence of nongenetic inheritance (NGI). In contrast, in our model, long development reduces the influence of the inherited state of the gene network. NGI thus had a negligible effect on the evolution of gene networks when the speed at which transcription levels reach equilibrium is not constrained. Nevertheless, simulations show that intergenerational transmission of the gene-network state negatively affects the evolution of robustness to environmental disturbances for either fast- or slow-developing organisms. Therefore, these results suggest that the evolutionary consequences of NGI might not be sought only in the way species respond to selection, but also on the evolution of emergent properties (such as environmental and genetic canalization) in complex genetic architectures. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

The Implications of the Cognitive Sciences for the Relation Between Religion and Science Education: The Case of Evolutionary Theory

NASA Astrophysics Data System (ADS)

Blancke, Stefaan; De Smedt, Johan; De Cruz, Helen; Boudry, Maarten; Braeckman, Johan

2012-08-01

This paper discusses the relationship between religion and science education in the light of the cognitive sciences. We challenge the popular view that science and religion are compatible, a view that suggests that learning and understanding evolutionary theory has no effect on students' religious beliefs and vice versa. We develop a cognitive perspective on how students manage to reconcile evolutionary theory with their religious beliefs. We underwrite the claim developed by cognitive scientists and anthropologists that religion is natural because it taps into people's intuitive understanding of the natural world which is constrained by essentialist, teleological and intentional biases. After contrasting the naturalness of religion with the unnaturalness of science, we discuss the difficulties cognitive and developmental scientists have identified in learning and accepting evolutionary theory. We indicate how religious beliefs impede students' understanding and acceptance of evolutionary theory. We explore a number of options available to students for reconciling an informed understanding of evolutionary theory with their religious beliefs. To conclude, we discuss the implications of our account for science and biology teachers.

Geographic mosaics of species' association: a definition and an example driven by plant-insect phenological synchrony.

PubMed

Singer, Michael C; McBride, Carolyn S

2012-12-01

Spatial mosaics occur in both evolutionary and ecological properties of species' interactions. Studies of these patterns have facilitated description and prediction of evolutionary responses of interacting species to each other and to changing environments. We propose seeking complementary understanding of community assembly and dynamics by studying ecological and mechanistic properties of mosaics. We define "species' association mosaics" as deviations from a null model in which spatial variation in the extent to which particular species interact ecologically is explained solely by variation in their densities. In extreme deviations from the null, a focal species interacts exclusively with different partners at different sites despite similar abundances of potential partners. We investigate this type of mosaic involving the butterfly Euphydryas editha and its hosts, the perennial Pedicularis semibarbata (Psem) and the ephemeral annual Collinsia torreyi (Ctor). A reciprocal transplant experiment showed that the proximate, mechanistic driver of the mosaic was variation in butterfly oviposition preference: the identity of the preferred host species depended on the site of origin of the insects, not that of the plants. In contrast, the evolutionary driver was phenological asynchrony between the insects and Ctor. Censuses showed that larvae hatching from eggs laid on Ctor would have suffered significantly greater mortality from host senescence at five sites where Ctor was avoided than at two sites where it was used. These differences among sites in phenological synchrony were caused by variation in life span of Ctor. At sites where Ctor was avoided, natural selection on host preference was stabilizing because Ctor life span was too short to accommodate the development time of most larvae. At sites where Ctor was used, selection on preference was also stabilizing because larvae lacked physiological adaptation to feed on Psem. These reciprocal forces of stabilizing selection formed a mosaic maintaining spatial variation in insect host preference that was the proximate cause of the species-association mosaic. In the Discussion, we examine the extent to which our findings hindcast an observed anthropogenic host shift by E. editha from Psem to Ctor. This example shows that elucidation of species-association mosaics can facilitate understanding of community evolution and dynamics.

Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

PubMed

Burdon, J J; Thrall, P H; Ericson, L

2013-08-01

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

PubMed Central

Stenseth, Nils Chr.; Ehrich, Dorothee; Rueness, Eli Knispel; Lingjærde, Ole Chr.; Chan, Kung-Sik; Boutin, Stan; O'Donoghue, Mark; Robinson, David A.; Viljugrein, Hildegunn; Jakobsen, Kjetill S.

2004-01-01

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics. PMID:15067131

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy.

PubMed

Trauner, Andrej; Liu, Qingyun; Via, Laura E; Liu, Xin; Ruan, Xianglin; Liang, Lili; Shi, Huimin; Chen, Ying; Wang, Ziling; Liang, Ruixia; Zhang, Wei; Wei, Wang; Gao, Jingcai; Sun, Gang; Brites, Daniela; England, Kathleen; Zhang, Guolong; Gagneux, Sebastien; Barry, Clifton E; Gao, Qian

2017-04-19

Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.

Hidden long evolutionary memory in a model biochemical network

NASA Astrophysics Data System (ADS)

Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2018-04-01

We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

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

PubMed

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

2012-01-01

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

Evolution of proliferation and the angiogenic switch in tumors with high clonal diversity.

PubMed

Bickel, Scott T; Juliano, Joseph D; Nagy, John D

2014-01-01

Natural selection among tumor cell clones is thought to produce hallmark properties of malignancy. Efforts to understand evolution of one such hallmark--the angiogenic switch--has suggested that selection for angiogenesis can "run away" and generate a hypertumor, a form of evolutionary suicide by extreme vascular hypo- or hyperplasia. This phenomenon is predicted by models of tumor angiogenesis studied with the techniques of adaptive dynamics. These techniques also predict that selection drives tumor proliferative potential towards an evolutionarily stable strategy (ESS) that is also convergence-stable. However, adaptive dynamics are predicated on two key assumptions: (i) no more than two distinct clones or evolutionary strategies can exist in the tumor at any given time; and (ii) mutations cause small phenotypic changes. Here we show, using a stochastic simulation, that relaxation of these assumptions has no effect on the predictions of adaptive dynamics in this case. In particular, selection drives proliferative potential towards, and angiogenic potential away from, their respective ESSs. However, these simulations also show that tumor behavior is highly contingent on mutational history, particularly for angiogenesis. Individual tumors frequently grow to lethal size before the evolutionary endpoint is approached. In fact, most tumor dynamics are predicted to be in the evolutionarily transient regime throughout their natural history, so that clinically, the ESS is often largely irrelevant. In addition, we show that clonal diversity as measured by the Shannon Information Index correlates with the speed of approach to the evolutionary endpoint. This observation dovetails with results showing that clonal diversity in Barrett's esophagus predicts progression to malignancy.

Evolution of resource cycling in ecosystems and individuals.

PubMed

Crombach, Anton; Hogeweg, Paulien

2009-06-01

Resource cycling is a defining process in the maintenance of the biosphere. Microbial communities, ranging from simple to highly diverse, play a crucial role in this process. Yet the evolutionary adaptation and speciation of micro-organisms have rarely been studied in the context of resource cycling. In this study, our basic questions are how does a community evolve its resource usage and how are resource cycles partitioned? We design a computational model in which a population of individuals evolves to take up nutrients and excrete waste. The waste of one individual is another's resource. Given a fixed amount of resources, this leads to resource cycles. We find that the shortest cycle dominates the ecological dynamics, and over evolutionary time its length is minimized. Initially a single lineage processes a long cycle of resources, later crossfeeding lineages arise. The evolutionary dynamics that follow are determined by the strength of indirect selection for resource cycling. We study indirect selection by changing the spatial setting and the strength of direct selection. If individuals are fixed at lattice sites or direct selection is low, indirect selection result in lineages that structure their local environment, leading to 'smart' individuals and stable patterns of resource dynamics. The individuals are good at cycling resources themselves and do this with a short cycle. On the other hand, if individuals randomly change position each time step, or direct selection is high, individuals are more prone to crossfeeding: an ecosystem based solution with turbulent resource dynamics, and individuals that are less capable of cycling resources themselves. In a baseline model of ecosystem evolution we demonstrate different eco-evolutionary trajectories of resource cycling. By varying the strength of indirect selection through the spatial setting and direct selection, the integration of information by the evolutionary process leads to qualitatively different results from individual smartness to cooperative community structures.

A Simple General Model of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Thurner, Stefan

Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense that it's predictions can be used to understand a series of experimental data ranging from the fossil record to macroeconomic indices.

A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

PubMed

Eirín-López, José M

2013-01-01

The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

PubMed

Mullon, Charles; Lehmann, Laurent

2017-08-01

Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is more efficient than between unrelated individuals. Copyright © 2017 Elsevier Inc. All rights reserved.

Global Warming Denial: The Human Brain on Extremes

NASA Astrophysics Data System (ADS)

Marrouch, N.; Johnson, B. T.; Slawinska, J. M.

2016-12-01

Future assessments of climate change rely on multi-model intercomparisons, and projections of the extreme events frequency are of particular interest as associated with significant economic costs and social threats. Notably, systematically simulated increases in the number of extreme weather events agree well with observational data over the last decade. At the same time, as the climate grows more volatile, widespread denial of climate change and its anthropocentric causes continues to proliferate (based on nationally representative U.S. polls). Simultaneous increases in both high-impact exposure and its denial is in stark contrast with our knowledge of socio-natural dynamics and its models. Disentangling this paradox requires an understanding of the origins of global warming denial at an individual level, and how subsequently it propagates across social networks of many scales, shaping global policies. However, as the real world and its dynamical models are complex (high-dimensional and coupled), separating the particular feedback of interest remains a challenge. Here, we demonstrate this feedback in a controlled experiment, where increasing unpredictability using helplessness-training paradigms induces changes in global warming denial, and the endorsement of conservative ideology. We explain these results in the context of evolutionary theory framing self-deception and denial as remnants of evolutionary processes that shaped and facilitated the survival of the human species. Further we link these findings to changes in neural and higher-level cognitive processes in response to unpredictable stimuli. We argue that climate change denial is an example of an extreme belief system that carries the potential to threaten the wellbeing of both humans and other species alike. It is therefore crucial to better quantify climate denial using social informatics tools that provide the means to improve its representations in coupled socio-geophysical models to mitigate its effects on global and local policies.

STELLAR POPULATIONS IN COMPACT GALAXY GROUPS: A MULTI-WAVELENGTH STUDY OF HCGs 16, 22, AND 42, THEIR STAR CLUSTERS, AND DWARF GALAXIES

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

Konstantopoulos, I. S.; Maybhate, A.; Charlton, J. C.

2013-06-20

We present a multi-wavelength analysis of three compact galaxy groups, Hickson compact groups (HCGs) 16, 22, and 42, which describe a sequence in terms of gas richness, from space- (Swift, Hubble Space Telescope (HST), and Spitzer) and ground-based (Las Campanas Observatory and Cerro Tololo Inter-American Observatory) imaging and spectroscopy. We study various signs of past interactions including a faint, dusty tidal feature about HCG 16A, which we tentatively age-date at <1 Gyr. This represents the possible detection of a tidal feature at the end of its phase of optical observability. Our HST images also resolve what were thought to bemore » double nuclei in HCG 16C and D into multiple, distinct sources, likely to be star clusters. Beyond our phenomenological treatment, we focus primarily on contrasting the stellar populations across these three groups. The star clusters show a remarkable intermediate-age population in HCG 22, and identify the time at which star formation was quenched in HCG 42. We also search for dwarf galaxies at accordant redshifts. The inclusion of 33 members and 27 ''associates'' (possible members) radically changes group dynamical masses, which in turn may affect previous evolutionary classifications. The extended membership paints a picture of relative isolation in HCGs 16 and 22, but shows HCG 42 to be part of a larger structure, following a dichotomy expected from recent studies. We conclude that (1) star cluster populations provide an excellent metric of evolutionary state, as they can age-date the past epochs of star formation; and (2) the extended dwarf galaxy population must be considered in assessing the dynamical state of a compact group.« less

Interspecific competition counteracts negative effects of dispersal on adaptation of an arthropod herbivore to a new host.

PubMed

Alzate, A; Bisschop, K; Etienne, R S; Bonte, D

2017-11-01

Dispersal and competition have both been suggested to drive variation in adaptability to a new environment, either positively or negatively. A simultaneous experimental test of both mechanisms is however lacking. Here, we experimentally investigate how population dynamics and local adaptation to a new host plant in a model species, the two-spotted spider mite (Tetranychus urticae), are affected by dispersal from a stock population (no-adapted) and competition with an already adapted spider mite species (Tetranychus evansi). For the population dynamics, we find that competition generally reduces population size and increases the risk of population extinction. However, these negative effects are counteracted by dispersal. For local adaptation, the roles of competition and dispersal are reversed. Without competition, dispersal exerts a negative effect on adaptation (measured as fecundity) to a novel host and females receiving the highest number of immigrants performed similarly to the stock population females. By contrast, with competition, adding more immigrants did not result in a lower fecundity. Females from populations with competition receiving the highest number of immigrants had a significantly higher fecundity than females from populations without competition (same dispersal treatment) and than the stock population females. We suggest that by exerting a stronger selection on the adapting populations, competition can counteract the migration load effect of dispersal. Interestingly, adaptation to the new host does not significantly reduce performance on the ancestral host, regardless of dispersal rate or competition. Our results highlight that assessments of how species can adapt to changing conditions need to jointly consider connectivity and the community context. © 2017 The Authors. Journal of Evolutionary Biology Published by John Wiley & Sons ltd on Behalf of European Society for Evolutionary Biology.

Stellar Populations in Compact Galaxy Groups: a Multi-wavelength Study of HCGs 16, 22, and 42, Their Star Clusters, and Dwarf Galaxies

NASA Technical Reports Server (NTRS)

Konstantopoulos, I. S.; Maybhate, A.; Charlton, J. C.; Fedotov, K.; Durrell, P. R.; Mulchaey, J. S.; English, J.; Desjardins, T. D.; Gallagher, S. C.; Walker, L. M.;

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

PubMed Central

Jack, Benjamin R.; Meyer, Austin G.; Echave, Julian; Wilke, Claus O.

2016-01-01

Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein–protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes. PMID:27138088

Evolutionary Nephrology.

PubMed

Chevalier, Robert L

2017-05-01

Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

Darwinism in quantum systems?

NASA Astrophysics Data System (ADS)

Iqbal, A.; Toor, A. H.

2002-03-01

We investigate the role of quantum mechanical effects in the central stability concept of evolutionary game theory, i.e., an evolutionarily stable strategy (ESS). Using two and three-player symmetric quantum games we show how the presence of quantum phenomenon of entanglement can be crucial to decide the course of evolutionary dynamics in a population of interacting individuals.

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

Evolutionary dynamics on graphs

NASA Astrophysics Data System (ADS)

Lieberman, Erez; Hauert, Christoph; Nowak, Martin A.

2005-01-01

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

The evolutionary language game: an orthogonal approach.

PubMed

Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

2005-08-21

Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning.

Feedbacks between geomorphology and biota controlling Earth surface processes and landforms: A review of foundation concepts and current understandings

NASA Astrophysics Data System (ADS)

Corenblit, Dov; Baas, Andreas C. W.; Bornette, Gudrun; Darrozes, José; Delmotte, Sébastien; Francis, Robert A.; Gurnell, Angela M.; Julien, Frédéric; Naiman, Robert J.; Steiger, Johannes

2011-06-01

This review article presents recent advances in the field of biogeomorphology related to the reciprocal coupling between Earth surface processes and landforms, and ecological and evolutionary processes. The aim is to present to the Earth Science community ecological and evolutionary concepts and associated recent conceptual developments for linking geomorphology and biota. The novelty of the proposed perspective is that (1) in the presence of geomorphologic-engineer species, which modify sediment and landform dynamics, natural selection operating at the scale of organisms may have consequences for the physical components of ecosystems, and particularly Earth surface processes and landforms; and (2) in return, these modifications of geomorphologic processes and landforms often feed back to the ecological characteristics of the ecosystem (structure and function) and thus to biological characteristics of engineer species and/or other species (adaptation and speciation). The main foundation concepts from ecology and evolutionary biology which have led only recently to an improved conception of landform dynamics in geomorphology are reviewed and discussed. The biogeomorphologic macroevolutionary insights proposed explicitly integrate geomorphologic niche-dimensions and processes within an ecosystem framework and reflect current theories of eco-evolutionary and ecological processes. Collectively, these lead to the definition of an integrated model describing the overall functioning of biogeomorphologic systems over ecological and evolutionary timescales.

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

Games of multicellularity.

PubMed

Kaveh, Kamran; Veller, Carl; Nowak, Martin A

2016-08-21

Evolutionary game dynamics are often studied in the context of different population structures. Here we propose a new population structure that is inspired by simple multicellular life forms. In our model, cells reproduce but can stay together after reproduction. They reach complexes of a certain size, n, before producing single cells again. The cells within a complex derive payoff from an evolutionary game by interacting with each other. The reproductive rate of cells is proportional to their payoff. We consider all two-strategy games. We study deterministic evolutionary dynamics with mutations, and derive exact conditions for selection to favor one strategy over another. Our main result has the same symmetry as the well-known sigma condition, which has been proven for stochastic game dynamics and weak selection. For a maximum complex size of n=2 our result holds for any intensity of selection. For n≥3 it holds for weak selection. As specific examples we study the prisoner's dilemma and hawk-dove games. Our model advances theoretical work on multicellularity by allowing for frequency-dependent interactions within groups. Copyright © 2016 Elsevier Ltd. All rights reserved.

The genomic and epidemiological dynamics of human influenza A virus.

PubMed

Rambaut, Andrew; Pybus, Oliver G; Nelson, Martha I; Viboud, Cecile; Taubenberger, Jeffery K; Holmes, Edward C

2008-05-29

The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.

The Effects of Predator Evolution and Genetic Variation on Predator-Prey Population-Level Dynamics.

PubMed

Cortez, Michael H; Patel, Swati

2017-07-01

This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory. With these four methods, we identify the conditions under which predator evolution alters system stability and shapes of predator-prey cycles, and how those effect depend on the amount of genetic variation in the predator population. We discuss the advantages and disadvantages of each method and the relations between the four methods. This work shows how the four methods can be used in tandem to make general predictions about eco-evolutionary dynamics and feedbacks.

Detection of timescales in evolving complex systems

PubMed Central

Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

2016-01-01

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

The co-evolutionary dynamics of directed network of spin market agents

NASA Astrophysics Data System (ADS)

Horváth, Denis; Kuscsik, Zoltán; Gmitra, Martin

2006-09-01

The spin market model [S. Bornholdt, Int. J. Mod. Phys. C 12 (2001) 667] is generalized by employing co-evolutionary principles, where strategies of the interacting and competitive traders are represented by local and global couplings between the nodes of dynamic directed stochastic network. The co-evolutionary principles are applied in the frame of Bak-Sneppen self-organized dynamics [P. Bak, K. Sneppen, Phys. Rev. Lett. 71 (1993) 4083] that includes the processes of selection and extinction actuated by the local (node) fitness. The local fitness is related to orientation of spin agent with respect to the instant magnetization. The stationary regime is formed due to the interplay of self-organization and adaptivity effects. The fat tailed distributions of log-price returns are identified numerically. The non-trivial model consequence is the evidence of the long time market memory indicated by the power-law range of the autocorrelation function of volatility with exponent smaller than one. The simulations yield network topology with broad-scale node degree distribution characterized by the range of exponents 1.3<γin<3 coinciding with social networks.

Evolutionary dynamics of group formation.

PubMed

Javarone, Marco Alberto; Marinazzo, Daniele

2017-01-01

Group formation is a quite ubiquitous phenomenon across different animal species, whose individuals cluster together forming communities of diverse size. Previous investigations suggest that, in general, this phenomenon might have similar underlying reasons across the interested species, despite genetic and behavioral differences. For instance improving the individual safety (e.g. from predators), and increasing the probability to get food resources. Remarkably, the group size might strongly vary from species to species, e.g. shoals of fishes and herds of lions, and sometimes even within the same species, e.g. tribes and families in human societies. Here we build on previous theories stating that the dynamics of group formation may have evolutionary roots, and we explore this fascinating hypothesis from a purely theoretical perspective, with a model using the framework of Evolutionary Game Theory. In our model we hypothesize that homogeneity constitutes a fundamental ingredient in these dynamics. Accordingly, we study a population that tries to form homogeneous groups, i.e. composed of similar agents. The formation of a group can be interpreted as a strategy. Notably, agents can form a group (receiving a 'group payoff'), or can act individually (receiving an 'individual payoff'). The phase diagram of the modeled population shows a sharp transition between the 'group phase' and the 'individual phase', characterized by a critical 'individual payoff'. Our results then support the hypothesis that the phenomenon of group formation has evolutionary roots.

Application of network methods for understanding evolutionary dynamics in discrete habitats.

PubMed

Greenbaum, Gili; Fefferman, Nina H

2017-06-01

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

A strategy with novel evolutionary features for the iterated prisoner's dilemma.

PubMed

Li, Jiawei; Kendall, Graham

2009-01-01

In recent iterated prisoner's dilemma tournaments, the most successful strategies were those that had identification mechanisms. By playing a predetermined sequence of moves and learning from their opponents' responses, these strategies managed to identify their opponents. We believe that these identification mechanisms may be very useful in evolutionary games. In this paper one such strategy, which we call collective strategy, is analyzed. Collective strategies apply a simple but efficient identification mechanism (that just distinguishes themselves from other strategies), and this mechanism allows them to only cooperate with their group members and defect against any others. In this way, collective strategies are able to maintain a stable population in evolutionary iterated prisoner's dilemma. By means of an invasion barrier, this strategy is compared with other strategies in evolutionary dynamics in order to demonstrate its evolutionary features. We also find that this collective behavior assists the evolution of cooperation in specific evolutionary environments.

Evolutionary perspectives on wildlife disease: concepts and applications

PubMed Central

Vander Wal, Eric; Garant, Dany; Pelletier, Fanie

2014-01-01

Wildlife disease has the potential to cause significant ecological, socioeconomic, and health impacts. As a result, all tools available need to be employed when host–pathogen dynamics merit conservation or management interventions. Evolutionary principles, such as evolutionary history, phenotypic and genetic variation, and selection, have the potential to unravel many of the complex ecological realities of infectious disease in the wild. Despite this, their application to wildlife disease ecology and management remains in its infancy. In this article, we outline the impetus behind applying evolutionary principles to disease ecology and management issues in the wild. We then introduce articles from this special issue on Evolutionary Perspectives on Wildlife Disease: Concepts and Applications, outlining how each is exemplar of a practical wildlife disease challenge that can be enlightened by applied evolution. Ultimately, we aim to bring new insights to wildlife disease ecology and its management using tools and techniques commonly employed in evolutionary ecology. PMID:25469154

Deciphering the Interdependence between Ecological and Evolutionary Networks.

PubMed

Melián, Carlos J; Matthews, Blake; de Andreazzi, Cecilia S; Rodríguez, Jorge P; Harmon, Luke J; Fortuna, Miguel A

2018-05-24

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator-prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2003-01-01

The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons. PMID:12966138

Mean-Potential Law in Evolutionary Games.

PubMed

Nałęcz-Jawecki, Paweł; Miękisz, Jacek

2018-01-12

The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1/3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

Time-Dependent Rate Phenomenon in Viruses

PubMed Central

Aiewsakun, Pakorn

2016-01-01

ABSTRACT Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies. PMID:27252529

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

PubMed Central

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Holmes, Edward C.; Bourhy, Hervé

2016-01-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. PMID:27977811

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

PubMed

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Duchene, Sebastián; Holmes, Edward C; Bourhy, Hervé

2016-12-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Evolutionary Games in Multi-Agent Systems of Weighted Social Networks

NASA Astrophysics Data System (ADS)

Du, Wen-Bo; Cao, Xian-Bin; Zheng, Hao-Ran; Zhou, Hong; Hu, Mao-Bin

Much empirical evidence has shown realistic networks are weighted. Compared with those on unweighted networks, the dynamics on weighted network often exhibit distinctly different phenomena. In this paper, we investigate the evolutionary game dynamics (prisoner's dilemma game and snowdrift game) on a weighted social network consisted of rational agents and focus on the evolution of cooperation in the system. Simulation results show that the cooperation level is strongly affected by the weighted nature of the network. Moreover, the variation of time series has also been investigated. Our work may be helpful in understanding the cooperative behavior in the social systems.

Restart Operator Meta-heuristics for a Problem-Oriented Evolutionary Strategies Algorithm in Inverse Mathematical MISO Modelling Problem Solving

NASA Astrophysics Data System (ADS)

Ryzhikov, I. S.; Semenkin, E. S.

2017-02-01

This study is focused on solving an inverse mathematical modelling problem for dynamical systems based on observation data and control inputs. The mathematical model is being searched in the form of a linear differential equation, which determines the system with multiple inputs and a single output, and a vector of the initial point coordinates. The described problem is complex and multimodal and for this reason the proposed evolutionary-based optimization technique, which is oriented on a dynamical system identification problem, was applied. To improve its performance an algorithm restart operator was implemented.

Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

PubMed

Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

2013-10-01

Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

Deep trees: Woodfall biodiversity dynamics in present and past oceans

NASA Astrophysics Data System (ADS)

Sigwart, Julia D.

2017-03-01

Marine deposits of sunken wood provide an important habitat for deep-sea biota, including an extensive wood-endemic invertebrate fauna. These habitats are important in their own right; many species on organic falls are not able to survive in other deep sea ecosystems. Evolutionary transitions of species among various chemosynthesis-based ecosystems does not proceed deliberately from organic falls toward hydrothermal vents. Polyplacophoran molluscs (chitons) are generally rare in deep-sea systems but are found in comparatively high diversity and abundance on tropical sunken wood. A new time-calibrated phylogeny for the predominantly deep-sea order Lepidopleurida shows the chiton lineages found in sunken wood habitats do not comprise a single clade or radiation, but represents a minimum of three independent radiations in the Pacific alone. Most marine invertebrate groups diversified in the deep sea following the end Cretaceous extinction event; by contrast, sunken-wood chitons may have persisted in these habitats for longer than other animals. Fossil chitons from the early Carboniferous (ca. 350 Mya) have strong similarities to modern wood-endemic taxa, yet the common ancestor of living Lepidopleurida occurred much later in the Triassic and did not apparently rely on woodfall. Clades within Lepidopleurida that occupy wood habitats in the tropical Pacific probably arose in the Jurassic, which corresponds to evidence from the fossil record, but with an additional separate colonisation more recently in the early Paleogene. Wood-endemic chiton species encompass multiple independent evolutionary origins of co-occurring wood species, and these separate lineages correspond to differences in micohabitat and feeding strategies. These patterns demonstrate the ongoing evolutionary linkages between terrestrial and deep marine environments, and the opportunistic adaptations of deep-sea organisms.

Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

PubMed Central

Chaillou, Stéphane; Lucquin, Isabelle; Najjari, Afef; Zagorec, Monique; Champomier-Vergès, Marie-Christine

2013-01-01

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products. PMID:24069179

Population genetics of Lactobacillus sakei reveals three lineages with distinct evolutionary histories.

PubMed

Chaillou, Stéphane; Lucquin, Isabelle; Najjari, Afef; Zagorec, Monique; Champomier-Vergès, Marie-Christine

2013-01-01

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.

PubMed

Hindersin, Laura; Traulsen, Arne

2015-11-01

We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.

Evolutionary dynamics of cooperation in neutral populations

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž

2018-01-01

Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

PubMed Central

Castoe, T.A.; Gu, W.; de Koning, A.P.J.; Daza, J.M.; Jiang, Z.J.; Parkinson, C.L.; Pollock, D.D.

2010-01-01

Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the ∼200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models. PMID:20215734

Evolving learning rules and emergence of cooperation in spatial prisoner's dilemma.

PubMed

Moyano, Luis G; Sánchez, Angel

2009-07-07

In the evolutionary Prisoner's dilemma (PD) game, agents play with each other and update their strategies in every generation according to some microscopic dynamical rule. In its spatial version, agents do not play with every other but, instead, interact only with their neighbours, thus mimicking the existing of a social or contact network that defines who interacts with whom. In this work, we explore evolutionary, spatial PD systems consisting of two types of agents, each with a certain update (reproduction, learning) rule. We investigate two different scenarios: in the first case, update rules remain fixed for the entire evolution of the system; in the second case, agents update both strategy and update rule in every generation. We show that in a well-mixed population the evolutionary outcome is always full defection. We subsequently focus on two-strategy competition with nearest-neighbour interactions on the contact network and synchronised update of strategies. Our results show that, for an important range of the parameters of the game, the final state of the system is largely different from that arising from the usual setup of a single, fixed dynamical rule. Furthermore, the results are also very different if update rules are fixed or evolve with the strategies. In these respect, we have studied representative update rules, finding that some of them may become extinct while others prevail. We describe the new and rich variety of final outcomes that arise from this co-evolutionary dynamics. We include examples of other neighbourhoods and asynchronous updating that confirm the robustness of our conclusions. Our results pave the way to an evolutionary rationale for modelling social interactions through game theory with a preferred set of update rules.

Genetic basis and fitness correlates of dynamic carotenoid-based ornamental coloration in male and female common kestrels Falco tinnunculus.

PubMed

Vergara, P; Fargallo, J A; Martínez-Padilla, J

2015-01-01

Knowledge of the genetic basis of sexual ornaments is essential to understand their evolution through sexual selection. Although carotenoid-based ornaments have been instrumental in the study of sexual selection, given the inability of animals to synthesize carotenoids de novo, they are generally assumed to be influenced solely by environmental variation. However, very few studies have directly estimated the role of genes and the environment in shaping variation in carotenoid-based traits. Using long-term individual-based data, we here explore the evolutionary potential of a dynamic, carotenoid-based ornament (namely skin coloration), in male and female common kestrels. We first estimate the amount of genetic variation underlying variation in hue, chroma and brightness. After correcting for sex differences, the chroma of the orange-yellow eye ring coloration was significantly heritable (h2±SE=0.40±0.17), whereas neither hue (h2=0) nor brightness (h2=0.02) was heritable. Second, we estimate the strength and shape of selection acting upon chromatic (hue and chroma) and achromatic (brightness) variation and show positive and negative directional selection on female but not male chroma and hue, respectively, whereas brightness was unrelated to fitness in both sexes. This suggests that different components of carotenoid-based signals traits may show different evolutionary dynamics. Overall, we show that carotenoid-based coloration is a complex and multifaceted trait. If we are to gain a better understanding of the processes responsible for the generation and maintenance of variation in carotenoid-based coloration, these complexities need to be taken into account. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Two-phase vesicles: a study on evolutionary and stationary models.

PubMed

Sahebifard, MohammadMahdi; Shahidi, Alireza; Ziaei-Rad, Saeed

2017-05-01

In the current article, the dynamic evolution of two-phase vesicles is presented as an extension to a previous stationary model and based on an equilibrium of local forces. In the simplified model, ignoring the effects of membrane inertia, a dynamic equilibrium between the membrane bending potential and local fluid friction is considered in each phase. The equilibrium equations at the domain borders are completed by extended introduction of membrane section reactions. We show that in some cases, the results of stationary and evolutionary models are in agreement with each other and also with experimental observations, while in others the two models differ markedly. The value of our approach is that we can account for unresponsive points of uncertainty using our equations with the local velocity of the lipid membranes and calculating the intermediate states (shapes) in the consequent evolutionary, or response, path.

Evolutionary dynamics on any population structure

NASA Astrophysics Data System (ADS)

Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

2017-03-01

Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.

PubMed

Jerison, Elizabeth R; Desai, Michael M

2015-12-01

Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Neutral tumor evolution in myeloma is associated with poor prognosis.

PubMed

Johnson, David C; Lenive, Oleg; Mitchell, Jonathan; Jackson, Graham; Owen, Roger; Drayson, Mark; Cook, Gordon; Jones, John R; Pawlyn, Charlotte; Davies, Faith E; Walker, Brian A; Wardell, Christopher; Gregory, Walter M; Cairns, David; Morgan, Gareth J; Houlston, Richard S; Kaiser, Martin F

2017-10-05

Recent studies suggest that the evolutionary history of a cancer is important in forecasting clinical outlook. To gain insight into the clonal dynamics of multiple myeloma (MM) and its possible influence on patient outcomes, we analyzed whole exome sequencing tumor data for 333 patients from Myeloma XI, a UK phase 3 trial and 434 patients from the CoMMpass study, all of which had received immunomodulatory drug (IMiD) therapy. By analyzing mutant allele frequency distributions in tumors, we found that 17% to 20% of MM is under neutral evolutionary dynamics. These tumors are associated with poorer patient survival in nonintensively treated patients, which is consistent with the reduced therapeutic efficacy of microenvironment-modulating IMiDs. Our findings provide evidence that knowledge of the evolutionary history of MM has relevance for predicting patient outcomes and personalizing therapy. © 2017 by The American Society of Hematology.

Darwin without borders? Looking at 'generalised Darwinism' through the prism of the 'hourglass model'.

PubMed

Levit, Georgy S; Hossfeld, Uwe

2011-12-01

This article critically analyzes the arguments of the 'generalized Darwinism' recently proposed for the analysis of social-economical systems. We argue that 'generalized Darwinism' is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical constraints. Arguing against 'generalised Darwinism' we present our vision of the history of evolutionary biology with the help of the 'hourglass model' reflecting the internal dynamic of competing theories of evolution.

An Application of Evolutionary Game Theory to Social Dilemmas: The Traveler's Dilemma and the Minimum Effort Coordination Game

PubMed Central

Iyer, Swami; Reyes, Joshua; Killingback, Timothy

2014-01-01

The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games. PMID:24709851

An application of evolutionary game theory to social dilemmas: the traveler's dilemma and the minimum effort coordination game.

PubMed

Iyer, Swami; Reyes, Joshua; Killingback, Timothy

2014-01-01

The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.

The contrasting phylodynamics of human influenza B viruses

PubMed Central

Vijaykrishna, Dhanasekaran; Holmes, Edward C; Joseph, Udayan; Fourment, Mathieu; Su, Yvonne CF; Halpin, Rebecca; Lee, Raphael TC; Deng, Yi-Mo; Gunalan, Vithiagaran; Lin, Xudong; Stockwell, Timothy B; Fedorova, Nadia B; Zhou, Bin; Spirason, Natalie; Kühnert, Denise; Bošková, Veronika; Stadler, Tanja; Costa, Anna-Maria; Dwyer, Dominic E; Huang, Q Sue; Jennings, Lance C; Rawlinson, William; Sullivan, Sheena G; Hurt, Aeron C; Maurer-Stroh, Sebastian; Wentworth, David E; Smith, Gavin JD; Barr, Ian G

2015-01-01

A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology. DOI: http://dx.doi.org/10.7554/eLife.05055.001 PMID:25594904

Extinction phase transitions in a model of ecological and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

2017-07-01

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms.

PubMed

Nadell, Carey D; Ricaurte, Deirdre; Yan, Jing; Drescher, Knut; Bassler, Bonnie L

2017-01-13

Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics in Pseudomonas aeruginosa biofilms. Irrespective of initial frequency, in competition with matrix mutants, wild-type cells always increase in relative abundance in planar microfluidic devices under simple flow regimes. By contrast, in microenvironments with complex, irregular flow profiles - which are common in natural environments - wild-type matrix-producing and isogenic non-producing strains can coexist. This result stems from local obstruction of flow by wild-type matrix producers, which generates regions of near-zero shear that allow matrix mutants to locally accumulate. Our findings connect the evolutionary stability of matrix production with the hydrodynamics and spatial structure of the surrounding environment, providing a potential explanation for the variation in biofilm matrix secretion observed among bacteria in natural environments.

The Limits of Natural Selection in a Nonequilibrium World.

PubMed

Brandvain, Yaniv; Wright, Stephen I

2016-04-01

Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance. Copyright © 2016 Elsevier Ltd. All rights reserved.

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

PubMed Central

2016-01-01

Mutualistic cooperation often requires multiple individuals to behave in a coordinated fashion. Hence, while the evolutionary stability of mutualistic cooperation poses no particular theoretical difficulty, its evolutionary emergence faces a chicken and egg problem: an individual cannot benefit from cooperating unless other individuals already do so. Here, we use evolutionary robotic simulations to study the consequences of this problem for the evolution of cooperation. In contrast with standard game-theoretic results, we find that the transition from solitary to cooperative strategies is very unlikely, whether interacting individuals are genetically related (cooperation evolves in 20% of all simulations) or unrelated (only 3% of all simulations). We also observe that successful cooperation between individuals requires the evolution of a specific and rather complex behaviour. This behavioural complexity creates a large fitness valley between solitary and cooperative strategies, making the evolutionary transition difficult. These results reveal the need for research on biological mechanisms which may facilitate this transition. PMID:27148874

Punctuated equilibrium and power law in economic dynamics

NASA Astrophysics Data System (ADS)

Gupta, Abhijit Kar

2012-02-01

This work is primarily based on a recently proposed toy model by Thurner et al. (2010) [3] on Schumpeterian economic dynamics (inspired by the idea of economist Joseph Schumpeter [9]). Interestingly, punctuated equilibrium has been shown to emerge from the dynamics. The punctuated equilibrium and Power law are known to be associated with similar kinds of biologically relevant evolutionary models proposed in the past. The occurrence of the Power law is a signature of Self-Organised Criticality (SOC). In our view, power laws can be obtained by controlling the dynamics through incorporating the idea of feedback into the algorithm in some way. The so-called 'feedback' was achieved by introducing the idea of fitness and selection processes in the biological evolutionary models. Therefore, we examine the possible emergence of a power law by invoking the concepts of 'fitness' and 'selection' in the present model of economic evolution.

Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

PubMed

Liao, David; Tlsty, Thea D

2014-08-06

Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

Evolutionary rescue: linking theory for conservation and medicine.

PubMed

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

2014-12-01

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

The role of selection on evolutionary rescue

NASA Astrophysics Data System (ADS)

Amirjanov, Adil

The paper investigates the role of selection on evolutionary rescue of population. The statistical mechanics technique is used to model dynamics of a population experiencing a natural selection and an abrupt change in the environment. The paper assesses the selective pressure produced by two different mechanisms: by strength of resistance and by strength of selection (by intraspecific competition). It is shown that both mechanisms are capable of providing an evolutionary rescue of population in particular conditions. However, for a small level of an extinction rate, the population cannot be rescued without intraspecific competition.

Extending and expanding the Darwinian synthesis: the role of complex systems dynamics.

PubMed

Weber, Bruce H

2011-03-01

Darwinism is defined here as an evolving research tradition based upon the concepts of natural selection acting upon heritable variation articulated via background assumptions about systems dynamics. Darwin's theory of evolution was developed within a context of the background assumptions of Newtonian systems dynamics. The Modern Evolutionary Synthesis, or neo-Darwinism, successfully joined Darwinian selection and Mendelian genetics by developing population genetics informed by background assumptions of Boltzmannian systems dynamics. Currently the Darwinian Research Tradition is changing as it incorporates new information and ideas from molecular biology, paleontology, developmental biology, and systems ecology. This putative expanded and extended synthesis is most perspicuously deployed using background assumptions from complex systems dynamics. Such attempts seek to not only broaden the range of phenomena encompassed by the Darwinian Research Tradition, such as neutral molecular evolution, punctuated equilibrium, as well as developmental biology, and systems ecology more generally, but to also address issues of the emergence of evolutionary novelties as well as of life itself. Copyright © 2010 Elsevier Ltd. All rights reserved.

Evolutionary dynamics of protein domain architecture in plants

PubMed Central

2012-01-01

Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution. PMID:22252370

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

PubMed Central

Ho, Cynthia K. Y.; Raghwani, Jayna; Koekkoek, Sylvie; Liang, Richard H.; Van der Meer, Jan T. M.; Van Der Valk, Marc; De Jong, Menno; Pybus, Oliver G.

2016-01-01

ABSTRACT In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms. IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations. PMID:28077634

Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

PubMed

Krasny, Darren P; Orin, David E

2004-08-01

Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

How mutation affects evolutionary games on graphs

PubMed Central

Allen, Benjamin; Traulsen, Arne; Tarnita, Corina E.; Nowak, Martin A.

2011-01-01

Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration. PMID:21473871

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

PubMed Central

Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

2016-01-01

Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

Deontic reasoning with emotional content: evolutionary psychology or decision theory?

PubMed

Perham, Nick; Oaksford, Mike

2005-09-10

Three experiments investigated the contrasting predictions of the evolutionary and decision-theoretic approaches to deontic reasoning. Two experiments embedded a hazard management (HM) rule in a social contract scenario that should lead to competition between innate modules. A 3rd experiment used a pure HM task. Threatening material was also introduced into the antecedent, p, of a deontic rule, if p then must q. According to the evolutionary approach, more HM responses (Cosmides & Tooby, 2000) are predicted when p is threatening, whereas decision theory predicts fewer. All 3 experiments were consistent with decision theory. Other theories are discussed, and it is concluded that they cannot account for the behavior observed in these experiments. 2005 Lawrence Erlbaum Associates, Inc.

Diversity-dependent evolutionary rates in early Palaeozoic zooplankton.

PubMed

Foote, Michael; Cooper, Roger A; Crampton, James S; Sadler, Peter M

2018-02-28

The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of approximately 1 Myr. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian. © 2018 The Author(s).

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities.

PubMed

Zhang, Lai; Andersen, Ken H; Dieckmann, Ulf; Brännström, Åke

2015-09-07

We investigate how four types of interference competition - which alternatively affect foraging, metabolism, survival, and reproduction - impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population׳s reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes.

PubMed

Near, Thomas J; Dornburg, Alex; Tokita, Masayoshi; Suzuki, Dai; Brandley, Matthew C; Friedman, Matt

2014-04-01

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils." © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Dynamics, morphogenesis and convergence of evolutionary quantum Prisoner's Dilemma games on networks

PubMed Central

Yong, Xi

2016-01-01

The authors proposed a quantum Prisoner's Dilemma (PD) game as a natural extension of the classic PD game to resolve the dilemma. Here, we establish a new Nash equilibrium principle of the game, propose the notion of convergence and discover the convergence and phase-transition phenomena of the evolutionary games on networks. We investigate the many-body extension of the game or evolutionary games in networks. For homogeneous networks, we show that entanglement guarantees a quick convergence of super cooperation, that there is a phase transition from the convergence of defection to the convergence of super cooperation, and that the threshold for the phase transitions is principally determined by the Nash equilibrium principle of the game, with an accompanying perturbation by the variations of structures of networks. For heterogeneous networks, we show that the equilibrium frequencies of super-cooperators are divergent, that entanglement guarantees emergence of super-cooperation and that there is a phase transition of the emergence with the threshold determined by the Nash equilibrium principle, accompanied by a perturbation by the variations of structures of networks. Our results explore systematically, for the first time, the dynamics, morphogenesis and convergence of evolutionary games in interacting and competing systems. PMID:27118882

Natural selection. IV. The Price equation*

PubMed Central

Frank, Steven A.

2012-01-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation’s greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection, and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. PMID:22487312

An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game.

PubMed

Hoffman, Moshe; Suetens, Sigrid; Gneezy, Uri; Nowak, Martin A

2015-03-06

Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium (NE), which is motivated by perfect rationality. NE specifies a strategy for everyone, such that no one would benefit by deviating unilaterally from his/her strategy. Another powerful tool available to game theorists are evolutionary dynamics (ED). Motivated by evolutionary and learning processes, ED specify changes in strategies over time in a population, such that more successful strategies typically become more frequent. A simple game that illustrates interesting ED is the generalized Rock-Paper-Scissors (RPS) game. The RPS game extends the children's game to situations where winning or losing can matter more or less relative to tying. Here we investigate experimentally three RPS games, where the NE is always to randomize with equal probability, but the evolutionary stability of this strategy changes. Consistent with the prediction of ED we find that aggregate behavior is far away from NE when it is evolutionarily unstable. Our findings add to the growing literature that demonstrates the predictive validity of ED in large-scale incentivized laboratory experiments with human subjects.

Cooperation in microbial communities and their biotechnological applications

PubMed Central

Cavaliere, Matteo; Feng, Song; Soyer, Orkun S.

2017-01-01

Summary Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross‐feeding, which can be understood in the general framework of ecological and evolutionary (eco‐evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of ‘cheating’ cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications. PMID:28447371

Niche construction theory: a practical guide for ecologists.

PubMed

Odling-Smee, John; Erwin, Douglas H; Palkovacs, Eric P; Feldman, Marcus W; Laland, Kevin N

2013-03-01

Niche construction theory (NCT) explicitly recognizes environmental modication by organisms ("niche construction") and their legacy overtime ("ecological inheritance") to be evolutionary processes in their own right. Here we illustrate how niche construction theory provides usedl conceptual tools and theoretical insights for integrating ecosystem ecology and evolutionary theory. We begin by briefly describing NCT, and illustrating how it deifers from conventional evolutionary approaches. We then distinguish between two aspects ofniche construction--environment alteration and subsequent evolution in response to constructed environments--equating the first of these with "ecosystem engineering." We describe some of the ecological and evolutionary impacts on ecosystems of niche construction, ecosystem engineering and ecological inheritance, and illustrate how these processes trigger ecological and evolutionary feedbacks and leave detectable ecological signatures that are open to investigation. FIinally, we provide a practical guide to how NCT could be deployed by ecologists and evolutionary biologists to aeplore ecoeoolutionay dynamics. We suggest that, by highlighting the ecological and evolutionay ramifications of changes that organisms bring about in ecosystems, NCT helps link ecosystem ecology to evolutionary biology, potentially leading to a deeper understanding of how ecosystems change over time.

Aspiration dynamics and the sustainability of resources in the public goods dilemma

NASA Astrophysics Data System (ADS)

Du, Jinming; Wu, Bin; Wang, Long

2016-04-01

How to exploit public non-renewable resources is a public goods dilemma. Individuals can choose to limit the depletion in order to use the resource for a longer time or consume more goods to benefit themselves. When the resource is used up, there is no benefit for the future generations any more, thus the evolutionary process ends. Here we investigate what mechanisms can extend the use of resources in the framework of evolutionary game theory under two updating rules based on imitation and aspiration, respectively. Compared with imitation process, aspiration dynamics may prolong the sustainable time of a public resource.

A SYMMETRY OF FIXATION TIMES IN EVOULTIONARY DYNAMICS

PubMed Central

TAYLOR, CHRISTINE; IWASA, YOH; NOWAK, MARTIN A.

2010-01-01

In this paper, we show that for evolutionary dynamics between two types that can be described by a Moran process, the conditional fixation time of either type is the same irrespective of the selective scenario. With frequency dependent selection between two strategies A and B of an evolutionary game, regardless of whether A dominates B, A and B are best replies to themselves, or A and B are best replies to each other, the conditional fixation times of a single A and a single B mutant are identical. This does not hold for Wright-Fisher models, nor when the mutants start from multiple copies. PMID:16890959

Learning dynamics explains human behaviour in prisoner's dilemma on networks.

PubMed

Cimini, Giulio; Sánchez, Angel

2014-05-06

Cooperative behaviour lies at the very basis of human societies, yet its evolutionary origin remains a key unsolved puzzle. Whereas reciprocity or conditional cooperation is one of the most prominent mechanisms proposed to explain the emergence of cooperation in social dilemmas, recent experimental findings on networked Prisoner's Dilemma games suggest that conditional cooperation also depends on the previous action of the player-namely on the 'mood' in which the player is currently in. Roughly, a majority of people behave as conditional cooperators if they cooperated in the past, whereas they ignore the context and free ride with high probability if they did not. However, the ultimate origin of this behaviour represents a conundrum itself. Here, we aim specifically to provide an evolutionary explanation of moody conditional cooperation (MCC). To this end, we perform an extensive analysis of different evolutionary dynamics for players' behavioural traits-ranging from standard processes used in game theory based on pay-off comparison to others that include non-economic or social factors. Our results show that only a dynamic built upon reinforcement learning is able to give rise to evolutionarily stable MCC, and at the end to reproduce the human behaviours observed in the experiments.

Evolutionary dynamics of public goods games with diverse contributions in finite populations

NASA Astrophysics Data System (ADS)

Wang, Jing; Wu, Bin; Chen, Xiaojie; Wang, Long

2010-05-01

The public goods game is a powerful metaphor for exploring the maintenance of social cooperative behavior in a group of interactional selfish players. Here we study the emergence of cooperation in the public goods games with diverse contributions in finite populations. The theory of stochastic process is innovatively adopted to investigate the evolutionary dynamics of the public goods games involving a diversity of contributions. In the limit of rare mutations, the general stationary distribution of this stochastic process can be analytically approximated by means of diffusion theory. Moreover, we demonstrate that increasing the diversity of contributions greatly reduces the probability of finding the population in a homogeneous state full of defectors. This increase also raises the expectation of the total contribution in the entire population and thus promotes social cooperation. Furthermore, by investigating the evolutionary dynamics of optional public goods games with diverse contributions, we find that nonparticipation can assist players who contribute more in resisting invasion and taking over individuals who contribute less. In addition, numerical simulations are performed to confirm our analytical results. Our results may provide insight into the effect of diverse contributions on cooperative behaviors in the real world.

Evolutionary dynamics of giant viruses and their virophages.

PubMed

Wodarz, Dominik

2013-07-01

Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested.

Evolutionary dynamics of giant viruses and their virophages

PubMed Central

Wodarz, Dominik

2013-01-01

Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested. PMID:23919155

Cognitive conflict without explicit conflict monitoring in a dynamical agent.

PubMed

Ward, Robert; Ward, Ronnie

2006-11-01

We examine mechanisms for resolving cognitive conflict in an embodied, situated, and dynamic agent, developed through an evolutionary learning process. The agent was required to solve problems of response conflict in a dual-target "catching" task, focusing response on one of the targets while ignoring the other. Conflict in the agent was revealed at the behavioral level in terms of increased latencies to the second target. This behavioral interference was correlated to peak violations of the network's stable state equation. At the level of the agent's neural network, peak violations were also correlated to periods of disagreement in source inputs to the agent's motor effectors. Despite observing conflict at these numerous levels, we did not find any explicit conflict monitoring mechanisms within the agent. We instead found evidence of a distributed conflict management system, characterized by competitive sources within the network. In contrast to the conflict monitoring hypothesis [Botvinick, M. M., Braver, T. S., Barch, D. M., Carter, C. S., & Cohen, J. D. (2001). Conflict monitoring and cognitive control. Psychological Review, 108(3), 624-652], this agent demonstrates that resolution of cognitive conflict does not require explicit conflict monitoring. We consider the implications of our results for the conflict monitoring hypothesis.

Demographic source-sink dynamics restrict local adaptation in Elliott's blueberry (Vaccinium elliottii).

PubMed

Anderson, Jill T; Geber, Monica A

2010-02-01

In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry (Vaccinium elliottii) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation.

Emergent properties of gene evolution: Species as attractors in phenotypic space

NASA Astrophysics Data System (ADS)

Reuveni, Eli; Giuliani, Alessandro

2012-02-01

The question how the observed discrete character of the phenotype emerges from a continuous genetic distance metrics is the core argument of two contrasted evolutionary theories: punctuated equilibrium (stable evolution scattered with saltations in the phenotype) and phyletic gradualism (smooth and linear evolution of the phenotype). Identifying phenotypic saltation on the molecular levels is critical to support the first model of evolution. We have used DNA sequences of ∼1300 genes from 6 isolated populations of the budding yeast Saccharomyces cerevisiae. We demonstrate that while the equivalent measure of the genetic distance show a continuum between lineage distance with no evidence of discrete states, the phenotypic space illustrates only two (discrete) possible states that can be associated with a saltation of the species phenotype. The fact that such saltation spans large fraction of the genome and follows by continuous genetic distance is a proof of the concept that the genotype-phenotype relation is not univocal and may have severe implication when looking for disease related genes and mutations. We used this finding with analogy to attractor-like dynamics and show that punctuated equilibrium could be explained in the framework of non-linear dynamics systems.

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes.

PubMed

Krajewski, C; Fain, M G; Buckley, L; King, D G

1999-11-01

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets. Copyright 1999 Academic Press.

Indirect evolutionary rescue: prey adapts, predator avoids extinction

PubMed Central

Yamamichi, Masato; Miner, Brooks E

2015-01-01

Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator–prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term ‘indirect evolutionary rescue’, has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change. PMID:26366196

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

PubMed Central

Jin, Wenfei; Wang, Sijia; Wang, Haifeng; Jin, Li; Xu, Shuhua

2012-01-01

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations. PMID:23103229

Revealing evolutionary pathways by fitness landscape reconstruction.

PubMed

Kogenaru, Manjunatha; de Vos, Marjon G J; Tans, Sander J

2009-01-01

The concept of epistasis has since long been used to denote non-additive fitness effects of genetic changes and has played a central role in understanding the evolution of biological systems. Owing to an array of novel experimental methodologies, it has become possible to experimentally determine epistatic interactions as well as more elaborate genotype-fitness maps. These data have opened up the investigation of a host of long-standing questions in evolutionary biology, such as the ruggedness of fitness landscapes and the accessibility of mutational trajectories, the evolution of sex, and the origin of robustness and modularity. Here we review this recent and timely marriage between systems biology and evolutionary biology, which holds the promise to understand evolutionary dynamics in a more mechanistic and predictive manner.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

Achieving sustainable plant disease management through evolutionary principles.

PubMed

Zhan, Jiasui; Thrall, Peter H; Burdon, Jeremy J

2014-09-01

Plants and their pathogens are engaged in continuous evolutionary battles and sustainable disease management requires novel systems to create environments conducive for short-term and long-term disease control. In this opinion article, we argue that knowledge of the fundamental factors that drive host-pathogen coevolution in wild systems can provide new insights into disease development in agriculture. Such evolutionary principles can be used to guide the formulation of sustainable disease management strategies which can minimize disease epidemics while simultaneously reducing pressure on pathogens to evolve increased infectivity and aggressiveness. To ensure agricultural sustainability, disease management programs that reflect the dynamism of pathogen population structure are essential and evolutionary biologists should play an increasing role in their design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dynamic evolution and biogenesis of small RNAs during sex reversal.

PubMed

Liu, Jie; Luo, Majing; Sheng, Yue; Hong, Qiang; Cheng, Hanhua; Zhou, Rongjia

2015-05-06

Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.

An Evolutionary Game Theory Model of Spontaneous Brain Functioning.

PubMed

Madeo, Dario; Talarico, Agostino; Pascual-Leone, Alvaro; Mocenni, Chiara; Santarnecchi, Emiliano

2017-11-22

Our brain is a complex system of interconnected regions spontaneously organized into distinct networks. The integration of information between and within these networks is a continuous process that can be observed even when the brain is at rest, i.e. not engaged in any particular task. Moreover, such spontaneous dynamics show predictive value over individual cognitive profile and constitute a potential marker in neurological and psychiatric conditions, making its understanding of fundamental importance in modern neuroscience. Here we present a theoretical and mathematical model based on an extension of evolutionary game theory on networks (EGN), able to capture brain's interregional dynamics by balancing emulative and non-emulative attitudes among brain regions. This results in the net behavior of nodes composing resting-state networks identified using functional magnetic resonance imaging (fMRI), determining their moment-to-moment level of activation and inhibition as expressed by positive and negative shifts in BOLD fMRI signal. By spontaneously generating low-frequency oscillatory behaviors, the EGN model is able to mimic functional connectivity dynamics, approximate fMRI time series on the basis of initial subset of available data, as well as simulate the impact of network lesions and provide evidence of compensation mechanisms across networks. Results suggest evolutionary game theory on networks as a new potential framework for the understanding of human brain network dynamics.

Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years.

PubMed

Haider, Md Shakir Hussain; Deeba, Farah; Khan, Wajihul Hasan; Naqvi, Irshad H; Ali, Sher; Ahmed, Anwar; Broor, Shobha; Alsenaidy, Hytham A; Alsenaidy, Abdulrahman M; Dohare, Ravins; Parveen, Shama

2018-06-01

Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011-15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10 -3 (95% HPD, 2.90-4.17 × 10 -3 ) and 3.56 × 10 -3 (95% HPD, 2.91 × 10 -3 -4.18 × 10 -3 ) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development. Copyright © 2018 Elsevier B.V. All rights reserved.

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.

PubMed

Gilpin, William; Feldman, Marcus W

2017-07-01

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.

Evolutionary disarmament in interspecific competition.

PubMed

Kisdi, E; Geritz, S A

2001-12-22

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

Evolutionary disarmament in interspecific competition.

PubMed Central

Kisdi, E.; Geritz, S. A.

2001-01-01

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races. PMID:11749715

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel

PubMed Central

Kim, Young Bun; Oh, Jung Hun; McIver, Lauren J.; Rashkovetsky, Eugenia; Michalak, Katarzyna; Garner, Harold R.; Kang, Lin; Nevo, Eviatar; Korol, Abraham B.; Michalak, Pawel

2014-01-01

Repeat sequences, especially mobile elements, make up large portions of most eukaryotic genomes and provide enormous, albeit commonly underappreciated, evolutionary potential. We analyzed repeatomes of Drosophila melanogaster that have been diverging in response to a microclimate contrast in Evolution Canyon (Mount Carmel, Israel), a natural evolutionary laboratory with two abutting slopes at an average distance of only 200 m, which pose a constant ecological challenge to their local biotas. Flies inhabiting the colder and more humid north-facing slope carried about 6% more transposable elements than those from the hot and dry south-facing slope, in parallel to a suite of other genetic and phenotypic differences between the two populations. Nearly 50% of all mobile element insertions were slope unique, with many of them disrupting coding sequences of genes critical for cognition, olfaction, and thermotolerance, consistent with the observed patterns of thermotolerance differences and assortative mating. PMID:25006263

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel.

PubMed

Kim, Young Bun; Oh, Jung Hun; McIver, Lauren J; Rashkovetsky, Eugenia; Michalak, Katarzyna; Garner, Harold R; Kang, Lin; Nevo, Eviatar; Korol, Abraham B; Michalak, Pawel

2014-07-22

Repeat sequences, especially mobile elements, make up large portions of most eukaryotic genomes and provide enormous, albeit commonly underappreciated, evolutionary potential. We analyzed repeatomes of Drosophila melanogaster that have been diverging in response to a microclimate contrast in Evolution Canyon (Mount Carmel, Israel), a natural evolutionary laboratory with two abutting slopes at an average distance of only 200 m, which pose a constant ecological challenge to their local biotas. Flies inhabiting the colder and more humid north-facing slope carried about 6% more transposable elements than those from the hot and dry south-facing slope, in parallel to a suite of other genetic and phenotypic differences between the two populations. Nearly 50% of all mobile element insertions were slope unique, with many of them disrupting coding sequences of genes critical for cognition, olfaction, and thermotolerance, consistent with the observed patterns of thermotolerance differences and assortative mating.

Evolutionary genetics of insect innate immunity.

PubMed

Viljakainen, Lumi

2015-11-01

Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. © The Author 2015. Published by Oxford University Press.

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

NASA Astrophysics Data System (ADS)

Wang, Lin; Liu, Gaozhi

2018-02-01

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

Galactic cannibalism. IV. The evidence-correlations between dynamical time scales and Bautz-Morgan type

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

McGlynn, T.A.; Ostriker, J.P.

1980-11-01

If the luminosity of supergiant cD galaxies in particular, and the Bautz-Morgan sequence of galaxy types in general, is produced by dynamical evolutionary processes, then one expects to find a correlation between dynamical times and ..delta..M/sub 12/, the magnitude difference between first and second brightest cluster members.

Methylome evolution in plants.

PubMed

Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank

2016-12-20

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.

PubMed

Kumar, Avishek; Butler, Brandon M; Kumar, Sudhir; Ozkan, S Banu

2015-12-01

Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations.

PubMed

Goitom, Eyerusalem; Kilsdonk, Laurens J; Brans, Kristien; Jansen, Mieke; Lemmens, Pieter; De Meester, Luc

2018-01-01

There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top-down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S-map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top-down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

Root foraging increases performance of the clonal plant Potentilla reptans in heterogeneous nutrient environments.

PubMed

Wang, Zhengwen; van Kleunen, Mark; During, Heinjo J; Werger, Marinus J A

2013-01-01

Plastic root-foraging responses have been widely recognized as an important strategy for plants to explore heterogeneously distributed resources. However, the benefits and costs of root foraging have received little attention. In a greenhouse experiment, we grew pairs of connected ramets of 22 genotypes of the stoloniferous plant Potentilla reptans in paired pots, between which the contrast in nutrient availability was set as null, medium and high, but with the total nutrient amount kept the same. We calculated root-foraging intensity of each individual ramet pair as the difference in root mass between paired ramets divided by the total root mass. For each genotype, we then calculated root-foraging ability as the slope of the regression of root-foraging intensity against patch contrast. For all genotypes, root-foraging intensity increased with patch contrast and the total biomass and number of offspring ramets were lowest at high patch contrast. Among genotypes, root-foraging intensity was positively related to production of offspring ramets and biomass in the high patch-contrast treatment, which indicates an evolutionary benefit of root foraging in heterogeneous environments. However, we found no significant evidence that the ability of plastic foraging imposes costs under homogeneous conditions (i.e. when foraging is not needed). Our results show that plants of P. reptans adjust their root-foraging intensity according to patch contrast. Moreover, the results show that the root foraging has an evolutionary advantage in heterogeneous environments, while costs of having the ability of plastic root foraging were absent or very small.

Topological enslavement in evolutionary games on correlated multiplex networks

NASA Astrophysics Data System (ADS)

Kleineberg, Kaj-Kolja; Helbing, Dirk

2018-05-01

Governments and enterprises strongly rely on incentives to generate favorable outcomes from social and strategic interactions between individuals. The incentives are usually modeled by payoffs in evolutionary games, such as the prisoners dilemma or the harmony game, with imitation dynamics. Adjusting the incentives by changing the payoff parameters can favor cooperation, as found in the harmony game, over defection, which prevails in the prisoner’s dilemma. Here, we show that this is not always the case if individuals engage in strategic interactions in multiple domains. In particular, we investigate evolutionary games on multiplex networks where individuals obtain an aggregate payoff. We explicitly control the strength of degree correlations between nodes in the different layers of the multiplex. We find that if the multiplex is composed of many layers and degree correlations are strong, the topology of the system enslaves the dynamics and the final outcome, cooperation or defection, becomes independent of the payoff parameters. The fate of the system is then determined by the initial conditions.

Promotion of cooperation in evolutionary game dynamics with local information.

PubMed

Liu, Xuesong; Pan, Qiuhui; He, Mingfeng

2018-01-21

In this paper, we propose a strategy-updating rule driven by local information, which is called Local process. Unlike the standard Moran process, the Local process does not require global information about the strategic environment. By analyzing the dynamical behavior of the system, we explore how the local information influences the fixation of cooperation in two-player evolutionary games. Under weak selection, the decreasing local information leads to an increase of the fixation probability when natural selection does not favor cooperation replacing defection. In the limit of sufficiently large selection, the analytical results indicate that the fixation probability increases with the decrease of the local information, irrespective of the evolutionary games. Furthermore, for the dominance of defection games under weak selection and for coexistence games, the decreasing of local information will lead to a speedup of a single cooperator taking over the population. Overall, to some extent, the local information is conducive to promoting the cooperation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses.

PubMed

Xiao, Yinghong; Dolan, Patrick Timothy; Goldstein, Elizabeth Faul; Li, Min; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

2017-08-29

RNA viruses, such as poliovirus, have a great evolutionary capacity, allowing them to quickly adapt and overcome challenges encountered during infection. Here we show that poliovirus infection in immune-competent mice requires adaptation to tissue-specific innate immune microenvironments. The ability of the virus to establish robust infection and virulence correlates with its evolutionary capacity. We further identify a region in the multi-functional poliovirus protein 2B as a hotspot for the accumulation of minor alleles that facilitate a more effective suppression of the interferon response. We propose that population genetic dynamics enables poliovirus spread between tissues through optimization of the genetic composition of low frequency variants, which together cooperate to circumvent tissue-specific challenges. Thus, intrahost virus evolution determines pathogenesis, allowing a dynamic regulation of viral functions required to overcome barriers to infection.RNA viruses, such as polioviruses, have a great evolutionary capacity and can adapt quickly during infection. Here, the authors show that poliovirus infection in mice requires adaptation to innate immune microenvironments encountered in different tissues.

Stability-based sorting: The forgotten process behind (not only) biological evolution.

PubMed

Toman, Jan; Flegr, Jaroslav

2017-12-21

Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Comet Cometh: Evolving Developmental Systems.

PubMed

Jaeger, Johannes; Laubichler, Manfred; Callebaut, Werner

In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule's prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach-which is based on reverse engineering, simulation, and mathematical analysis-the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

Strategy selection in structured populations.

PubMed

Tarnita, Corina E; Ohtsuki, Hisashi; Antal, Tibor; Fu, Feng; Nowak, Martin A

2009-08-07

Evolutionary game theory studies frequency dependent selection. The fitness of a strategy is not constant, but depends on the relative frequencies of strategies in the population. This type of evolutionary dynamics occurs in many settings of ecology, infectious disease dynamics, animal behavior and social interactions of humans. Traditionally evolutionary game dynamics are studied in well-mixed populations, where the interaction between any two individuals is equally likely. There have also been several approaches to study evolutionary games in structured populations. In this paper we present a simple result that holds for a large variety of population structures. We consider the game between two strategies, A and B, described by the payoff matrix(abcd). We study a mutation and selection process. For weak selection strategy A is favored over B if and only if sigma a+b>c+sigma d. This means the effect of population structure on strategy selection can be described by a single parameter, sigma. We present the values of sigma for various examples including the well-mixed population, games on graphs, games in phenotype space and games on sets. We give a proof for the existence of such a sigma, which holds for all population structures and update rules that have certain (natural) properties. We assume weak selection, but allow any mutation rate. We discuss the relationship between sigma and the critical benefit to cost ratio for the evolution of cooperation. The single parameter, sigma, allows us to quantify the ability of a population structure to promote the evolution of cooperation or to choose efficient equilibria in coordination games.

Reciprocity in spatial evolutionary public goods game on double-layered network

NASA Astrophysics Data System (ADS)

Kim, Jinho; Yook, Soon-Hyung; Kim, Yup

2016-08-01

Spatial evolutionary games have mainly been studied on a single, isolated network. However, in real world systems, many interaction topologies are not isolated but many different types of networks are inter-connected to each other. In this study, we investigate the spatial evolutionary public goods game (SEPGG) on double-layered random networks (DRN). Based on the mean-field type arguments and numerical simulations, we find that SEPGG on DRN shows very rich interesting phenomena, especially, depending on the size of each layer, intra-connectivity, and inter-connected couplings, the network reciprocity of SEPGG on DRN can be drastically enhanced through the inter-connected coupling. Furthermore, SEPGG on DRN can provide a more general framework which includes the evolutionary dynamics on multiplex networks and inter-connected networks at the same time.

Reciprocity in spatial evolutionary public goods game on double-layered network

PubMed Central

Kim, Jinho; Yook, Soon-Hyung; Kim, Yup

2016-01-01

Spatial evolutionary games have mainly been studied on a single, isolated network. However, in real world systems, many interaction topologies are not isolated but many different types of networks are inter-connected to each other. In this study, we investigate the spatial evolutionary public goods game (SEPGG) on double-layered random networks (DRN). Based on the mean-field type arguments and numerical simulations, we find that SEPGG on DRN shows very rich interesting phenomena, especially, depending on the size of each layer, intra-connectivity, and inter-connected couplings, the network reciprocity of SEPGG on DRN can be drastically enhanced through the inter-connected coupling. Furthermore, SEPGG on DRN can provide a more general framework which includes the evolutionary dynamics on multiplex networks and inter-connected networks at the same time. PMID:27503801

An emerging synthesis between community ecology and evolutionary biology.

PubMed

Johnson, Marc T J; Stinchcombe, John R

2007-05-01

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.

The evolution of parasite manipulation of host dispersal

PubMed Central

Lion, Sébastien; van Baalen, Minus; Wilson, William G

2006-01-01

We investigate the evolution of manipulation of host dispersal behaviour by parasites using spatially explicit individual-based simulations. We find that when dispersal is local, parasites always gain from increasing their hosts' dispersal rate, although the evolutionary outcome is determined by the costs-to-benefits ratio. However, when dispersal can be non-local, we show that parasites investing in an intermediate dispersal distance of their hosts are favoured even when the manipulation is not costly, due to the intrinsic spatial dynamics of the host–parasite interaction. Our analysis highlights the crucial importance of ecological spatial dynamics in evolutionary processes and reveals the theoretical possibility that parasites could manipulate their hosts' dispersal. PMID:16600882

Evolutionary history predicts plant defense against an invasive pest.

PubMed

Desurmont, Gaylord A; Donoghue, Michael J; Clement, Wendy L; Agrawal, Anurag A

2011-04-26

It has long been hypothesized that invasive pests may be facilitated by the evolutionary naïveté of their new hosts, but this prediction has never been examined in a phylogenetic framework. To address the hypothesis, we have been studying the invasive viburnum leaf beetle (Pyrrhalta viburni), which is decimating North American native species of Viburnum, a clade of worldwide importance as understory shrubs and ornamentals. In a phylogenetic field experiment using 16 species of Viburnum, we show that old-world Viburnum species that evolved in the presence of Pyrrhalta beetles mount a massive defensive wound response that crushes eggs of the pest insect; in contrast, naïve North American species that share no evolutionary history with Pyrrhalta beetles show a markedly lower response. This convergent continental difference in the defensive response of Viburnum spp. against insect oviposition contrasts with little difference in the quality of leaves for beetle larvae. Females show strong oviposition preferences that correspond with larval performance regardless of continental origin, which has facilitated colonization of susceptible North American species. Thus, although much attention has been paid to escape from enemies as a factor in the establishment and spread of nonnative organisms, the colonization of undefended resources seems to play a major role in the success of invasive species such as the viburnum leaf beetle.

Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

PubMed Central

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

“Trojan” is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules. PMID:25803627

Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints.

PubMed

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

PubMed

Chen, Bor-Sen; Yeh, Chin-Hsun

2017-12-01

We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

PubMed Central

Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A.; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe

2014-01-01

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation. PMID:24699231

Social monogamy vs. polyandry: ecological factors associated with sex roles in two closely related birds within the same habitat.

PubMed

Goymann, W; Makomba, M; Urasa, F; Schwabl, I

2015-07-01

Why mainly males compete and females take a larger share in parental care remains an exciting question in evolutionary biology. Role-reversed species are of particular interest, because such 'exceptions' help to test the rule. Using mating systems theory as a framework, we compared the reproductive ecology of the two most contrasting coucals with regard to sexual dimorphism and parental care: the black coucal with male-only care and the biparental white-browed coucal. Both species occur in the same lush habitat and face similar ecological conditions, but drastically differ in mating system and sexual dimorphism. Black coucals were migratory and occurred at high breeding densities. With females being obligatory polyandrous and almost twice as heavy as males, black coucals belong to the most extreme vertebrates with reversed sexual dimorphism. Higher variance in reproductive success in fiercely competing females suggests that sexual selection is stronger in females than in males. In contrast, resident white-browed coucals bred at low densities and invariably in pairs. They were almost monomorphic and the variance in reproductive success was similar between the sexes. Black coucals were more likely to lose nests than white-browed coucals, probably facilitating female emancipation of parental care in black coucals. We propose that a combination of high food abundance, high population density, high degree of nest loss and male bias in the adult sex ratio represent ecological conditions that facilitate role reversal and polyandry in coucals and terrestrial vertebrates in general. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

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

Makarov, Pavel V., E-mail: pvm@ispms.tsc.ru

An evolutionary approach to earthquake development is proposed. A medium under loading is treated as a multiscale nonlinear dynamic system. Its failure involves a number of stages typical of any dynamic system: dynamic chaos, self-organized criticality, and global stability loss in the final stage of its evolution. In the latter stage, the system evolves in a blow-up mode accompanied by catastrophic superfast movements of the elements of this geomedium.

Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect.

PubMed

Borregaard, Michael K; Amorim, Isabel R; Borges, Paulo A V; Cabral, Juliano S; Fernández-Palacios, José M; Field, Richard; Heaney, Lawrence R; Kreft, Holger; Matthews, Thomas J; Olesen, Jens M; Price, Jonathan; Rigal, Francois; Steinbauer, Manuel J; Triantis, Konstantinos A; Valente, Luis; Weigelt, Patrick; Whittaker, Robert J

2017-05-01

The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space-for-time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non-native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research. © 2016 Cambridge Philosophical Society.

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamic fractals in spatial evolutionary games

NASA Astrophysics Data System (ADS)

Kolotev, Sergei; Malyutin, Aleksandr; Burovski, Evgeni; Krashakov, Sergei; Shchur, Lev

2018-06-01

We investigate critical properties of a spatial evolutionary game based on the Prisoner's Dilemma. Simulations demonstrate a jump in the component densities accompanied by drastic changes in average sizes of the component clusters. We argue that the cluster boundary is a random fractal. Our simulations are consistent with the fractal dimension of the boundary being equal to 2, and the cluster boundaries are hence asymptotically space filling as the system size increases.

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.

The experimental evolution of herbicide resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides.

PubMed

Vogwill, T; Lagator, M; Colegrave, N; Neve, P

2012-10-01

Pleiotropic fitness trade-offs will be key determinants of the evolutionary dynamics of selection for pesticide resistance. However, for herbicide resistance, empirical support for a fitness cost of resistance is mixed, and it is therefore also questionable what further ecological trade-offs can be assumed to apply to herbicide resistance. Here, we test the existence of trade-offs by experimentally evolving herbicide resistance in Chlamydomonas reinhardtii. Although fitness costs are detected for all herbicides, we find that, counterintuitively, the most resistant populations also have the lowest fitness costs as measured by growth rate in the ancestral environment. Furthermore, after controlling for differences in the evolutionary dynamics of resistance to different herbicides, we also detect significant positive correlations between resistance, fitness in the ancestral environment and cross-resistance to other herbicides. We attribute this to the highest levels of nontarget-site resistance being achieved by fixing mutations that more broadly affect cellular physiology, which results in both more cross-resistance and less overall antagonistic pleiotropy on maximum growth rate. Consequently, the lack of classical ecological trade-offs could present a major challenge for herbicide resistance management. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Cis-regulatory Evolution of Chalcone-Synthase Expression in the Genus Arabidopsis

PubMed Central

de Meaux, Juliette; Pop, A.; Mitchell-Olds, T.

2006-01-01

The contribution of cis-regulation to adaptive evolutionary change is believed to be essential, yet little is known about the evolutionary rules that govern regulatory sequences. Here, we characterize the short-term evolutionary dynamics of a cis-regulatory region within and among two closely related species, A. lyrata and A. halleri, and compare our findings to A. thaliana. We focused on the cis-regulatory region of chalcone synthase (CHS), a key enzyme involved in the synthesis of plant secondary metabolites. We observed patterns of nucleotide diversity that differ among species but do not depart from neutral expectations. Using intra- and interspecific F1 progeny, we have evaluated functional cis-regulatory variation in response to light and herbivory, environmental cues, which are known to induce CHS expression. We find that substantial cis-regulatory variation segregates within and among populations as well as between species, some of which results from interspecific genetic introgression. We further demonstrate that, in A. thaliana, CHS cis-regulation in response to herbivory is greater than in A. lyrata or A. halleri. Our work indicates that the evolutionary dynamics of a cis-regulatory region is characterized by pervasive functional variation, achieved mostly by modification of response modules to one but not all environmental cues. Our study did not detect the footprint of selection on this variation. PMID:17028316

Stochastic evolutionary voluntary public goods game with punishment in a Quasi-birth-and-death process.

PubMed

Quan, Ji; Liu, Wei; Chu, Yuqing; Wang, Xianjia

2017-11-23

Traditional replication dynamic model and the corresponding concept of evolutionary stable strategy (ESS) only takes into account whether the system can return to the equilibrium after being subjected to a small disturbance. In the real world, due to continuous noise, the ESS of the system may not be stochastically stable. In this paper, a model of voluntary public goods game with punishment is studied in a stochastic situation. Unlike the existing model, we describe the evolutionary process of strategies in the population as a generalized quasi-birth-and-death process. And we investigate the stochastic stable equilibrium (SSE) instead. By numerical experiments, we get all possible SSEs of the system for any combination of parameters, and investigate the influence of parameters on the probabilities of the system to select different equilibriums. It is found that in the stochastic situation, the introduction of the punishment and non-participation strategies can change the evolutionary dynamics of the system and equilibrium of the game. There is a large range of parameters that the system selects the cooperative states as its SSE with a high probability. This result provides us an insight and control method for the evolution of cooperation in the public goods game in stochastic situations.

Between “design” and “bricolage”: Genetic networks, levels of selection, and adaptive evolution

PubMed Central

Wilkins, Adam S.

2007-01-01

The extent to which “developmental constraints” in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a “network perspective” may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed. PMID:17494754

Between "design" and "bricolage": genetic networks, levels of selection, and adaptive evolution.

PubMed

Wilkins, Adam S

2007-05-15

The extent to which "developmental constraints" in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a "network perspective" may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed.

Role-separating ordering in social dilemmas controlled by topological frustration

NASA Astrophysics Data System (ADS)

Amaral, Marco A.; Perc, Matjaž; Wardil, Lucas; Szolnoki, Attila; da Silva Júnior, Elton J.; da Silva, Jafferson K. L.

2017-03-01

``Three is a crowd" is an old proverb that applies as much to social interactions as it does to frustrated configurations in statistical physics models. Accordingly, social relations within a triangle deserve special attention. With this motivation, we explore the impact of topological frustration on the evolutionary dynamics of the snowdrift game on a triangular lattice. This topology provides an irreconcilable frustration, which prevents anticoordination of competing strategies that would be needed for an optimal outcome of the game. By using different strategy updating protocols, we observe complex spatial patterns in dependence on payoff values that are reminiscent to a honeycomb-like organization, which helps to minimize the negative consequence of the topological frustration. We relate the emergence of these patterns to the microscopic dynamics of the evolutionary process, both by means of mean-field approximations and Monte Carlo simulations. For comparison, we also consider the same evolutionary dynamics on the square lattice, where of course the topological frustration is absent. However, with the deletion of diagonal links of the triangular lattice, we can gradually bridge the gap to the square lattice. Interestingly, in this case the level of cooperation in the system is a direct indicator of the level of topological frustration, thus providing a method to determine frustration levels in an arbitrary interaction network.

A crucial step toward realism: responses to climate change from an evolving metacommunity perspective.

PubMed

Urban, Mark C; De Meester, Luc; Vellend, Mark; Stoks, Robby; Vanoverbeke, Joost

2012-02-01

We need to understand joint ecological and evolutionary responses to climate change to predict future threats to biological diversity. The 'evolving metacommunity' framework emphasizes that interactions between ecological and evolutionary mechanisms at both local and regional scales will drive community dynamics during climate change. Theory suggests that ecological and evolutionary dynamics often interact to produce outcomes different from those predicted based on either mechanism alone. We highlight two of these dynamics: (i) species interactions prevent adaptation of nonresident species to new niches and (ii) resident species adapt to changing climates and thereby prevent colonization by nonresident species. The rate of environmental change, level of genetic variation, source-sink structure, and dispersal rates mediate between these potential outcomes. Future models should evaluate multiple species, species interactions other than competition, and multiple traits. Future experiments should manipulate factors such as genetic variation and dispersal to determine their joint effects on responses to climate change. Currently, we know much more about how climates will change across the globe than about how species will respond to these changes despite the profound effects these changes will have on global biological diversity. Integrating evolving metacommunity perspectives into climate change biology should produce more accurate predictions about future changes to species distributions and extinction threats.

Evolutionary Dynamics of Fearfulness and Boldness: A Stochastic Simulation Model

PubMed Central

Lu, Nan; Ji, Ting; Zhang, Jia-Hua; Sun, Yue-Hua; Tao, Yi

2012-01-01

A stochastic simulation model is investigated for the evolution of anti-predator behavior in birds. The main goal is to reveal the effects of population size, predation threats, and energy lost per escape on the evolutionary dynamics of fearfulness and boldness. Two pure strategies, fearfulness and boldness, are assumed to have different responses for the predator attacks and nonlethal disturbance. On the other hand, the co-existence mechanism of fearfulness and boldness is also considered. For the effects of total population size, predation threats, and energy lost per escape, our main results show that: (i) the fearful (bold) individuals will be favored in a small (large) population, i.e. in a small (large) population, the fearfulness (boldness) can be considered to be an ESS; (ii) in a population with moderate size, fearfulness would be favored under moderate predator attacks; and (iii) although the total population size is the most important factor for the evolutionary dynamics of both fearful and bold individuals, the small energy lost per escape enables the fearful individuals to have the ability to win the advantage even in a relatively large population. Finally, we show also that the co-existence of fearful and bold individuals is possible when the competitive interactions between individuals are introduced. PMID:22412859

Evolutionary dynamics of fearfulness and boldness: a stochastic simulation model.

PubMed

Lu, Nan; Ji, Ting; Zhang, Jia-Hua; Sun, Yue-Hua; Tao, Yi

2012-01-01

A stochastic simulation model is investigated for the evolution of anti-predator behavior in birds. The main goal is to reveal the effects of population size, predation threats, and energy lost per escape on the evolutionary dynamics of fearfulness and boldness. Two pure strategies, fearfulness and boldness, are assumed to have different responses for the predator attacks and nonlethal disturbance. On the other hand, the co-existence mechanism of fearfulness and boldness is also considered. For the effects of total population size, predation threats, and energy lost per escape, our main results show that: (i) the fearful (bold) individuals will be favored in a small (large) population, i.e. in a small (large) population, the fearfulness (boldness) can be considered to be an ESS; (ii) in a population with moderate size, fearfulness would be favored under moderate predator attacks; and (iii) although the total population size is the most important factor for the evolutionary dynamics of both fearful and bold individuals, the small energy lost per escape enables the fearful individuals to have the ability to win the advantage even in a relatively large population. Finally, we show also that the co-existence of fearful and bold individuals is possible when the competitive interactions between individuals are introduced.

A crucial step toward realism: responses to climate change from an evolving metacommunity perspective

PubMed Central

Urban, Mark C; De Meester, Luc; Vellend, Mark; Stoks, Robby; Vanoverbeke, Joost

2012-01-01

We need to understand joint ecological and evolutionary responses to climate change to predict future threats to biological diversity. The ‘evolving metacommunity’ framework emphasizes that interactions between ecological and evolutionary mechanisms at both local and regional scales will drive community dynamics during climate change. Theory suggests that ecological and evolutionary dynamics often interact to produce outcomes different from those predicted based on either mechanism alone. We highlight two of these dynamics: (i) species interactions prevent adaptation of nonresident species to new niches and (ii) resident species adapt to changing climates and thereby prevent colonization by nonresident species. The rate of environmental change, level of genetic variation, source-sink structure, and dispersal rates mediate between these potential outcomes. Future models should evaluate multiple species, species interactions other than competition, and multiple traits. Future experiments should manipulate factors such as genetic variation and dispersal to determine their joint effects on responses to climate change. Currently, we know much more about how climates will change across the globe than about how species will respond to these changes despite the profound effects these changes will have on global biological diversity. Integrating evolving metacommunity perspectives into climate change biology should produce more accurate predictions about future changes to species distributions and extinction threats. PMID:25568038

Evolutionary history of Pacific salmon in dynamic environments

PubMed Central

Waples, Robin S; Pess, George R; Beechie, Tim

2008-01-01

Contemporary evolution of Pacific salmon (Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forged during recurrent episodes of Pleistocene glaciation. In northwestern North America, dominant habitat features have been relatively stable for the past 5000 years, but salmon ecosystems remain dynamic because of disturbance regimes (volcanic eruptions, landslides, wildfires, floods, variations in marine and freshwater productivity) that occur on a variety of temporal and spatial scales. These disturbances both create selective pressures for adaptive responses by salmon and inhibit long-term divergence by periodically extirpating local populations and creating episodic dispersal events that erode emerging differences. Recent anthropogenic changes are replicated pervasively across the landscape and interrupt processes that allow natural habitat recovery. If anthropogenic changes can be shaped to produce disturbance regimes that more closely mimic (in both space and time) those under which the species evolved, Pacific salmon should be well-equipped to deal with future challenges, just as they have throughout their evolutionary history. PMID:25567626

Role-separating ordering in social dilemmas controlled by topological frustration.

PubMed

Amaral, Marco A; Perc, Matjaž; Wardil, Lucas; Szolnoki, Attila; da Silva Júnior, Elton J; da Silva, Jafferson K L

2017-03-01

''Three is a crowd" is an old proverb that applies as much to social interactions as it does to frustrated configurations in statistical physics models. Accordingly, social relations within a triangle deserve special attention. With this motivation, we explore the impact of topological frustration on the evolutionary dynamics of the snowdrift game on a triangular lattice. This topology provides an irreconcilable frustration, which prevents anticoordination of competing strategies that would be needed for an optimal outcome of the game. By using different strategy updating protocols, we observe complex spatial patterns in dependence on payoff values that are reminiscent to a honeycomb-like organization, which helps to minimize the negative consequence of the topological frustration. We relate the emergence of these patterns to the microscopic dynamics of the evolutionary process, both by means of mean-field approximations and Monte Carlo simulations. For comparison, we also consider the same evolutionary dynamics on the square lattice, where of course the topological frustration is absent. However, with the deletion of diagonal links of the triangular lattice, we can gradually bridge the gap to the square lattice. Interestingly, in this case the level of cooperation in the system is a direct indicator of the level of topological frustration, thus providing a method to determine frustration levels in an arbitrary interaction network.

Evolutionary dynamics of incubation periods

PubMed Central

Ottino-Loffler, Bertrand; Scott, Jacob G

2017-01-01

The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease. PMID:29266000

Evolutionary dynamics of incubation periods.

PubMed

Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H

2017-12-21

The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.

Stability of Mixed-Strategy-Based Iterative Logit Quantal Response Dynamics in Game Theory

PubMed Central

Zhuang, Qian; Di, Zengru; Wu, Jinshan

2014-01-01

Using the Logit quantal response form as the response function in each step, the original definition of static quantal response equilibrium (QRE) is extended into an iterative evolution process. QREs remain as the fixed points of the dynamic process. However, depending on whether such fixed points are the long-term solutions of the dynamic process, they can be classified into stable (SQREs) and unstable (USQREs) equilibriums. This extension resembles the extension from static Nash equilibriums (NEs) to evolutionary stable solutions in the framework of evolutionary game theory. The relation between SQREs and other solution concepts of games, including NEs and QREs, is discussed. Using experimental data from other published papers, we perform a preliminary comparison between SQREs, NEs, QREs and the observed behavioral outcomes of those experiments. For certain games, we determine that SQREs have better predictive power than QREs and NEs. PMID:25157502

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

PubMed

Shanahan, Timothy

2008-03-01

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

Importance of tie strengths in the prisoner's dilemma game on social networks

NASA Astrophysics Data System (ADS)

Xu, Bo; Liu, Lu; You, Weijia

2011-06-01

Though numerous researches have shown that tie strengths play a key role in the formation of collective behavior in social networks, little work has been done to explore their impact on the outcome of evolutionary games. In this Letter, we studied the effect of tie strength in the dynamics of evolutionary prisoner's dilemma games by using online social network datasets. The results show that the fraction of cooperators has a non-trivial dependence on tie strength. Weak ties, just like previous researches on epidemics and information diffusion have shown, play a key role by the maintenance of cooperators in evolutionary prisoner's dilemma games.

Langley's CSI evolutionary model: Phase O

NASA Technical Reports Server (NTRS)

Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.

1991-01-01

A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.

Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

PubMed

Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

2016-01-01

In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

Dynamic tests on the NASA Langley CSI evolutionary model

NASA Technical Reports Server (NTRS)

Troidl, H.; Elliott, K. B.

1993-01-01

A modal analysis study, representing one of the anticipated 'Cooperative Spacecraft Structural Dynamics Experiments on the NASA Langley CSI Evolutionary Model', was carried out as a sub-task under the NASA/DLR collaboration in dynamics and control of large space systems. The CSI evolutionary testbed (CEM) is designed for the development of Controls-Structures Interaction (CSI) technology to improve space science platform pointing. For orbiting space structures like large flexible trusses, new identification challenges arise due to their specific dynamic characteristics (low frequencies and high modal density) on the one hand, and the limited possibilities of exciting such structures and measuring their responses on orbit on the other. The main objective was to investigate the modal identification potential of several different types of forcing functions that could possibly be realized with on-board excitation equipment using a minimum number of exciter locations as well as response locations. These locations were defined in an analytical test prediction process used to study the implications of measuring and analyzing the responses thus produced. It turned out that broadband excitation is needed for a general modal survey, but if only certain modes are of particular interest, combinations of exponentially decaying sine functions provide favorable excitation conditions as they allow to concentrate the available energy on the modes being of special interest. From a practical point-of-view structural nonlinearities as well as noisy measurements make the analysis more difficult, especially in the low frequency range and when the modes are closely spaced.

A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape

PubMed Central

2017-01-01

In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the “edge of chaos” while creating a wide distribution of opportunities for speciation during epochs of disruptive selection—a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies. PMID:28678792

Evolutionary Preference/Utility Functions: A Dynamic Perspective

ERIC Educational Resources Information Center

DeSarbo, Wayne S.; Fong, Duncan K. H.; Liechty, John; Coupland, Jennifer Chang

2005-01-01

The collection of repeated measures in psychological research is one of the most common data collection formats employed in survey and experimental research. The behavioral decision theory literature documents the existence of the dynamic evolution of preferences that occur over time and experience due to learning, exposure to additional…

Elucidation of molecular dynamics of invasive species of rice

USDA-ARS?s Scientific Manuscript database

Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

PubMed

Steinacher, Arno; Bates, Declan G; Akman, Ozgur E; Soyer, Orkun S

2016-01-01

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

PubMed

Vlachostergios, Panagiotis J; Faltas, Bishoy M

2018-05-02

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

Evolutionary characterization of the West Nile Virus complete genome.

PubMed

Gray, R R; Veras, N M C; Santos, L A; Salemi, M

2010-07-01

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. Copyright 2010 Elsevier Inc. All rights reserved.

The replicator equation and other game dynamics

PubMed Central

Cressman, Ross; Tao, Yi

2014-01-01

The replicator equation is the first and most important game dynamics studied in connection with evolutionary game theory. It was originally developed for symmetric games with finitely many strategies. Properties of these dynamics are briefly summarized for this case, including the convergence to and stability of the Nash equilibria and evolutionarily stable strategies. The theory is then extended to other game dynamics for symmetric games (e.g., the best response dynamics and adaptive dynamics) and illustrated by examples taken from the literature. It is also extended to multiplayer, population, and asymmetric games. PMID:25024202

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

Parada, Javiera; Richer, Harvey; Heyl, Jeremy

Blue stragglers (BSS) are stars whose position in the color–magnitude diagram (CMD) places them above the main sequence (MS) turn-off (TO) point of a star cluster. Using data from the core of 47 Tuc in the ultraviolet (UV), we have identified various stellar populations in the CMD, and used their radial distributions to study the evolution and origin of BSS, and obtain a dynamical estimate of the mass of BSS systems. When we separate the BSS into two samples by their magnitude, we find that the bright BSS show a much more centrally concentrated radial distribution and thus higher massmore » estimate (over twice the TO mass for these BSS systems), suggesting an origin involving triple or multiple stellar systems. In contrast, the faint BSS are less concentrated, with a radial distribution similar to the MS binaries, pointing to the MS binaries as the likely progenitors of these BSS. Putting our data together with available photometric data in the visible and using MESA evolutionary models, we calculate the expected number of stars in each evolutionary stage for the normal evolution of stars and the number of stars coming from the evolution of BSS. The results indicate that BSS have a post-MS evolution comparable to that of a normal star of the same mass and a MS BSS lifetime of about 200–300 Myr. We also find that the excess population of asymptotic giant branch stars in 47 Tuc is due to evolved BSS.« less

[Sexual attraction: a concept analysis using an evolutionary perspective].

PubMed

Yang, Shu-Chin; Chu, Chun-Hong; Lu, Zxy-Yann Jane

2015-02-01

Medical technology has transformed the body image of women and altered perceptions of beauty and sexual attraction. While "sexual attraction" is a fundamental concept in sexology, the characteristics of this concept have not been studied in the field of nursing. Because nurses provide advice and health education for women, it is essential to clarify the concept of sexual attraction for the benefit of related nursing research and for the further development of nursing knowledge. This study explores the concept of sexual attraction in a Taiwanese social context using concept analysis based on an evolutionary perspective. Inductive inquiry is used to compare and contrast articles from the academic literature, magazines, and newspapers, and data from participant observation and interviews are used to generate exemplars. The process by which the concept of sexual attraction has evolved over time is captured from three distinct aspects: significance, use, and application. The definitional statement of sexual attraction includes the five dimensions of: 1. sexual-oriented psychological dynamics; 2. personal aesthetics and sensory experience; 3. instinct body forces; 4. body language of self; and 5. social and cultural norms. This study scrutinized the changes in attributes that emphasize the biological, objectified body, and stereotyped gender roles of women. Further directions for research and nursing knowledge development are suggested. Examples include identifying the changes in the concept of sexual attraction that result from technological advancement and further clarifying the experiential knowledge of sexual attraction that represents the selfhood and independence of women in Taiwan.

Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity.

PubMed

de Bruyn, Mark; Stelbrink, Björn; Morley, Robert J; Hall, Robert; Carvalho, Gary R; Cannon, Charles H; van den Bergh, Gerrit; Meijaard, Erik; Metcalfe, Ian; Boitani, Luigi; Maiorano, Luigi; Shoup, Robert; von Rintelen, Thomas

2014-11-01

Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

On the Dynamics of Small-Scale Solar Magnetic Elements

NASA Technical Reports Server (NTRS)

Berger, T. E.; Title, A. M.

1996-01-01

We report on the dynamics of the small-scale solar magnetic field, based on analysis of very high resolution images of the solar photosphere obtained at the Swedish Vacuum Solar Telescope. The data sets are movies from 1 to 4 hr in length, taken in several wavelength bands with a typical time between frames of 20 s. The primary method of tracking small-scale magnetic elements is with very high contrast images of photospheric bright points, taken through a 12 A bandpass filter centered at 4305 A in the Fraunhofer 'G band.' Previous studies have established that such bright points are unambiguously associated with sites of small-scale magnetic flux in the photosphere, although the details of the mechanism responsible for the brightening of the flux elements remain uncertain. The G band bright points move in the intergranular lanes at speeds from 0.5 to 5 km/s. The motions appear to be constrained to the intergranular lanes and are primarily driven by the evolution of the local granular convection flow field. Continual fragmentation and merging of flux is the fundamental evolutionary mode of small-scale magnetic structures in the solar photosphere. Rotation and folding of chains or groups of bright points are also observed. The timescale for magnetic flux evolution in active region plage is on the order of the correlation time of granulation (typically 6-8 minutes), but significant morphological changes can occur on timescales as short as 100 S. Smaller fragments are occasionally seen to fade beyond observable contrast. The concept of a stable, isolated subarcsecond magnetic 'flux tube' in the solar photosphere is inconsistent with the observations presented here.

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

PubMed Central

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

2016-01-01

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments. PMID:26824236

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

PubMed

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

2016-01-01

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

Co-Evolution of Opinion and Strategy in Persuasion Dynamics:. AN Evolutionary Game Theoretical Approach

NASA Astrophysics Data System (ADS)

Ding, Fei; Liu, Yun; Li, Yong

In this paper, a new model of opinion formation within the framework of evolutionary game theory is presented. The model simulates strategic situations when people are in opinion discussion. Heterogeneous agents adjust their behaviors to the environment during discussions, and their interacting strategies evolve together with opinions. In the proposed game, we take into account payoff discount to join a discussion, and the situation that people might drop out of an unpromising game. Analytical and emulational results show that evolution of opinion and strategy always tend to converge, with utility threshold, memory length, and decision uncertainty parameters influencing the convergence time. The model displays different dynamical regimes when we set differently the rule when people are at a loss in strategy.

Fast stochastic algorithm for simulating evolutionary population dynamics

NASA Astrophysics Data System (ADS)

Tsimring, Lev; Hasty, Jeff; Mather, William

2012-02-01

Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

Multiobjective optimization of temporal processes.

PubMed

Song, Zhe; Kusiak, Andrew

2010-06-01

This paper presents a dynamic predictive-optimization framework of a nonlinear temporal process. Data-mining (DM) and evolutionary strategy algorithms are integrated in the framework for solving the optimization model. DM algorithms learn dynamic equations from the process data. An evolutionary strategy algorithm is then applied to solve the optimization problem guided by the knowledge extracted by the DM algorithm. The concept presented in this paper is illustrated with the data from a power plant, where the goal is to maximize the boiler efficiency and minimize the limestone consumption. This multiobjective optimization problem can be either transformed into a single-objective optimization problem through preference aggregation approaches or into a Pareto-optimal optimization problem. The computational results have shown the effectiveness of the proposed optimization framework.

Effects of in situ climate warming on monarch caterpillar (Danaus plexippus) development.

PubMed

Lemoine, Nathan P; Capdevielle, Jillian N; Parker, John D

2015-01-01

Climate warming will fundamentally alter basic life history strategies of many ectothermic insects. In the lab, rising temperatures increase growth rates of lepidopteran larvae but also reduce final pupal mass and increase mortality. Using in situ field warming experiments on their natural host plants, we assessed the impact of climate warming on development of monarch (Danaus plexippus) larvae. Monarchs were reared on Asclepias tuberosa grown under 'Ambient' and 'Warmed' conditions. We quantified time to pupation, final pupal mass, and survivorship. Warming significantly decreased time to pupation, such that an increase of 1 °C corresponded to a 0.5 day decrease in pupation time. In contrast, survivorship and pupal mass were not affected by warming. Our results indicate that climate warming will speed the developmental rate of monarchs, influencing their ecological and evolutionary dynamics. However, the effects of climate warming on larval development in other monarch populations and at different times of year should be investigated.

Adaptation as process: the future of Darwinism and the legacy of Theodosius Dobzhansky.

PubMed

Depew, David J

2011-03-01

Conceptions of adaptation have varied in the history of genetic Darwinism depending on whether what is taken to be focal is the process of adaptation, adapted states of populations, or discrete adaptations in individual organisms. I argue that Theodosius Dobzhansky's view of adaptation as a dynamical process contrasts with so-called "adaptationist" views of natural selection figured as "design-without-a-designer" of relatively discrete, enumerable adaptations. Correlated with these respectively process and product oriented approaches to adaptive natural selection are divergent pictures of organisms themselves as developmental wholes or as "bundles" of adaptations. While even process versions of genetical Darwinism are insufficiently sensitive to the fact much of the variation on which adaptive selection works consists of changes in the timing, rate, or location of ontogenetic events, I argue that articulations of the Modern Synthesis influenced by Dobzhansky are more easily reconciled with the recent shift to evolutionary developmentalism than are versions that make discrete adaptations central. Copyright © 2010 Elsevier Ltd. All rights reserved.

Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity

PubMed Central

Bhattacharyya, Sanchari; Bershtein, Shimon; Yan, Jin; Argun, Tijda; Gilson, Amy I; Trauger, Sunia A; Shakhnovich, Eugene I

2016-01-01

Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization – molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between ‘E. coli’s self’ and ‘foreign’ proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness. DOI: http://dx.doi.org/10.7554/eLife.20309.001 PMID:27938662

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

PubMed

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G; Helland, Aslaug; Rye, Inga H; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-02-13

Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and posttreatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of cellular diversity for genetic and phenotypic features

PubMed Central

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; Rye, Inga H.; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L.; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-01-01

SUMMARY Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor subtype-specific and it did not change during treatment in tumors with partial or no response. However, lower pre-treatment genetic diversity was significantly associated with complete pathologic response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. PMID:24462293

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity

DOE PAGES

Almendro, Vanessa; Cheng, Yu -Kang; Randles, Amanda; ...

2014-02-01

Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatialmore » distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.« less

Bayesian inference of a historical bottleneck in a heavily exploited marine mammal.

PubMed

Hoffman, J I; Grant, S M; Forcada, J; Phillips, C D

2011-10-01

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology. © 2011 Blackwell Publishing Ltd.

[Static and dynamic contrast sensitivity of myopic eyes before and after laser in situ keratomileusis].

PubMed

Liu, Xiao-wei; Pang, Guo-xiang; Liu, Xi-pu; Jiang, Ru-xin; Jin, Yu-mei; Sun, Yu-min; Wang, Zhong-hai

2003-10-01

To evaluate the static and dynamic contrast sensitivity changes in myopic patients before and after laser in situ keratomileusis (LASIK). Seventy-three eyes in 37 patients with myopia (with or without astigmatism) who received LASIK were tested for static and dynamic contrast sensitivities using the METRO VISION MON ELEC I system at 0.7, 1.4, 2.7, 5.5, 11, and 22 cpd and cps prior to LASIK, and at one-, three-, and six-month intervals after LASIK. All eyes gained naked visual acuity of more than 0.5 after LASIK. The contrast sensitivity was depressed at all frequencies 1 month after LASIK, as compared to one week prior to LASIK. The depression at 2.7, 5.5, 11 (P < 0.01) and 22 cpd (P < 0.05) was statistically significant for static contrast sensitivity, and also at 5.5 (P < 0.01) and 11 cps (P < 0.05) for dynamic contrast sensitivity. Myopic eyes between 6.25 D and 14.0 D, and astigmatic eyes 2 DC and more, suffered more static and dynamic contrast sensitivity depression than the myopic eyes between 1.25 D and 6.00 D and astigmatic eyes less than 2 DC. Contrast sensitivities were improved and exceeded preoperative levels 3 months after LASIK, and improved even more 6 months after LASIK. All sequences were statistically significant for static contrast sensitivity (P < 0.01), while only 2.7, 5.5, and 11 cps were statistically significant for dynamic contrast sensitivity (P < 0.01). The astigmatic eyes 2 DC and more showed less improvement, even below the preoperative level at 1.4 cps of dynamic contrast sensitivity. While temporary depression of contrast sensitivity for myopic eyes after LASIK was seen, contrast sensitivity soon returned to exceed preoperative levels at 3 months after LASIK, while improving even more 6 months after LASIK.

Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes

PubMed Central

Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

2016-01-01

Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success. PMID:26784357

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

PubMed Central

Vanneste, Kevin; Baele, Guy; Maere, Steven; Van de Peer, Yves

2014-01-01

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids. PMID:24835588

Ecology of hemiepiphytism in fig species is based on evolutionary correlation of hydraulics and carbon economy.

PubMed

Hao, Guang-You; Goldstein, Guillermo; Sack, Lawren; Holbrook, N Michele; Liu, Zhi-Hui; Wang, Ai-Ying; Harrison, Rhett D; Su, Zhi-Hui; Cao, Kun-Fang

2011-11-01

Woody hemiepiphytic species (Hs) are important components of tropical rain forests, and they have been hypothesized to differ from non-hemiepiphytic tree species (NHs) in adaptations relating to water relations and carbon economy; but few studies have been conducted comparing ecophysiological traits between the two growth forms especially in an evolutionary context. Using common-garden plants of the genus Ficus, functional traits related to plant hydraulics and carbon economy were compared for seven NHs and seven Hs in their adult terrestrial "tree-like" growth phase. We used phylogenetically independent contrasts to test the hypothesis that differences in water availability selected for contrasting suites of traits in Hs and NHs, driving evolutionary correlations among functional traits including hydraulic conductivity and photosynthetic traits. Species of the two growth forms differed in functional traits; Hs had substantially lower xylem hydraulic conductivity and stomatal conductance, and higher instantaneous photosynthetic water use efficiency. Leaf morphological and structural traits also differed strikingly between the two growth forms. The Hs had significantly smaller leaves, higher leaf mass per area (LMA), and smaller xylem vessel lumen diameters. Across all the species, hydraulic conductivity was positively correlated with leaf gas exchange indicating high degrees of hydraulic-photosynthetic coordination. More importantly, these correlations were supported by correlations implemented on phylogenetic independent contrasts, suggesting that most trait correlations arose through repeated convergent evolution rather than as a result of chance events in the deep nodes of the lineage. Vatiation in xylem hydraulic conductivity was also centrally associated with a suite of other functional traits related to carbon economy and growth, such as LMA, water use efficiency, leaf nutrient concentration, and photosynthetic nutrient use efficiency, indicating important physiological constraints or trade-offs among functional traits. Shifts in this trait cluster apparently related to the adaptation to drought-prone canopy growth during the early life cycle of Hs and clearly affected ecophysiology of the later terrestrial stage of these species. Evolutionary flexibility in hydraulics and associated traits might be one basis for the hyper-diversification of Ficus species in tropical rain forests.

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

PubMed

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

The role of biotic forces in driving macroevolution: beyond the Red Queen

PubMed Central

Voje, Kjetil L.; Holen, Øistein H.; Liow, Lee Hsiang; Stenseth, Nils Chr.

2015-01-01

A multitude of hypotheses claim that abiotic factors are the main drivers of macroevolutionary change. By contrast, Van Valen's Red Queen hypothesis is often put forward as the sole representative of the view that biotic forcing is the main evolutionary driver. This imbalance of hypotheses does not reflect our current knowledge: theoretical work demonstrates the plausibility of biotically driven long-term evolution, whereas empirical work suggests a central role for biotic forcing in macroevolution. We call for a more pluralistic view of how biotic forces may drive long-term evolution that is compatible with both phenotypic stasis in the fossil record and with non-constant extinction rates. Promising avenues of research include contrasting predictions from relevant theories within ecology and macroevolution, as well as embracing both abiotic and biotic proxies while modelling long-term evolutionary data. By fitting models describing hypotheses of biotically driven macroevolution to data, we could dissect their predictions and transcend beyond pattern description, possibly narrowing the divide between our current understanding of micro- and macroevolution. PMID:25948685

Metabolism in Fungal Pathogenesis

PubMed Central

Ene, Iuliana V.; Brunke, Sascha; Brown, Alistair J.P.; Hube, Bernhard

2014-01-01

Fungal pathogens must assimilate local nutrients to establish an infection in their mammalian host. We focus on carbon, nitrogen, and micronutrient assimilation mechanisms, discussing how these influence host–fungus interactions during infection. We highlight several emerging trends based on the available data. First, the perturbation of carbon, nitrogen, or micronutrient assimilation attenuates fungal pathogenicity. Second, the contrasting evolutionary pressures exerted on facultative versus obligatory pathogens have led to contemporary pathogenic fungal species that display differing degrees of metabolic flexibility. The evolutionarily ancient metabolic pathways are conserved in most fungal pathogen, but interesting gaps exist in some species (e.g., Candida glabrata). Third, metabolic flexibility is generally essential for fungal pathogenicity, and in particular, for the adaptation to contrasting host microenvironments such as the gastrointestinal tract, mucosal surfaces, bloodstream, and internal organs. Fourth, this metabolic flexibility relies on complex regulatory networks, some of which are conserved across lineages, whereas others have undergone significant evolutionary rewiring. Fifth, metabolic adaptation affects fungal susceptibility to antifungal drugs and also presents exciting opportunities for the development of novel therapies. PMID:25190251

Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe

PubMed Central

Kolář, Filip; Lučanová, Magdalena; Vít, Petr; Urfus, Tomáš; Chrtek, Jindřich; Fér, Tomáš; Ehrendorfer, Friedrich; Suda, Jan

2013-01-01

Background and Aims Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. Methods DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. Key Results The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. Conclusions The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the evolutionary dynamics and speciation rates in the dramatically changing environments of Northern Europe. PMID:23589633

Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies.

PubMed

de Roode, J C; de Castillejo, C Lopez Fernandez; Faits, T; Alizon, S

2011-04-01

Host resistance to parasites can come in two main forms: hosts may either reduce the probability of parasite infection (anti-infection resistance) or reduce parasite growth after infection has occurred (anti-growth resistance). Both resistance mechanisms are often imperfect, meaning that they do not fully prevent or clear infections. Theoretical work has suggested that imperfect anti-growth resistance can select for higher parasite virulence by favouring faster-growing and more virulent parasites that overcome this resistance. In contrast, imperfect anti-infection resistance is thought not to select for increased parasite virulence, because it is assumed that it reduces the number of hosts that become infected, but not the fitness of parasites in successfully infected hosts. Here, we develop a theoretical model to show that anti-infection resistance can in fact select for higher virulence when such resistance reduces the effective parasite dose that enters a host. Our model is based on a monarch butterfly-parasite system in which larval food plants confer resistance to the monarch host. We carried out an experiment and showed that this environmental resistance is most likely a form of anti-infection resistance, through which toxic food plants reduce the effective dose of parasites that initiates an infection. We used these results to build a mathematical model to investigate the evolutionary consequences of food plant-induced resistance. Our model shows that when the effective infectious dose is reduced, parasites can compensate by evolving a higher per-parasite growth rate, and consequently a higher intrinsic virulence. Our results are relevant to many insect host-parasite systems, in which larval food plants often confer imperfect anti-infection resistance. Our results also suggest that - for parasites where the infectious dose affects the within-host dynamics - vaccines that reduce the effective infectious dose can select for increased parasite virulence. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

An information entropy model on clinical assessment of patients based on the holographic field of meridian

NASA Astrophysics Data System (ADS)

Wu, Jingjing; Wu, Xinming; Li, Pengfei; Li, Nan; Mao, Xiaomei; Chai, Lihe

2017-04-01

Meridian system is not only the basis of traditional Chinese medicine (TCM) method (e.g. acupuncture, massage), but also the core of TCM's basic theory. This paper has introduced a new informational perspective to understand the reality and the holographic field of meridian. Based on maximum information entropy principle (MIEP), a dynamic equation for the holographic field has been deduced, which reflects the evolutionary characteristics of meridian. By using self-organizing artificial neural network as algorithm, the evolutionary dynamic equation of the holographic field can be resolved to assess properties of meridians and clinically diagnose the health characteristics of patients. Finally, through some cases from clinical patients (e.g. a 30-year-old male patient, an apoplectic patient, an epilepsy patient), we use this model to assess the evolutionary properties of meridians. It is proved that this model not only has significant implications in revealing the essence of meridian in TCM, but also may play a guiding role in clinical assessment of patients based on the holographic field of meridians.

Evolutionary Perspective on Collective Decision Making

NASA Astrophysics Data System (ADS)

Farrell, Dene; Sayama, Hiroki; Dionne, Shelley D.; Yammarino, Francis J.; Wilson, David Sloan

Team decision making dynamics are investigated from a novel perspective by shifting agency from decision makers to representations of potential solutions. We provide a new way to navigate social dynamics of collective decision making by interpreting decision makers as constituents of an evolutionary environment of an ecology of evolving solutions. We demonstrate distinct patterns of evolution with respect to three forms of variation: (1) Results with random variations in utility functions of individuals indicate that groups demonstrating minimal internal variation produce higher true utility values of group solutions and display better convergence; (2) analysis of variations in behavioral patterns within a group shows that a proper balance between selective and creative evolutionary forces is crucial to producing adaptive solutions; and (3) biased variations of the utility functions diminish the range of variation for potential solution utility, leaving only the differential of convergence performance static. We generally find that group cohesion (low random variation within a group) and composition (appropriate variation of behavioral patterns within a group) are necessary for a successful navigation of the solution space, but performance in both cases is susceptible to group level biases.

Life's attractors : understanding developmental systems through reverse engineering and in silico evolution.

PubMed

Jaeger, Johannes; Crombach, Anton

2012-01-01

We propose an approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary simulations. We infer regulatory parameters for gene networks by fitting computational models to quantitative expression data. This allows us to characterize the regulatory structure and dynamical repertoire of evolving gene regulatory networks with a reasonable amount of experimental and computational effort. We use the resulting network models to identify those regulatory interactions that are conserved, and those that have diverged between different species. Moreover, we use the models obtained by data fitting as starting points for simulations of evolutionary transitions between species. These simulations enable us to investigate whether such transitions are random, or whether they show stereotypical series of regulatory changes which depend on the structure and dynamical repertoire of an evolving network. Finally, we present a case study-the gap gene network in dipterans (flies, midges, and mosquitoes)-to illustrate the practical application of the proposed methodology, and to highlight the kind of biological insights that can be gained by this approach.

Emergence of communities and diversity in social networks

PubMed Central

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross

2017-01-01

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics. PMID:28235785

Emergence of communities and diversity in social networks.

PubMed

Han, Xiao; Cao, Shinan; Shen, Zhesi; Zhang, Boyu; Wang, Wen-Xu; Cressman, Ross; Stanley, H Eugene

2017-03-14

Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society. An elusive question is how communities with common internal properties arise in social networks with great individual diversity. Here, we answer this question using the ultimatum game, which has been a paradigm for characterizing altruism and fairness. We experimentally show that stable local communities with different internal agreements emerge spontaneously and induce social diversity into networks, which is in sharp contrast to populations with random interactions. Diverse communities and social norms come from the interaction between responders with inherent heterogeneous demands and rational proposers via local connections, where the former eventually become the community leaders. This result indicates that networks are significant in the emergence and stabilization of communities and social diversity. Our experimental results also provide valuable information about strategies for developing network models and theories of evolutionary games and social dynamics.

Examples of equilibrium and non-equilibrium behavior in evolutionary systems

NASA Astrophysics Data System (ADS)

Soulier, Arne

With this thesis, we want to shed some light into the darkness of our understanding of simply defined statistical mechanics systems and the surprisingly complex dynamical behavior they exhibit. We will do so by presenting in turn one equilibrium and then one non-equilibrium system with evolutionary dynamics. In part 1, we will present the seceder-model, a newly developed system that cannot equilibrate. We will then study several properties of the system and obtain an idea of the richness of the dynamics of the seceder model, which is particular impressive given the minimal amount of modeling necessary in its setup. In part 2, we will present extensions to the directed polymer in random media problem on a hypercube and its connection to the Eigen model of evolution. Our main interest will be the influence of time-dependent and time-independent changes in the fitness landscape viewed by an evolving population. This part contains the equilibrium dynamics. The stochastic models and the topic of evolution and non-equilibrium in general will allow us to point out similarities to the various lines of thought in game theory.

Evolutionary dynamics of language systems

PubMed Central

Wu, Chieh-Hsi; Hua, Xia; Dunn, Michael; Levinson, Stephen C.; Gray, Russell D.

2017-01-01

Understanding how and why language subsystems differ in their evolutionary dynamics is a fundamental question for historical and comparative linguistics. One key dynamic is the rate of language change. While it is commonly thought that the rapid rate of change hampers the reconstruction of deep language relationships beyond 6,000–10,000 y, there are suggestions that grammatical structures might retain more signal over time than other subsystems, such as basic vocabulary. In this study, we use a Dirichlet process mixture model to infer the rates of change in lexical and grammatical data from 81 Austronesian languages. We show that, on average, most grammatical features actually change faster than items of basic vocabulary. The grammatical data show less schismogenesis, higher rates of homoplasy, and more bursts of contact-induced change than the basic vocabulary data. However, there is a core of grammatical and lexical features that are highly stable. These findings suggest that different subsystems of language have differing dynamics and that careful, nuanced models of language change will be needed to extract deeper signal from the noise of parallel evolution, areal readaptation, and contact. PMID:29073028

Evolutionary Determinants of Cancer

PubMed Central

Greaves, Mel

2015-01-01

‘Nothing in biology makes sense except in the light of evolution’ Th. Dobzhansky, 1973 Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as complex, dynamic and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints facilitating increasing complexity and longevity of species. But our own has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. PMID:26193902

Joint evolution of specialization and dispersal in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2011-04-21

We study the joint evolution of dispersal and specialization concerning resource usage in a mechanistically underpinned structured discrete-time metapopulation model. We show that dispersal significantly affects the evolution of specialization and that specialization is a key factor that determines the possibility of evolutionary branching in dispersal propensity. Allowing both dispersal propensity and specialization to evolve as a consequence of natural selection is necessary in order to understand the evolutionary dynamics. The joint evolution of dispersal and specialization forms a natural evolutionary path leading to the coexistence of generalists and specialists. We show that in this process, the number of different patch types and the resource distribution are essential. Copyright © 2011 Elsevier Ltd. All rights reserved.

Packets Distributing Evolutionary Algorithm Based on PSO for Ad Hoc Network

NASA Astrophysics Data System (ADS)

Xu, Xiao-Feng

2018-03-01

Wireless communication network has such features as limited bandwidth, changeful channel and dynamic topology, etc. Ad hoc network has lots of difficulties in accessing control, bandwidth distribution, resource assign and congestion control. Therefore, a wireless packets distributing Evolutionary algorithm based on PSO (DPSO)for Ad Hoc Network is proposed. Firstly, parameters impact on performance of network are analyzed and researched to obtain network performance effective function. Secondly, the improved PSO Evolutionary Algorithm is used to solve the optimization problem from local to global in the process of network packets distributing. The simulation results show that the algorithm can ensure fairness and timeliness of network transmission, as well as improve ad hoc network resource integrated utilization efficiency.