Inbreeding depression (i.e. negative fitness effects of inbreeding) is central in evolutionary biology, affecting numerous aspects of population dynamics and demography, such as the evolution of mating systems, dispersal behaviour and the genetics of quantitative traits. Inbreeding depression is commonly observed in animals and plants. Here, we demonstrate that, in addition to genetic processes, epigenetic processes may play an important role in causing inbreeding effects. We compared epigenetic markers of outbred and inbred offspring of the perennial plant Scabiosa columbaria and found that inbreeding increases DNA methylation. Moreover, we found that inbreeding depression disappears when epigenetic variation is modified by treatment with a demethylation agent, linking inbreeding depression firmly to epigenetic variation. Our results suggest an as yet unknown mechanism for inbreeding effects and demonstrate the importance of evaluating the role of epigenetic processes in inbreeding depression.

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.

Metrics of success or impact in academia may do more harm than good. To explore the value of citations, the reported efficacy of treatments in ecology and evolution from close to 1,500 publications was examined. If citation behavior is rationale, i.e. studies that successfully applied a treatment and detected greater biological effects are cited more frequently, then we predict that larger effect sizes increases study relative citation rates. This prediction was not supported. Citations are likely thus a poor proxy for the quantitative merit of a given treatment in ecology and evolutionary biology—unlike evidence-based medicine wherein the success of a drug or treatment on human health is one of the critical attributes. Impact factor of the journal is a broader metric, as one would expect, but it also unrelated to the mean effect sizes for the respective populations of publications. The interpretation by the authors of the treatment effects within each study differed depending on whether the hypothesis was supported or rejected. Significantly larger effect sizes were associated with rejection of a hypothesis. This suggests that only the most rigorous studies reporting negative results are published or that authors set a higher burden of proof in rejecting a hypothesis. The former is likely true to a major extent since only 29 % of the studies rejected the hypotheses tested. These findings indicate that the use of citations to identify important papers in this specific discipline—at least in terms of designing a new experiment or contrasting treatments—is of limited value.

Producing equal amounts of male and female offspring has long been considered an evolutionarily stable strategy. Nevertheless, exceptions to this general rule (i.e. male and female biases) are documented in many taxa, making sex allocation an important domain in current evolutionary biology research. Pinpointing the underlying mechanism of sex ratio bias is challenging owing to the multitude of potential sex ratio-biasing factors. In the dwarf spider, Oedothorax gibbosus, infection with the bacterial endosymbiont Wolbachia results in a female bias. However, pedigree analysis reveals that other factors influence sex ratio variation. In this paper, we investigate whether this additional variation can be explained by the unequal production of male- and female-determining sperm cells during sperm production. Using flow cytometry, we show that males produce equal amounts of male- and female-determining sperm cells; thus bias in sperm production does not contribute to the sex ratio bias observed in this species. This demonstrates that other factors such as parental genes suppressing endosymbiont effects and cryptic female choice might play a role in sex allocation in this species.

An overview of the scientific literature shows that the concept of function is central in physiology. However, the concept itself is not defined by physiologists. On the other hand, the teleological, namely, the ‘goal-directed’ dimension of function, and its subsequent explanatory relevance, is a philosophical problem. Intuitively, the function of a trait in a system explains why this trait is present, but, in the early 1960s, Ernest Nagel and Carl Hempel have shown that this inference cannot be logically founded. However, they showed that self-regulated systems are teleological. According to the selectionist theories, the function of an item is its effect that has been selected by natural selection, a process that explains its presence. As they restrict the functional attribution of a trait to its past selective value and not its current properties, these theories are inconsistent with the concept of function in physiology. A more adequate one is the causal role theory, for which a function of a trait in a system is its causal contribution to the functional capacity of the system. However, this leaves unsolved the question of the ‘surplus meaning’ of the teleological dimension of function. The significance of considering organisms as ‘purpose-like’ (teleological) systems may reside not in its explanatory power but in its methodological fruitfulness in physiology. In this view...

The rates and properties of new mutations affecting fitness have implications for a number of outstanding questions in evolutionary biology. Obtaining estimates of mutation rates and effects has historically been challenging, and little theory has been available for predicting the distribution of fitness effects (DFE); however, there have been recent advances on both fronts. Extreme-value theory predicts the DFE of beneficial mutations in well-adapted populations, while phenotypic fitness landscape models make predictions for the DFE of all mutations as a function of the initial level of adaptation and the strength of stabilizing selection on traits underlying fitness. Direct experimental evidence confirms predictions on the DFE of beneficial mutations and favors distributions that are roughly exponential but bounded on the right. A growing number of studies infer the DFE using genomic patterns of polymorphism and divergence, recovering a wide range of DFE. Future work should be aimed at identifying factors driving the observed variation in the DFE. We emphasize the need for further theory explicitly incorporating the effects of partial pleiotropy and heterogeneity in the environment on the expected DFE.

Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals. Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice (Peromyscus polionotus). One mainland subspecies has a cryptic dark brown dorsal coat, while a younger beach-dwelling subspecies has a lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, we identified three chromosomal regions (two of major and one of minor effect) associated with differences in pigmentation traits. Two candidate genes, the melanocortin-1 receptor (Mc1r) and its antagonist, the Agouti signaling protein (Agouti), map to independent regions that together are responsible for most of the difference in pigmentation between subspecies. A derived mutation in the coding region of Mc1r, rather than change in its expression level, contributes to light pigmentation. Conversely, beach mice have a derived increase in Agouti mRNA expression but no changes in protein sequence. These two genes also interact epistatically: the phenotypic effects of Mc1r are visible only in genetic backgrounds containing the derived Agouti allele. These results demonstrate that cryptic coloration can be based largely on a few interacting genes of major effect.; Organismic and Evolutionary Biology

A large body of theoretical work suggests that analyses of variation at the maternally inherited mitochondrial (mt)DNA and the paternally inherited non-recombining portion of the Y chromosome (NRY) are a potentially powerful way to reveal the differing migratory histories of men and women across human societies. However, the few empirical studies comparing mtDNA and NRY variation and known patterns of sex-biased migration have produced conflicting results. Here we review some methodological reasons for these inconsistencies, and take them into account to provide an unbiased characterization of mtDNA and NRY variation in chimpanzees, one of the few mammalian taxa where males routinely remain in and females typically disperse from their natal groups. We show that patterns of mtDNA and NRY variation are more strongly contrasting in patrilocal chimpanzees compared with patrilocal human societies. The chimpanzee data we present here thus provide a valuable comparative benchmark of the patterns of mtDNA and NRY variation to be expected in a society with extremely female-biased dispersal.; Anthropology; Human Evolutionary Biology

The spatiotemporal distribution of females is thought to drive variation in mating systems, and hence plays a central role in understanding animal behavior, ecology and evolution. Previous research has focused on investigating the links between female spatiotemporal distribution and the number of males in haplorhine primates. However, important questions remain concerning the importance of spatial cohesion, the generality of the pattern across haplorhine and strepsirrhine primates, and the consistency of previous findings given phylogenetic uncertainty. To address these issues, we examined how the spatiotemporal distribution of females influences the number of males in primate groups using an expanded comparative dataset and recent advances in Bayesian phylogenetic and statistical methods. Specifically, we investigated the effect of female distributional factors (female number, spatial cohesion, estrous synchrony, breeding season duration and breeding seasonality) on the number of males in primate groups. Using Bayesian approaches to control for uncertainty in phylogeny and the model of trait evolution, we found that the number of females exerted a strong influence on the number of males in primate groups. In a multiple regression model that controlled for female number...

Punishment offers a powerful mechanism for the maintenance of cooperation in human and animal societies, but the maintenance of costly punishment itself remains problematic. Game theory has shown that corruption, where punishers can defect without being punished themselves, may sustain cooperation. However, in many human societies and some insect ones, high levels of cooperation coexist with low levels of corruption, and such societies show greater wellbeing than societies with high corruption. Here we show that small payments from cooperators to punishers can destabilize corrupt societies and lead to the spread of punishment without corruption (righteousness). Righteousness can prevail even in the face of persistent power inequalities. The resultant righteous societies are highly stable and have higher wellbeing than corrupt ones. This result may help to explain the persistence of costly punishing behavior, and indicates that corruption is a sub-optimal tool for maintaining cooperation in human societies.; Organismic and Evolutionary Biology

The Neotropics is rich in biodiversity and arguably contains some of the least understood and most understudied predators of the world. Jaguars and other carnivores represent the highest trophic levels within Neotropical areas that can markedly alter vertebrate communities and indirectly plant communities—leading to greater overall biodiversity. Their elusive nature and diffuse distributions within difficult to access areas make their data extremely difficult, time consuming and expensive to obtain. Thus, we considered it essential to bring together the world’s leading Neotropical carnivore specialists to compile their most recent data altogether in a single publication that would be available to conservation managers of Neotropical areas. This chapter describes the book’s main themes (molecular population genetics, evolutionary biology, and biological conservation) and how itpresents Neotropical carnivore data in different categories such as by guild (all Neotropical carnivores), by family, and when appropriate, by species. The remaining part of this chapter describes specific species of interest (jaguar, jaguarundi, guigna, pampas cat, Andean mountain cat...

An enduring problem in evolutionary biology is the near ubiquity of sexual reproduction despite the inherent cost of transmitting only half the parent's genes to progeny. Queens of some ant species circumvent this cost by using selectively both sexual reproduction and parthenogenesis: workers arise from fertilized eggs, while new queens are produced by parthenogenesis. We show that queens of the ant Cataglyphis cursor maximize the transmission rate of their genes by regulating the proportion of fertilized and parthenogenetic eggs laid over time. Parthenogenetic offspring are produced in early spring, when workers raise the brood into sexuals. After the mating period, queens lay mostly fertilized eggs that will be reared as the non-reproductive caste.

Many forms of developmental plasticity have been observed and these are usually beneficial to the organism. The Predictive Adaptive Response (PAR) hypothesis refers to a form of developmental plasticity in which cues received in early life influence the development of a phenotype that is normally adapted to the environmental conditions of later life. When the predicted and actual environments differ, the mismatch between the individual's phenotype and the conditions in which it finds itself can have adverse consequences for Darwinian fitness and, later, for health. Numerous examples exist of the long-term effects of cues indicating a threatening environment affecting the subsequent phenotype of the individual organism. Other examples consist of the long-term effects of variations in environment within a normal range, particularly in the individual's nutritional environment. In mammals the cues to developing offspring are often provided by the mother's plane of nutrition, her body composition or stress levels. This hypothetical effect in humans is thought to be important by some scientists and controversial by others. In resolving the conflict, distinctions should be drawn between PARs induced by normative variations in the developmental environment and the ill effects on development of extremes in environment such as a very poor or very rich nutritional environment. Tests to distinguish between different developmental processes impacting on adult characteristics are proposed. Many of the mechanisms underlying developmental plasticity involve molecular epigenetic processes...

Computational methods have revolutionized evolutionary biology. In this paper we explore the impact these methods are now having on our understanding of the forces that both affect the diversification of human languages and shape human cognition. We show

In the past years, a remarkable mapping has been found between the dynamics of a population of M individuals undergoing random mutations and selection, and that of a single system in contact with a thermal bath with temperature 1/M. This correspondence holds under the somewhat restrictive condition that the population is dominated by a single type at almost all times, punctuated by rare successive mutations. Here we argue that such thermal dynamics will hold more generally, specifically in systems with rugged fitness landscapes. This includes cases with strong clonal interference, where a number of concurrent mutants dominate the population. The problem becomes closely analogous to the experimental situation of glasses subjected to controlled variations of parameters such as temperature, pressure or magnetic fields. Non-trivial suggestions from the field of glasses may be thus proposed for evolutionary systems - including a large part of the numerical simulation procedures - that in many cases would have been counter intuitive without this background.

The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key must lie in the creation of increased variability in offspring, causing enhanced response to selection. Rigorously quantifying the effects of assorted mechanisms which might lead to such increased variability, and establishing that these beneficial effects outweigh the immediate costs of sexual reproduction has, however, proved problematic. Here we introduce an approach which does not focus on particular mechanisms influencing factors such as the fixation of beneficial mutants or the ability of populations to deal with deleterious mutations, but rather tracks the entire distribution of a population of genotypes as it moves across vast fitness landscapes. In this setting simulations now show sex robustly outperforming asex across a broad spectrum of finite or infinite population models. Concentrating on the additive infinite populations model, we are able to give a rigorous mathematical proof establishing that sexual reproduction acts as a more efficient optimiser of mean fitness, thereby solving the problem for this model. Some of the key features of this analysis carry through to the finite populations case.

Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have received relatively less attention. Here we present a structured population model where different individuals are best suited to different regions of their environment. The underlying structure is a graph: individuals occupy vertices, which are connected by edges. If an individual is suited for their vertex, they receive an increase in fecundity. This framework allows attention to be restricted to the spatial arrangement of suitable habitat. We prove some basic properties of this model and find some counter-intuitive results. Notably, 1) the arrangement of suitable sites is as important as their proportion, and, 2) decreasing the proportion of suitable sites may result in a decrease in the fixation time of an allele.

Energy efficiency is gaining importance in wireless communication networks which have nodes with limited energy supply and signal processing capabilities. We present a numerical study of cooperative communication scenarios based on simple local rules. This is in contrast to most of the approaches in the literature which enforce cooperation by using complex algorithms and require strategic complexity of the network nodes. The approach is motivated by recent results in evolutionary biology which suggest that, if certain mechanism is at work, cooperation can be favoured by natural selection, i. e. even selfish actions of the individual nodes can lead to emergence of cooperative behaviour in the network. The results of the simulations in the context of wireless communication networks verify these observations and indicate that uncomplicated local rules, followed by simple fitness evaluation, can generate network behaviour which yields global energy efficiency.; Comment: The paper is accepted for publication at the International Workshop on Physics-inspired Paradigms in Wireless Communications and Networks - PHYSCOMNET 2014, in conjunction with the 12th Intl. Symposium on Modelling and Optimization in Mobile, Ad Hoc, and Wireless Networks - WIOPT...

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This

The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000 species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting via a web-based interface at "http://kb.phenoscape.org":http://kb.phenoscape.org.