The evolution of genetic architectures underlying quantitative traits

In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in QTL mapping have begun to elucidate the genetic architectures underlying vast numbers of phenotypes across diverse taxa, producing observations that sometimes contrast with Fisher's blueprint. Despite these considerable empirical efforts to map the genetic determinants of traits, it remains poorly understood how the genetic architecture of a trait should evolve, or how it depends on the selection pressures on the trait. Here we develop a simple, population-genetic model for the evolution of genetic architectures. Our model predicts that traits under moderate selection should be encoded by many loci with highly variable effects, whereas traits under either weak or strong selection should be encoded by relatively few loci. We compare these theoretical predictions to qualitative trends in the genetics of human traits, and to systematic data on the genetics of gene expression levels in yeast. Our analysis provides an evolutionary explanation for broad empirical patterns in the genetic basis of traits, and it introduces a single framework that unifies the diversity of observed genetic architectures, ranging from Mendelian to Fisherian.Comment: Minor changes in the text; Added supplementary materia

Small games and long memories promote cooperation

Complex social behaviors lie at the heart of many of the challenges facing evolutionary biology, sociology, economics, and beyond. For evolutionary biologists in particular the question is often how such behaviors can arise \textit{de novo} in a simple evolving system. How can group behaviors such as collective action, or decision making that accounts for memories of past experience, emerge and persist? Evolutionary game theory provides a framework for formalizing these questions and admitting them to rigorous study. Here we develop such a framework to study the evolution of sustained collective action in multi-player public-goods games, in which players have arbitrarily long memories of prior rounds of play and can react to their experience in an arbitrary way. To study this problem we construct a coordinate system for memory-$m$ strategies in iterated $n$-player games that permits us to characterize all the cooperative strategies that resist invasion by any mutant strategy, and thus stabilize cooperative behavior. We show that while larger games inevitably make cooperation harder to evolve, there nevertheless always exists a positive volume of strategies that stabilize cooperation provided the population size is large enough. We also show that, when games are small, longer-memory strategies make cooperation easier to evolve, by increasing the number of ways to stabilize cooperation. Finally we explore the co-evolution of behavior and memory capacity, and we find that longer-memory strategies tend to evolve in small games, which in turn drives the evolution of cooperation even when the benefits for cooperation are low

The collapse of cooperation in evolving games

Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner's Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players' strategies as well as their payoffs to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions, and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the co-evolution of strategies and payoffs in arbitrary iterated games. We show that, as payoffs evolve, a trade-off between the benefits and costs of cooperation precipitates a dramatic loss of cooperation under the Iterated Prisoner's Dilemma; and eventually to evolution away from the Prisoner's Dilemma altogether. The collapse of cooperation is so extreme that the average payoff in a population may decline, even as the potential payoff for mutual cooperation increases. Our work offers a new perspective on the Prisoner's Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the co-evolution of strategies and payoffs in iterated interactions.Comment: 33 pages, 13 figure

The evolution of complex gene regulation by low specificity binding sites

Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained and lost. Nevertheless, we have a relatively poor understanding of what evolutionary forces determine the specificity of binding sites. Here we address this question by studying regulatory modules composed of multiple binding sites. Using a population-genetic model, we show that more complex regulatory modules, composed of a greater number of binding sites, must employ binding sites that are individually less specific, compared to less complex regulatory modules. This effect is extremely general, and it hold regardless of the regulatory logic of a module. We attribute this phenomenon to the inability of stabilising selection to maintain highly specific sites in large regulatory modules. Our analysis helps to explain broad empirical trends in the yeast regulatory network: those genes with a greater number of transcriptional regulators feature by less specific binding sites, and there is less variance in their specificity, compared to genes with fewer regulators. Likewise, our results also help to explain the well-known trend towards lower specificity in the transcription factor binding sites of higher eukaryotes, which perform complex regulatory tasks, compared to prokaryotes

Historical contingency and entrenchment in protein evolution under purifying selection

The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the course of protein evolution across divergent species. Whereas epistasis between adaptive substitutions has been the subject of extensive study, relatively little is known about epistasis under purifying selection. Here we use mechanistic models of thermodynamic stability in a ligand-binding protein to explore the structure of epistatic interactions between substitutions that fix in protein sequences under purifying selection. We find that the selection coefficients of mutations that are nearly-neutral when they fix are highly contingent on the presence of preceding mutations. Conversely, mutations that are nearly-neutral when they fix are subsequently entrenched due to epistasis with later substitutions. Our evolutionary model includes insertions and deletions, as well as point mutations, and so it allows us to quantify epistasis within each of these classes of mutations, and also to study the evolution of protein length. We find that protein length remains largely constant over time, because indels are more deleterious than point mutations. Our results imply that, even under purifying selection, protein sequence evolution is highly contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the wild-type sequence.Comment: 42 pages, 13 figure