History of development of evolutionary methods in St. Petersburg school of computer simulation in biology

The work presents a short history of development of evolutionary methods in the St. Petersburg school of computer simulation of biological processes. Several moments confirm priority of this school in modeling of micro- and macroevolutionary processes. A peculiarity of the school is a combination of the applied and theoretical study, penetration into the biological essence of phenomenon, consideration of real interrelationships of ecological and physiological parameters. The natural tendency for transition to modeling at the level of single individuals and then-to imitation of evolutionary processes on computer is traced. Paradoxically, such detalization sometimes does not worsen, but improves prognostic properties of models of populations, communities, and ecosystems, and besides, makes unnecessary monitoring of some variable characteristics, because the individual-based approach allows to direct account for adaptive processes and hidden evolutionary relationships between the life history parameters. Problems and perspectives of development of evolutionary methods of modeling are analyzed.     

A cascade of evolutionary change alters consumer-resource dynamics and ecosystem function

It is becoming increasingly clear that intraspecific evolutionary divergence influences the properties of populations, communities and ecosystems. The different ecological impacts of phenotypes and genotypes may alter selection on many species and promote a cascade of ecological and evolutionary change throughout the food web. Theory predicts that evolutionary interactions across trophic levels may contribute to hypothesized feedbacks between ecology and evolution. However, the importance of 'cascading evolutionary change' in a natural setting is unknown. In lakes in Connecticut, USA, variation in migratory behaviour and feeding morphology of a fish predator, the alewife (Alosa pseudoharengus), drives life-history evolution in a species of zooplankton prey (Daphnia ambigua). Here we evaluated the reciprocal impacts of Daphnia evolution on ecological processes in laboratory mesocosms. We show that life-history evolution in Daphnia facilitates divergence in rates of population growth, which in turn significantly alters consumer-resource dynamics and ecosystem function. These experimental results parallel trends observed in lakes. Such results argue that a cascade of evolutionary change, which has occurred over contemporary timescales, alters community and ecosystem processes.     

Artificial evolution of life history and behavior

We present an individual-based model that uses artificial evolution to predict fit behavior and life-history traits on the basis of environmental data and organism physiology. Our main purpose is to investigate whether artificial evolution is a suitable tool for studying life history and behavior of real biological organisms. The evolutionary adaptation is founded on a genetic algorithm that searches for improved solutions to the traits under scrutiny. From the genetic algorithm's "genetic code," behavior is determined using an artificial neural network. The marine planktivorous fish Müller's pearlside (Maurolicus muelleri) is used as the model organism because of the broad knowledge of its behavior and life history, by which the model's performance is evaluated. The model adapts three traits: habitat choice, energy allocation, and spawning strategy. We present one simulation with, and one without, stochastic juvenile survival. Spawning pattern, longevity, and energy allocation are the life-history traits most affected by stochastic juvenile survival. Predicted behavior is in good agreement with field observations and with previous modeling results, validating the usefulness of the presented model in particular and artificial evolution in ecological modeling in general. The advantages, possibilities, and limitations of this modeling approach are further discussed.     

Longevity and ageing: appraising the evolutionary consequences of growing old

Senescence or ageing is an increase in mortality and/or decline in fertility with increasing age. Evolutionary theories predict that ageing or longevity evolves in response to patterns of extrinsic mortality or intrinsic damage. If ageing is viewed as the outcome of the processes of behaviour, growth and reproduction then it should be possible to predict mortality rate. Recent developments have shown that it is now possible to integrate these ecological and physiological processes and predict the shape of mortality trajectories. By drawing on the key exciting developments in the cellular, physiological and ecological process of longevity the evolutionary consequences of ageing are reviewed. In presenting these ideas an evolutionary demographic framework is used to argue how trade-offs in life-history strategies are important in the maintenance of variation in longevity within and between species. Evolutionary processes associated with longevity have an important role in explaining levels of biological diversity and speciation. In particular, the effects of life-history trait trade-offs in maintaining and promoting species diversity are explored. Such trade-offs can alleviate the effects of intense competition between species and promote species coexistence and diversification. These results have important implications for understanding a number of core ecological processes such as how species are divided among niches, how closely related species co-occur and the rules by which species assemble into food-webs. Theoretical work reveals that the proximate physiological processes are as important as the ecological factors in explaining the variation in the evolution of longevity. Possible future research challenges integrating work on the evolution and mechanisms of growing old are briefly discussed.     

附生蕨类植物的克隆性研究进展

石松类及蕨类植物在高等植物中处于比较特殊的进化与系统发育地位, 同时具有孢子植物(孢子)与种子植物(维管束)的双重特征。附生蕨类植物是蕨类植物中占据独特生境的一个大类群, 其生活史策略及进化历史与其附生生长的森林生态系统紧密相关。大部分附生蕨类植物的克隆生长习性及克隆生活史性状在其生态适应中具有重要作用, 但这方面未引起广泛关注。本文主要综述了中国山地森林中附生蕨类植物的根状茎克隆生长、克隆性与生态适应性、不同克隆生长方式与进化等方面, 并展望了蕨类植物克隆性在森林生态系统过程与功能中的作用, 以及今后如何将蕨类植物生态学研究与气候变化、植被恢复、土地利用变化等全球变化的主流方向进行结合。     

The role of size-specific predation in the evolution and diversification of prey life histories

Some of the best empirical examples of life-history evolution involve responses to predation. Nevertheless, most life-history theory dealing with responses to predation has not been formulated within an explicit dynamic food-web context. In particular, most previous theory does not explicitly consider the coupled population dynamics of the focal species and its predators and resources. Here we present a model of life-history evolution that explores the evolutionary consequences of size-specific predation on small individuals when there is a trade-off between growth and reproduction. The model explicitly describes the population dynamics of a predator, the prey of interest, and its resource. The selective forces that cause life-history evolution in the prey species emerge from the ecological interactions embodied by this model and can involve important elements of frequency dependence. Our results demonstrate that the strength of the coupling between predator and prey in the community determines many aspects of life-history evolution. If the coupling is weak (as is implicitly assumed in many previous models), differences in resource productivity have no effect on the nature of life-history evolution. A single life-history strategy is favored that minimizes the equilibrium resource density (if possible). If the coupling is strong, then higher resource productivities select for faster growth into the predation size refuge. Moreover, under strong coupling it is also possible for natural selection to favor an evolutionary diversification of life histories, possibly resulting in two coexisting species with divergent life-history strategies.     

Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history

Background

Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions.

Methology/Principal Findings

Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns.

Conclusion/Significance

Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes.     

The Price equation framework to study disease within-host evolution

The evolution of infectious diseases is known to affect epidemiological dynamics, but, for some viruses and bacteria, this evolution also takes place inside a host during the course of an infection. I develop an original approach to study intrahost evolutionary dynamics of quantitative disease traits. This approach can be expressed mathematically using the ‘Price equation’ framework recently developed in evolutionary epidemiology. This framework combines population genetics and within-host population dynamics models to identify trade-offs that affect disease intrahost evolution and to predict short-term evolutionary dynamics of life-history traits. I show that this can be applied to study the evolution of viruses competing for host cells or to study the coevolution between parasites and the immune system of the host. This framework can also easily incorporate experimental data. Studying intrahost evolutionary dynamics provides insight at the within-host level, because it allows us to better understand the course of chronic infections, and at the epidemiological level, because it helps to study multi-scale evolutionary processes. This framework can be used to address important biological issues, from immune escape to disease evolutionary response to treatments.     

Directionality theory: an empirical study of an entropic principle in life-history evolution

Understanding the relationship between ecological constraints and life-history properties constitutes a central problem in evolutionary ecology. Directionality theory, a model of the evolutionary process based on demographic entropy, a measure of the uncertainty in the age of the mother of a randomly chosen newborn, provides an analytical framework for addressing this problem. The theory predicts that in populations that spend the greater part of their evolutionary history in the stationary growth phase (equilibrium species), entropy will increase. Equilibrium species will be characterized by high iteroparity and strong demographic stability. In populations that spend the greater part of their evolutionary history in the exponential growth phase (opportunistic species), entropy will decrease when population size is large, and will undergo random variation when population size is small. Opportunistic species will be characterized by weak iteroparity and weak demographic stability when population size is large, and random variations in these attributes when population size is small. This paper assesses the validity of these predictions by employing a demographic dataset of 66 species of perennial plants. This empirical analysis is consistent with directionality theory and provides support for its significance as an explanatory and predictive model of life-history evolution.     

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.     

Toward a synthetic understanding of the role of phenology in ecology and evolution

Phenology affects nearly all aspects of ecology and evolution. Virtually all biological phenomena—from individual physiology to interspecific relationships to global nutrient fluxes—have annual cycles and are influenced by the timing of abiotic events. Recent years have seen a surge of interest in this topic, as an increasing number of studies document phenological responses to climate change. Much recent research has addressed the genetic controls on phenology, modelling techniques and ecosystem-level and evolutionary consequences of phenological change. To date, however, these efforts have tended to proceed independently. Here, we bring together some of these disparate lines of inquiry to clarify vocabulary, facilitate comparisons among habitat types and promote the integration of ideas and methodologies across different disciplines and scales. We discuss the relationship between phenology and life history, the distinction between organismal- and population-level perspectives on phenology and the influence of phenology on evolutionary processes, communities and ecosystems. Future work should focus on linking ecological and physiological aspects of phenology, understanding the demographic effects of phenological change and explicitly accounting for seasonality and phenology in forecasts of ecological and evolutionary responses to climate change.     

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.     

Morphological interpretation of darwinism

The development of evolutionary theory requires the resolution of the problem of relationships between random and regular processes in historical development of biological systems. According to the theory of natural selection, ecological factors play a leading role in evolution. Variations are nondirectional, unpredictable, and provide chaotic diversity of variants, only some of which are potentially useful. However, based on random processes, new variants that are useful for organisms and remain adaptive significance in various ecological situations are infrequent. At the same time, morphology demonstrates certain evolutionary patterns. The morphological approach takes into account the role in evolution of structural features of organism and social systems and evolutionary significance of “constructive technologies,” which distinguish morphological interpretation of evolutionary processes. The constructive and evolutionary patterns revealed in biological systems provide the basis for morphological interpretation of the principle of natural selection: both natural and artificial selection is interaction between social systems (populations, ecosystems, biogeocoenoses) and organisms composing them.     

Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild

The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life-history components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies.     

Plant reproductive systems and evolution during biological invasion

Recent biological invasions provide opportunities to investigate microevolution during contemporary timescales. The tempo and scope of local adaptation will be determined by the intensity of natural selection and the amounts and kinds of genetic variation within populations. In flowering plants, genetic diversity is strongly affected by interactions between reproductive systems and stochastic forces associated with immigration history and range expansion. Here, we explore the significance of reproductive system diversity for contemporary evolution during plant invasion. We focus in particular on how reproductive modes influence the genetic consequences of long-distance colonization and determine the likelihood of adaptive responses during invasion. In many clonal invaders, strong founder effects and restrictions on sexual reproduction limit opportunities for local adaptation. In contrast, adaptive changes to life-history traits should be a general expectation in both outbreeding and inbreeding species. We provide evidence that evolutionary modifications to reproductive systems promote the colonizing ability of invading populations and that reproductive timing is an important target of selection during range expansion. Knowledge of the likelihood and speed at which local adaptation evolves in invasive plants will be particularly important for management practices when evolutionary changes enhance ecological opportunities and invasive spread.     

Optimal annual routines: behaviour in the context of physiology and ecology

Organisms in a seasonal environment often schedule activities in a regular way over the year. If we assume that such annual routines have been shaped by natural selection then life-history theory should provide a basis for explaining them. We argue that many life-history trade-offs are mediated by underlying physiological variables that act on various time scales. The dynamics of these variables often preclude considering one period of the year in isolation. In order to capture the essence of annual routines, and many life-history traits, a detailed model of changes in physiological state over the annual cycle is required. We outline a modelling approach based on suitable physiological and ecological state variables that can capture this underlying biology, and describe how models based on this approach can be used to generate a range of insights and predictions.     

Developmental palaeontology in synapsids: the fossil record of ontogeny in mammals and their closest relatives

The study of fossilized ontogenies in mammals is mostly restricted to postnatal and late stages of growth, but nevertheless can deliver great insights into life history and evolutionary mechanisms affecting all aspects of development. Fossils provide evidence of developmental plasticity determined by ecological factors, as when allometric relations are modified in species which invaded a new space with a very different selection regime. This is the case of dwarfing and gigantism evolution in islands. Skeletochronological studies are restricted to the examination of growth marks mostly in the cement and dentine of teeth and can provide absolute age estimates. These, together with dental replacement data considered in a phylogenetic context, provide life-history information such as maturation time and longevity. Palaeohistology and dental replacement data document the more or less gradual but also convergent evolution of mammalian growth features during early synapsid evolution. Adult phenotypes of extinct mammals can inform developmental processes by showing a combination of features or levels of integration unrecorded in living species. Some adult features such as vertebral number, easily recorded in fossils, provide indirect information about somitogenesis and hox-gene expression boundaries. Developmental palaeontology is relevant for the discourse of ecological developmental biology, an area of research where features of growth and variation are fundamental and accessible among fossil mammals.     

What have two decades of laboratory life-history evolution studies onDrosophila melanogaster taught us?

A series of laboratory selection experiments onDrosophila melanogaster over the past two decades has provided insights into the specifics of life-history tradeoffs in the species and greatly refined our understanding of how ecology and genetics interact in life-history evolution. Much of what has been learnt from these studies about the subtlety of the microevolutionary process also has significant implications for experimental design and inference in organismal biology beyond life-history evolution, as well as for studies of evolution in the wild. Here we review work on the ecology and evolution of life-histories in laboratory populations ofD. melanogaster, emphasizing how environmental effects on life-history-related traits can influence evolutionary change. We discuss life-history tradeoffs—many unexpected—revealed by selection experiments, and also highlight recent work that underscores the importance to life-history evolution of cross-generation and cross-life-stage effects and interactions, sexual antagonism and sexual dimorphism, population dynamics, and the possible role of biological clocks in timing life-history events. Finally, we discuss some of the limitations of typical selection experiments, and how these limitations might be transcended in the future by a combination of more elaborate and realistic selection experiments, developmental evolutionary biology, and the emerging discipline of phenomics.     

Bridging scales in the evolution of infectious disease life histories: application

Within- and between-host disease processes occur on the same timescales, therefore changes in the within-host dynamics of parasites, resources, and immunity can interact with changes in the epidemiological dynamics to affect evolutionary outcomes. Consequently, studies of the evolution of disease life histories, that is, infection-age-specific patterns of transmission and virulence, have been constrained by the need for a mechanistic understanding of within-host disease dynamics. In a companion paper (Day et al. 2011), we develop a novel approach that quantifies the relevant within-host aspects of disease through genetic covariance functions. Here, we demonstrate how to apply this theory to data. Using two previously published datasets from rodent malaria infections, we show how to translate experimental measures into disease life-history traits, and how to quantify the covariance in these traits. Our results show how patterns of covariance can interact with epidemiological dynamics to affect evolutionary predictions for disease life history. We also find that the selective constraints on disease life-history evolution can vary qualitatively, and that "simple" virulence-transmission trade-offs that are often the subject of experimental investigation can be obscured by trade-offs within one trait alone. Finally, we highlight the type and quality of data required for future applications.     

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo,Evo-Eco and Evolutionary Transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.