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Cooperation driven by mutations in multi-person Prisoner's Dilemma.

The n-person Prisoner's Dilemma is a widely used model for populations where individuals interact in groups. The evolutionary stability of populations has been analysed in the literature for the case where mutations in the population may be considered as isolated events. For this case, and assuming simple trigger strategies and many iterations per game, we analyse the rate of convergence to the evolutionarily stable populations. We find that for some values of the payoff parameters of the Prisoner's Dilemma this rate is so low that the assumption, that mutations in the population are infrequent on that time-scale, is unreasonable. Furthermore, the problem is compounded as the group size is increased. In order to address this issue, we derive a deterministic approximation of the evolutionary dynamics with explicit, stochastic mutation processes, valid when the population size is large. We then analyse how the evolutionary dynamics depends on the following factors: mutation rate, group size, the value of the payoff parameters, and the structure of the initial population. In order to carry out the simulations for groups of more than just a few individuals, we derive an efficient way of calculating the fitness values. We find that when the mutation rate per individual and generation is very low, the dynamics is characterized by populations which are evolutionarily stable. As the mutation rate is increased, other fixed points with a higher degree of cooperation become stable. For some values of the payoff parameters, the system is characterized by (apparently) stable limit cycles dominated by cooperative behaviour. The parameter regions corresponding to high degree of cooperation grow in size with the mutation rate, and in number with the group size. For some parameter values, we find more than one stable fixed point, corresponding to different structures of the initial population.

Animals↗

Lineage-specific differences in evolutionary mode in a salamander courtship pheromone.

Functionally equivalent genes may evolve heterogeneously across closely related taxa as a consequence of lineage-specific selective pressures. Such disparate evolutionary modes are especially prevalent in genes that encode postcopulatory reproductive proteins, presumably as a result of sexual selection. We might therefore expect genes that mediate reproduction prior to insemination to evolve in a similar manner. Plethodontid receptivity factor (PRF), a proteinaceous salamander pheromone produced by the male, increases female receptivity during courtship interactions. To test for lineage-specific differences in PRF's evolution, we intensively sampled PRF genes across the eastern Plethodon phylogeny (27 spp.; 34 populations) to compare gene diversification, rates of evolution, modes of selection, and types of amino acid substitution. Our analyses indicate that PRF evolutionary dynamics vary considerably from lineage to lineage. Underlying this heterogeneity, however, are two well-defined transitions in evolutionary mode. The first mode is representative of a typical protein profile, wherein neutral divergence and purifying selection are the dominant features. The second mode is characterized by incessant, cyclical evolution driven by positive selection. In this mode, the positively selected sites are bound by a limited assortment of acceptable amino acids that appear to evolve independently of other sites, resulting in a tremendous number of unique PRF alleles. Several of these selected sites are implicated in receptor binding. These sites are apparently involved in a molecular tango in which the male signal and female receptors coevolve within a confined molecular space. PRF's lineage-specific evolutionary dynamics, in combination with evidence of a molecular tango, highlight the molecular action of sexual selection on a chemical signal that is used during courtship.

Amino Acid Sequence↗

Convergence to a novel environment: comparative method versus experimental evolution.

Laboratory adaptation allows researchers to contrast temporal studies of experimental evolution with comparative studies. The comparative method is here taken to mean the inference of microevolutionary processes from comparisons among contemporaneous populations of diverse origins, from one or multiple species. The data contrasted here come from Drosophila subobscura populations that were introduced to the laboratory at several different times and from two different locations. Two questions were addressed. First, can we correctly infer evolutionary dynamics from comparative data collected simultaneously from disparate populations? In most cases, we could, except for the character of starvation resistance. Second, are the evolutionary dynamics inferred from the comparative approach similar to those revealed by temporal studies of experimental evolution? For fecundity characters, they were. Overall the results show that both comparative and temporal studies are useful, though the former can be uninformative for characters with complex evolutionary trajectories.

Adaptation, Biological↗

Population dynamics and the evolution of virulence in epidemiological models with discrete host generations

Chaos is the likely outcome of the interaction between a parasite and a host with discrete generations, if the parasite's virulence is high and if transmission from one generation to the next is held constant. We studied two alternative routes of transmission-vertical transmission from infecteds to their offspring, and transmission via long-lasting spores produced in those individuals that were killed by the infection-to investigate the influence of the transmission route on the system's evolution and population dynamics. The major results are: (1) vertical transmission often leads to low virulence, thus confirming most epidemiological models. However, if hosts can become super-infected, the evolutionary dynamics of virulence can have several equilibrium points, including 100% disease-induced mortality; (2) when parasites are transmitted with long-lasting spores, the evolutionary dynamics of virulence can become unstable, leading to the repeated bifurcation of two sub-populations with high and low virulence or to punctuated equilibria with sudden changes in the average level of virulence; (3) in general, the evolution of virulence moves the system to an area where the population dynamics are stable. When evolution leads to chaos, the system most often becomes extinct. Only for a restricted parameter space in the system where transmission from one generation to the next is via long-lasting spores do the dynamics become chaotic without extinction of the system. Copyright 1999 Academic Press.

Journal Article↗

Food-web formation with recursive evolutionary branching.

A reaction-diffusion model describing the evolutionary dynamics of a food-web was constructed. In this model, predator-prey relationships among organisms were determined by their position in a two-dimensional phenotype space defined by two traits: as prey and as predator. The mutation process is expressed with a diffusion process of biomass in the phenotype space. Numerical simulation of this model showed co-evolutionary dynamics of isolated phenotypic clusters, including various types of evolutionary branching, which were classified into branching as prey, branching as predators, and co-evolutionary branching of both prey and predators. A complex food-web develops with recursive evolutionary branching from a single phenotypic cluster. Biodiversity peaks at the medium strength of the predator-prey interaction, where the food-web is maintained at medium biomass by a balanced frequency between evolutionary branching and extinction.

Animals↗

An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes.

Self-splicing group I and II introns are selfish genetic elements that are widely yet patchily distributed across the tree of life. Their selfish behavior comes from super-Mendelian inheritance behaviors, collectively called "homing", which allow them to rapidly spread within populations to the specific genomic sites they home into. Observations of self-splicing intron evolutionary dynamics have led to the formulation of an intron "lifecycle" model where, once fixed in a population, the introns lose selection for homing and undergo an extensive period of degradation until their eventual loss. Here, we find that self-splicing introns are common in the mitochondrial genomes of Epichloë species, endophytic fungi that live in symbioses with grasses. However, these introns show substantial intron presence-absence polymorphism, with our analyses suggesting that these result from a combination of vertical intron inheritance coupled with multiple invasion and loss events over the course of Epichloë evolution. Surprisingly, we find little evidence for the extensive intron degradation expected under the existing intron lifecycle model. Instead, these introns in Epichloë appear to be lost soon after fixation, suggesting that Epichloë self-splicing introns have a different lifecycle. However, rapid intron loss alone cannot explain our results, indicating that additional factors, such as the evolution of homing suppressors, also contribute to Epichloë self-splicing intron dynamics. This work shows that self-splicing introns have more diverse evolutionary dynamics than previously appreciated.

Introns↗

The linear process of somatic evolution.

Cancer is the consequence of an unwanted evolutionary process. Cells receive mutations that alter their phenotype. Especially dangerous are those mutations that increase the net reproductive rate of cells, thereby leading to neoplasia and later to cancer. The standard models of evolutionary dynamics consider well mixed populations of individuals in symmetric positions. Here we introduce a spatially explicit, asymmetric stochastic process that captures the essential architecture of evolutionary dynamics operating within tissues of multicellular organisms. The "linear process" has the property of cancelling out selective differences among cells yet retaining the protective function of apoptosis. This design can slow down the rate of somatic evolution dramatically and therefore delay the onset of cancer.

Animals↗

The universal ancestor.

A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

Animals↗

Stochastic processes are key determinants of short-term evolution in influenza a virus.

Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.

Antigenic Variation↗

Ancient origin of the tryptophan operon and the dynamics of evolutionary change.

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.

Evolution, Molecular↗

The evolution of molecular genetic pathways and networks.

There is growing interest in the evolutionary dynamics of molecular genetic pathways and networks, and the extent to which the molecular evolution of a gene depends on its position within a pathway or network, as well as over-all network topology. Investigations on the relationships between network organization, topological architecture and evolutionary dynamics provide intriguing hints as to how networks evolve. Recent studies also suggest that genetic pathway and network structures may influence the action of evolutionary forces, and may play a role in maintaining phenotypic robustness in organisms.

Animals↗

Temporal variation can facilitate niche evolution in harsh sink environments.

We examine the impact of temporal variation on adaptive evolution in "sink" environments, where a species encounters conditions outside its niche. Sink populations persist because of recurrent immigration from sources. Prior studies have highlighted the importance of demographic constraints on adaptive evolution in sinks and revealed that adaptation is less likely in harsher sinks. We examine two complementary models of population and evolutionary dynamics in sinks: a continuous-state quantitative-genetics model and an individual-based model. In the former, genetic variance is fixed; in the latter, genetic variance varies because of mutation, drift, and sampling. In both models, a population in a constant harsh sink environment can exist in alternative states: local maladaptation (phenotype comparable to immigrants from the source) or adaptation (phenotype near the local optimum). Temporal variation permits transitions between these states. We show that moderate amounts of temporal variation can facilitate adaptive evolution in sinks, permitting niche evolution, particularly for slow or autocorrelated variation. Such patterns of temporal variation may particularly pertain to sinks caused by biotic interactions (e.g., predation). Our results are relevant to the evolutionary dynamics of species' ranges, the fate of exotic invasive species, and the evolutionary emergence of infectious diseases into novel hosts.

Adaptation, Biological↗

The evolution of resource specialization through frequency-dependent and frequency-independent mechanisms.

Levins's fitness set approach has shaped the intuition of many evolutionary ecologists about resource specialization: if the set of possible phenotypes is convex, a generalist is favored, while either of the two specialists is predicted for concave phenotype sets. An important aspect of Levins's approach is that it explicitly excludes frequency-dependent selection. Frequency dependence emerged in a series of models that studied the degree of character displacement of two consumers coexisting on two resources. Surprisingly, the evolutionary dynamics of a single consumer type under frequency dependence has not been studied in detail. We analyze a model of one evolving consumer feeding on two resources and show that, depending on the trait considered to be subject to evolutionary change, selection is either frequency independent or frequency dependent. This difference is explained by the effects different foraging traits have on the consumer-resource interactions. If selection is frequency dependent, then the population can become dimorphic through evolutionary branching at the trait value of the generalist. Those traits with frequency-independent selection, however, do indeed follow the predictions based on Levins's fitness set approach. This dichotomy in the evolutionary dynamics of traits involved in the same foraging process was not previously recognized.

Conservation of Natural Resources↗

Maternal effects, paternal effects and sexual selection.

Maternal and paternal effects can lead to complicated evolutionary dynamics, including evolution in the opposite direction to selection. Recent studies demonstrate that parental effects on sexually selected traits, as well as preferences for those traits, might be large. Although these findings are likely to have consequences for both the evolutionary dynamics and equilibria of sexual selection, theory is lacking. Because parents are expected to maximize their own fitness, rather than that of a specific offspring, the magnitude (and even direction) of parental effects are context dependent. By extension, this dynamic nature of parental effects might help to explain the maintenance of variation in many sexually selected traits.

Journal Article↗

The mammalian model for population studies of B chromosomes: the wood mouse (Apodemus).

The presence of B chromosomes was reported in six species of the genus Apodemus (A. peninsulae, A. agrarius, A. sylvaticus, A. flavicollis, A. mystacinus, A. argenteus). High frequencies of Bs were recorded particularly in A. peninsulae and A. flavicollis. The origin of Bs in Apodemus seems to be rather ancient, and it is possible that the supernumerary elements, and/or a tendency for their appearance, were inherited from the common ancestor of the extant species. We have not found any correlated changes between frequencies of Bs and the level of protein polymorphism and/or heterozygosity assessed in electrophoretic studies. No measurable effect of Bs on overall genetic variability was thus revealed in studied populations. The pattern of evolutionary dynamics of Bs can be distinctly different between geographical populations, and both the parasitic and the heterotic models can be applied to explain the maintenance of Bs in different populations. Further studies are desirable to improve our understanding of the complicated evolutionary dynamics of Bs in the Apodemus species. An essential condition for success in this respect is much more detailed information on inheritance and the molecular structure of Bs.

Animals↗

The role of epistatic gene interactions in the response to selection and the evolution of evolvability.

It has been argued that the architecture of the genotype-phenotype map determines evolvability, but few studies have attempted to quantify these effects. In this article we use the multilinear epistatic model to study the effects of different forms of epistasis on the response to directional selection. We derive an analytical prediction for the change in the additive genetic variance, and use individual-based simulations to understand the dynamics of evolvability and the evolution of genetic architecture. This shows that the major determinant for the evolution of the additive variance, and thus the evolvability, is directional epistasis. Positive directional epistasis leads to an acceleration of evolvability, while negative directional epistasis leads to canalization. In contrast, pure non-directional epistasis has little effect on the response to selection. One consequence of this is that the classical epistatic variance components, which do not distinguish directional and non-directional effects, are useless as predictors of evolutionary dynamics. The build-up of linkage disequilibrium also has negligible effects. We argue that directional epistasis is likely to have major effects on evolutionary dynamics and should be the focus of empirical studies of epistasis.

Biological Evolution↗

Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins.

By analytical theory and computer simulation the expected evolutionary dynamics of P transposable element spread in an infinite population are investigated. The analysis is based on the assumption that, unlike transposable elements which move via RNA intermediates, the harmful effects of P elements arise primarily in the act of transposition, and that this causes their evolutionary dynamics to be unusual. It is suggested that a situation of transposition-selection balance will be superceded by the buildup of a cytoplasmically inherited repression or by the elimination of active transposase-encoding elements from the chromosomes, a process which may be accompanied by the evolution of elements which encode proteins which repress transposition.

Animals↗

Computational and evolutionary aspects of language.

Language is our legacy. It is the main evolutionary contribution of humans, and perhaps the most interesting trait that has emerged in the past 500 million years. Understanding how darwinian evolution gives rise to human language requires the integration of formal language theory, learning theory and evolutionary dynamics. Formal language theory provides a mathematical description of language and grammar. Learning theory formalizes the task of language acquisition it can be shown that no procedure can learn an unrestricted set of languages. Universal grammar specifies the restricted set of languages learnable by the human brain. Evolutionary dynamics can be formulated to describe the cultural evolution of language and the biological evolution of universal grammar.

Biological Evolution↗