Evolutionary dynamics in structured populations

Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.     

Two Explanations of Evolutionary Progress

Natural selection explains how living forms are fitted to theirconditions of life. Darwin argued that selection also explains what hecalled the gradual advancement of the organisation, i.e.evolutionary progress. Present-day selectionists disagree. In theirview, it is happenstance that sustains conditions favorable to progress,and therefore happenstance, not selection, that explains progress. Iargue that the disagreement here turns not on whether there exists aselection-based condition bias – a belief now attributed to Darwin – but on whether there needs to be such a bias for selection to count as explaining progress. In Darwin's own view, selection explained progressso far as more complex organisms have the selective advantage whenselection operates unimpeded. I show that these two explanations ofevolutionary progress, selection and happenstance, answer for theirobjectivity to different standards, and for their truth or falsehood todifferent features of the world.     

Evolutionary dynamics of endogenous Jaagsiekte sheep retroviruses proliferation in the domestic sheep,mouflon and Pyrenean chamois

The oncogenic exogenous Jaagsiekte sheep retrovirus (JSRV), responsible for ovine pulmonary adenocarcinoma, has several endogenous counterparts termed enJSRVs. Although many of these elements have been inactivated over time by the accumulation of deleterious mutations or internal recombination leading to solo long terminal repeat (LTR) formation, several members of enJSRVs have been identified as nearly intact and probably represent recent integration events. To determine the level of enJSRV polymorphism in the sheep population and related species, we have undertaken a study by characterizing enJSRVs copies and independent integration sites in six domestic sheep and two wild species of the sheep lineage. enJSRVs copies were detected by amplifying the env-LTR region by PCR, and for the detection of the insertion sites, we used two approaches: (1) an in silico approach based on the recently published Sheep Reference Genome Assembly (OARv3.0) and (2) an experimental approach based on PCR suppression and inverse PCR techniques. In total, 103 enJSRV sequences were generated across 10 individuals and enJSRV integrations were found on 11 of the 28 sheep chromosomes. These findings suggest that there are still uncharacterized enJSRVs, and that some of the integration sites are variable among the different species, breeds of the same species, subspecies and geographic locations.     

Evolutionary and Ecological Effects of Multi-Generational Exposures to Anthropogenic Stressors

Biological and ecological responses to stress are dictated by duration and frequency, as well as instantaneous magnitude. Conditional compensatory responses at the physiological and behavioral levels, referred to as ‘acclimation’, may mitigate effects on individuals experiencing brief or infrequent periods of moderate stress. However, even modest stress over extended periods may reduce the fitness of some or all exposed individuals. In this way, specific stress that persists over multiple generations will increase probabilities for extinction of populations composed of sensitive individuals. For populations whose members demonstrate variance and heritability for stressor response, this selective loss of sensitive individuals may result in populations dominated by resistant individuals. The formation of these ‘adapted’ populations may be considered an ecological compensatory mechanism to multi-generational stress. Paradoxically, the biological costs to individuals of toxicity and physiological acclimation may result in obvious signs of stress in affected wildlife populations while the costs of genetic adaptation may be more covert. It is important to consider such costs because recent evidence suggests that anthropogenic stressors have acted as powerful selection agents that have modified the composition of wildlife populations subjected for successive generational exposures to specific stressors. This essay focuses on a case study where adaptation has been demonstrated in fish populations with a history of chronic exposure to persistent, bioaccumulative and toxic environmental contaminants. Because the magnitude, breadth and long-term outcomes of such changes are unknown, ecological risk assessments that are limited in focus to short-term exposures and consequences may seriously underestimate the ecological and evolutionary impacts of anthropogenic stressors.     

Evolutionary dynamics of taxonomic structure

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth-death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record.     

Evolutionary perspectives on human height variation

Human height is a highly variable trait, both within and between populations, has a high heritability, and influences the manner in which people behave and are treated in society. Although we know much about human height, this information has rarely been brought together in a comprehensive, systematic fashion. Here, we present a synthetic review of the literature on human height from an explicit evolutionary perspective, addressing its phylogenetic history, development, and environmental and genetic influences on growth and stature. In addition to presenting evidence to suggest the past action of natural selection on human height, we also assess the evidence that natural and sexual selection continues to act on height in contemporary populations. Although there is clear evidence to suggest that selection acts on height, mainly through life‐history processes but perhaps also directly, it is also apparent that methodological factors reduce the confidence with which such inferences can be drawn, and there remain surprising gaps in our knowledge. The inability to draw firm conclusions about the adaptiveness of such a highly visible and easily measured trait suggests we should show an appropriate degree of caution when dealing with other human traits in evolutionary perspective.     

Extensive evolutionary rate variation in floral color determining genes in the genus Ipomoea

Flower color is an important adaptive trait in many plant species because it determines reproductive success through differential attractiveness to insect pollinators. The genus Ipomoea is a pan tropically distributed plant genus characterized by showy flowers that often differ in color among closely related species. Flower color is determined primarily by products of the anthocyanin biosynthesis pathway. To determine whether flower color evolution among members of the genus is driven by adaptive molecular evolution of the anthocyanin pathway genes, we analyzed data from 10 genes sequenced from 19 species of Ipomoea . Six protein-coding genes from the anthocyanin pathway were drawn for evolutionary analysis in addition to three genes from the unrelated leucine biosynthesis pathway and one MADS box regulatory gene for comparison. The analyses provided: (i) no convincing evidence for positive selection on anthocyanin pathway structural genes, or on the other sampled genes, despite shifts in flower color among species included in the sample; (ii) pathway position correlated weakly with estimates of the intensity of evolutionary constraint on the anthocyanin pathway enzyme coding genes; and (iii) there was substantial gene-specific heterogeneity in the rates of synonymous site evolution. Synonymous rate heterogeneity does not appear to be accounted for by codon bias or local contextual or compositional sequence differences, leading us to implicate heterogeneous rates of mutation among genes as the most probable cause of synonymous rate heterogeneity.     

Evolutionary rates for multivariate traits: the role of selection and genetic variation

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders'' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.     

Eco-evolutionary dynamics

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.     

Deconstructing Darwin: Evolutionary theory in context

The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwins contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory.     

Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism

Like many phenotypic traits, biomechanical systems are defined by both an underlying morphology and an emergent functional property. The relationship between these levels may have a profound impact on how selection for functional performance is translated into morphological evolution. In particular, complex mechanical systems are likely to be highly redundant, because many alternative morphologies yield equivalent functions. We suggest that this redundancy weakens the relationship between morphological and functional diversity, and we illustrate this effect using an evolutionary model of the four-bar lever system of labrid fishes. Our results demonstrate that, when traits are complex, the morphological diversity of a clade may only weakly predict its mechanical diversity. Furthermore, parallel or convergent selection on function does not necessarily produce convergence in morphology. Empirical observations suggest that this weak form-function relationship has contributed to the morphological diversity of labrid fishes, as functionally equivalent species may nevertheless possess morphologically distinct jaws. We suggest that partial decoupling of morphology and mechanics due to redundancy is a major factor in morphological diversification.     

Evolutionary dynamics of collective action in N-person stag hunt dilemmas

In the animal world, collective action to shelter, protect and nourish requires the cooperation of group members. Among humans, many situations require the cooperation of more than two individuals simultaneously. Most of the relevant literature has focused on an extreme case, the N-person Prisoner's Dilemma. Here we introduce a model in which a threshold less than the total group is required to produce benefits, with increasing participation leading to increasing productivity. This model constitutes a generalization of the two-person stag hunt game to an N-person game. Both finite and infinite population models are studied. In infinite populations this leads to a rich dynamics that admits multiple equilibria. Scenarios of defector dominance, pure coordination or coexistence may arise simultaneously. On the other hand, whenever one takes into account that populations are finite and when their size is of the same order of magnitude as the group size, the evolutionary dynamics is profoundly affected: it may ultimately invert the direction of natural selection, compared with the infinite population limit.     

Eco-evolutionary dynamics in Pacific salmon

Increasing acceptance of the idea that evolution can proceed rapidly has generated considerable interest in understanding the consequences of ongoing evolutionary change for populations, communities and ecosystems. The nascent field of 'eco-evolutionary dynamics' considers these interactions, including reciprocal feedbacks between evolution and ecology. Empirical support for eco-evolutionary dynamics has emerged from several model systems, and we here present some possibilities for diverse and strong effects in Pacific salmon (Oncorhynchus spp.). We specifically focus on the consequences that natural selection on body size can have for salmon population dynamics, community (bear-salmon) interactions and ecosystem process (fluxes of salmon biomass between habitats). For example, we find that shifts in body size because of selection can alter fluxes across habitats by up to 11% compared with ecological (that is, numerical) effects. More generally, we show that selection within a generation can have large effects on ecological dynamics and so should be included within a complete eco-evolutionary framework.     

Evolutionary rescue and the limits of adaptation

Populations subject to severe stress may be rescued by natural selection, but its operation is restricted by ecological and genetic constraints. The cost of natural selection expresses the limited capacity of a population to sustain the load of mortality or sterility required for effective selection. Genostasis expresses the lack of variation that prevents many populations from adapting to stress. While the role of relative fitness in adaptation is well understood, evolutionary rescue emphasizes the need to recognize explicitly the importance of absolute fitness. Permanent adaptation requires a range of genetic variation in absolute fitness that is broad enough to provide a few extreme types capable of sustained growth under a stress that would cause extinction if they were not present. This principle implies that population size is an important determinant of rescue. The overall number of individuals exposed to selection will be greater when the population declines gradually under a constant stress, or is progressively challenged by gradually increasing stress. In gradually deteriorating environments, survival at lethal stress may be procured by prior adaptation to sublethal stress through genetic correlation. Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.     

Evolutionary ecology of the tropane alkaloids of Datura stramonium L. (Solanaceae)

Abstract.— Although insect herbivory is frequently assumed to be responsible for the maintenance of plant secondary metabolites such as alkaloids, the assumption is controversial and experimental evidence for this assumption is sparse. We examined natural selection on the two major alkaloids present in the leaves of Datura stramonium and found that both alkaloids came under active selection. We found negative directional selection for scopolamine (natural selection acting to reduce scopolamine levels) and stabilizing selection for hyoscyamine (natural selection acting to maintain an intermediate level of hyoscyamine). We also present evidence that insect herbivores act as the agents of selection on these alkaloids. Finally, we show that there were no trade-offs in resistance to different species of insects.     

数量遗传学理论框架下的进化生态学研究：以动物模型的运用为例

目前,生态学家越来越关注深入的生物学问题,例如,1)理解生态和进化过程的互作和关系;2)种群中一个重要的表型特征,受遗传基因影响多大?即其可遗传程度,表示该性状的进化潜能;3)基因是怎样影响表型性状,及其对应的个体适合度以及种群动态?4)决定多个重要表型性状的基因之间关系和互作如何?随着生物统计软件尤其是线性混合模型的发展,结合经典数量遗传学的理论,发展出了针对上述问题的动物模型(Animal Model),使得我们可以对野外种群进行上述研究。本文首先介绍了经典数量遗传学的重要概念,随后在其理论框架下,举例介绍了动物模型的操作和使用,最后探讨和展望了利用数量遗传学方法进行进化生态学研究的前景。     

The use of retroviruses as pharmaceutical tools for target discovery and validation in the field of functional genomics

Retrovirally mediated functional genomics enables identification of physiologically relevant cellular therapeutic targets. Unique properties of retroviruses make them ideal tools for the introduction of large and diverse libraries of potential genetic effectors to a variety of cell types. The identification and recovery of intracellular library elements responsible for altered disease responses establishes a direct basis for pharmaceutical development. Recent innovations in retroviral infection efficiency and expression control have broadened application of the methodology to include libraries of mutagenized cDNAs, peptides and ribozyme genetic effectors.     

On the Explanatory Roles of Natural Selection

Can selection explain why individuals have the traits they do? This question has generated significant controversy. I will argue that the debate encompasses two separable aspects, to detrimental effect: (1) the role of selection in explaining the origin and evolution of biological traits and (2) the implications this may have for explaining why individuals have the traits they do. (1) can be settled on the basis of evolutionary theory while (2) requires additional, extra-scientific assumptions. By making a distinction between traits affected by a single factor and traits affected by multiple factors I show that selection can, under certain conditions, help explain the origin of traits. Resolving the first aspect enables us to critically assess the various incompatible and independent philosophical commitments made within the second aspect of the debate.     

Evolutionary dynamics of a sexual ornament in the house sparrow (Passer domesticus): the role of indirect selection within and between sexes

The relative contribution of sexual and natural selection to evolution of sexual ornaments has rarely been quantified under natural conditions. In this study we used a long-term dataset of house sparrows in which parents and offspring were matched genetically to estimate the within- and across-sex genetic basis for variation and covariation among morphological traits. By applying two-sex multivariate "animal models" to estimate genetic parameters, we estimated evolutionary changes in a male sexual ornament, badge size, from the contribution of direct and indirect selection on correlated traits within males and females, after accounting for overlapping generations and age-structure. Indirect natural selection on genetically correlated traits in males and females was the major force causing evolutionary change in the male ornament. Thus, natural selection on female morphology may cause indirect evolutionary changes in male ornaments. We observed however no directional phenotypic change in the ornament size of one-year-old males during the study period. On the other hand, changes were recorded in other morphological characters of both sexes. Our analyses of evolutionary dynamics in sexual characters require application of appropriate two-sex models to account for how selection on correlated traits in both sexes affects the evolutionary outcome of sexual selection.