Epigenetics and the environment: emerging patterns and implications

The rarer-sex effect

The study of sex allocation-that is, the investment of resources into male versus female reproductive effort-yields among the best quantitative evidence for Darwinian adaptation, and has long enjoyed a tight and productive interplay of theoretical and empirical research. The fitness consequences of an individual's sex allocation decisions depend crucially upon the sex allocation behaviour of others and, accordingly, sex allocation is readily conceptualized in terms of an evolutionary game. Here, I investigate the historical development of understanding of a fundamental driver of the evolution of sex allocation-the rarer-sex effect-from its inception in the writing of Charles Darwin in 1871 through to its explicit framing in terms of consanguinity and reproductive value by William D. Hamilton in 1972. I show that step-wise development of theory proceeded through refinements in the conceptualization of the strategy set, the payoff function and the unbeatable strategy. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Evolutionarily stable strategy analysis and its links to demography and genetics through invasion fitness

Evolutionarily stable strategy (ESS) analysis pioneered by Maynard Smith and Price took off in part because it often does not require explicit assumptions about the genetics and demography of a population in contrast to population genetic models. Though this simplicity is useful, it obscures the degree to which ESS analysis applies to populations with more realistic genetics and demography: for example, how does ESS analysis handle complexities such as kin selection, group selection and variable environments when phenotypes are affected by multiple genes? In this paper, I review the history of the ESS concept and show how early uncertainty about the method lead to important mathematical theory linking ESS analysis to general population genetic models. I use this theory to emphasize the link between ESS analysis and the concept of invasion fitness. I give examples of how invasion fitness can measure kin selection, group selection and the evolution of linked modifier genes in response to variable environments. The ESSs in these examples depend crucially on demographic and genetic parameters, which highlights how ESS analysis will continue to be an important tool in understanding evolutionary patterns as new models address the increasing abundance of genetic and long-term demographic data in natural populations. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Stackelberg evolutionary game theory: how to manage evolving systems

Stackelberg evolutionary game (SEG) theory combines classical and evolutionary game theory to frame interactions between a rational leader and evolving followers. In some of these interactions, the leader wants to preserve the evolving system (e.g. fisheries management), while in others, they try to drive the system to extinction (e.g. pest control). Often the worst strategy for the leader is to adopt a constant aggressive strategy (e.g. overfishing in fisheries management or maximum tolerable dose in cancer treatment). Taking into account the ecological dynamics typically leads to better outcomes for the leader and corresponds to the Nash equilibria in game-theoretic terms. However, the leader's most profitable strategy is to anticipate and steer the eco-evolutionary dynamics, leading to the Stackelberg equilibrium of the game. We show how our results have the potential to help in fields where humans try to bring an evolutionary system into the desired outcome, such as, among others, fisheries management, pest management and cancer treatment. Finally, we discuss limitations and opportunities for applying SEGs to improve the management of evolving biological systems. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Game theory in biology: 50 years and onwards

Game theory in biology gained prominence 50 years ago, when Maynard Smith & Price formulated the concept of an evolutionarily stable strategy (ESS). Their aim was to explain why conflicts between animals of the same species usually are of a 'limited war' type, not causing serious injury. They emphasized that game theory is an alternative to previous ideas about group selection, which were used by ethologists to explain limited aggression. Subsequently, the ESS concept was applied to many phenomena with frequency dependence in the evolutionary success of strategies, including sex allocation, alternative mating types, contest behaviour and signalling, cooperation, and parental care. Both the analyses of signalling and cooperation were inspired by similar problems in economics and attracted much attention in biology. Here we give a perspective on which of the ambitions in the field have been achieved, with a focus on contest behaviour and cooperation. We evaluate whether the game-theoretical study of the evolution of cooperation has measured up to expectations in explaining the behaviour of non-human animals. We also point to potentially fruitful directions for the field, and emphasize the importance of incorporating realistic behavioural mechanisms into models. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Evolutionary game theory of continuous traits from a causal perspective

Modern evolutionary game theory typically deals with the evolution of continuous, quantitative traits under weak selection, allowing the incorporation of rich biological detail and complicated nonlinear interactions. While these models are commonly used to find candidates for evolutionary endpoints and to approximate evolutionary trajectories, a less appreciated property is their potential to expose and clarify the causal structure of evolutionary processes. The mathematical step of differentiation breaks a nonlinear model into additive components which are more intuitive to interpret, and when combined with a proper causal hypothesis, partial derivatives in such models have a causal meaning. Such an approach has been used in the causal analysis of game-theoretical models in an informal manner. Here we formalize this approach by linking evolutionary game theory to concepts developed in causal modelling over the past century, from path coefficients to the recently proposed causal derivative. There is a direct correspondence between the causal derivative and the derivative used in evolutionary game theory. Some game theoretical models (e.g. kin selection) consist of multiple causal derivatives. Components of these derivatives correspond to components of the causal derivative, to path coefficients, and to edges on a causal graph, formally linking evolutionary game theory to causal modelling. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

The early rise and spread of evolutionary game theory: perspectives based on recollections of early workers

Though the first attempts to introduce game theory into evolutionary biology failed, new formalism by Maynard Smith and Price in 1973 had almost instant success. We use information supplied by early workers to analyse how and why evolutionary game theory (EGT) spread so rapidly in its earliest years. EGT was a major tool for the rapidly expanding discipline of behavioural ecology in the 1970s; each catalysed the other. The first models were applied to animal contests, and early workers sought to improve their biological reality to compare predictions with observations. Furthermore, it was quickly realized that EGT provided a general evolutionary modelling method; not only was it swiftly applied to diverse phenotypic adaptations in evolutionary biology, it also attracted researchers from other disciplines such as mathematics and economics, for which game theory was first devised. Lastly, we pay attention to exchanges with population geneticists, considering tensions between the two modelling methods, as well as efforts to bring them closer. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Evolutionary game theory and the adaptive dynamics approach: adaptation where individuals interact

Evolutionary game theory and the adaptive dynamics approach have made invaluable contributions to understanding how gradual evolution leads to adaptation when individuals interact. Here, we review some of the basic tools that have come out of these contributions to model the evolution of quantitative traits in complex populations. We collect together mathematical expressions that describe directional and disruptive selection in class- and group-structured populations in terms of individual fitness, with the aims of bridging different models and interpreting selection. In particular, our review of disruptive selection suggests there are two main paths that can lead to diversity: (i) when individual fitness increases more than linearly with trait expression; (ii) when trait expression simultaneously increases the probability that an individual is in a certain context (e.g. a given age, sex, habitat, size or social environment) and fitness in that context. We provide various examples of these and more broadly argue that population structure lays the ground for the emergence of polymorphism with unique characteristics. Beyond this, we hope that the descriptions of selection we present here help see the tight links among fundamental branches of evolutionary biology, from life history to social evolution through evolutionary ecology, and thus favour further their integration. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

The evolutionarily stable strategy, animal contests, parasitoids, pest control and sociality

The evolutionarily stable strategy, ESS, concept was first used in biology to understand sex ratio bias and, shortly afterwards, to explore the logic of contests over essential and indivisible resources. ESS models formed the basis of much subsequent research on animal behaviour and placed game-theoretic thinking firmly within the behavioural ecology approach. Among behavioural ecologists studying parasitoids, it was those asking questions about the evolution of sex ratios who first made extensive use of the game-theoretic approach. A later growth of interest in parasitoid host defence and fighting behaviour made use of these tractable study species to explore contests and their connections to further aspects of life-history evolution plus some pest control applications. Our aims are to (i) introduce the topic of contests, which are engaged in by a very wide array of animal taxa, and the importance, both historical and conceptual, of the game-theoretic approach to their study, and (ii) review recent studies of parasitoid contests, including those that have considered the context of social evolution and the performance of parasitoids as agents of biological control. We consider that game-theoretic models are eminently testable and applicable and will likely endure as valuable tools in studies of parasitoid biology. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Variance in offspring sex ratio and maternal allocation in a highly invasive mammal

Skewed sex ratios at birth are widely reported in wild populations, however, the extent to which parents are able to modulate the sex ratio of offspring to maximize their own fitness remains unclear. This is particularly true for highly polytocous species as maximizing fitness may include trade-offs between sex ratio and the size and number of offspring in litters. In such cases, it may be adaptive for mothers to adjust both the number of offspring per litter and offspring sex to maximize individual fitness. Investigating maternal sex allocation in wild pigs (Sus scrofa) under stochastic environmental conditions, we predicted that under favorable conditions, high-quality mothers (larger and older) would produce male-biased litters and invest more in producing larger litters with more males. We also predicted sex ratio would vary relative to litter size, with a male-bias among smaller litters. We found evidence that increasing wild boar ancestry, maternal age and condition, and resource availability may weakly contribute to male-biased sex ratio, however, unknown factors not measured in this study are assumed to be more influential. High-quality mothers allocated more resources to litter production, but this relationship was driven by adjustment of litter size, not sex ratio. There was no relationship between sex ratio and litter size. Collectively, our results emphasized that adjustment of litter size appeared to be the primary reproductive characteristic manipulated in wild pigs to increase fitness rather than adjustment of offspring sex ratio.

Population growth of Tetranychus truncatus (Acari: Tetranychidae) on different drought-tolerant potato cultivars

Tetranychus truncatus Ehara (Acari: Tetranychidae) has become one of the major phytophagous pests in China in recent years, and is found on a wide range of host plants. However, little information is available on the population performance of this arthropod pest on potatoes. In this study, we explored the population growth of T. truncatus on two drought-tolerant potato (Solanum tuberosum L.) cultivars under laboratory conditions using the age-stage, two-sex life table. Tetranychus truncatus completed its entire life history on both potato cultivars tested, Holland 15 and Longshu 10. There was no significant difference between two potato cultivars in developmental duration. Tetranychus truncatus had shorter adult longevity (20.61 days), adult female longevity (20.41 days), and total female longevity (33.66 days) on Longshu 10 than Holland 15 (21.16 days, 21.19 days, and 34.38 days, respectively). However, it exhibited a higher preadult survival rate, higher fecundity (F = 88.32 eggs per female), and relatively higher population parameters when reared on Longshu 10 than on Holland 15 (F = 75.70 eggs per female). Growth projection also showed that the population size of T. truncatus on Longshu 10 (expand 750-fold) was larger than that on Holland 15 (expand 273-fold) after 60 days. Our results demonstrate that the drought-sensitive potato variety, Holland 15, is relatively resistant to T. truncatus compared with the drought-tolerant variety, Longshu 10, and suggest that T. truncatus exhibited a trade-off between longevity and reproduction on both potato cultivars. Our findings provide information on population prediction, which may aid the management of this pest mite species of potatoes.

Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park

Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model's predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.

Female preference for rare males is maintained by indirect selection in Trinidadian guppies

When females prefer mates with rare phenotypes, sexual selection can maintain rather than deplete genetic variation. However, there is no consensus on why this widespread and frequently observed preference might evolve and persist. We examine the fitness consequences of female preference for rare male color patterns in a natural population of Trinidadian guppies, using a pedigree that spans 10 generations. We demonstrate (i) a rare male reproductive advantage, (ii) that females that mate with rare males gain an indirect fitness advantage through the mating success of their sons, and (iii) the fitness benefit that females accrue through their "sexy sons" evaporates for their grandsons as their phenotype becomes common. Counter to prevailing theory, we show that female preference can be maintained through indirect selection.

Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster

Fertility is a major component of fitness but its genetic architecture remains poorly understood. Using a full diallel cross of 50 Drosophila Genetic Reference Panel inbred lines with whole genome sequences, we found substantial genetic variation in fertility largely attributable to females. We mapped genes associated with variation in female fertility by genome-wide association analysis of common variants in the fly genome. Validation of candidate genes by RNAi knockdown confirmed the role of the dopamine 2-like receptor (Dop2R) in promoting egg laying. We replicated the Dop2R effect in an independently collected productivity dataset and showed that the effect of the Dop2R variant was mediated in part by regulatory gene expression variation. This study demonstrates the strong potential of genome-wide association analysis in this diverse panel of inbred strains and subsequent functional analyses for understanding the genetic architecture of fitness traits.

Molecular patterns and processes in evolving sociality: lessons from insects

Social insects have provided some of the clearest insights into the origins and evolution of collective behaviour. Over 20 years ago, Maynard Smith and Szathmáry defined the most complex form of insect social behaviour-superorganismality-among the eight major transitions in evolution that explain the emergence of biological complexity. However, the mechanistic processes underlying the transition from solitary life to superorganismal living in insects remain rather elusive. An overlooked question is whether this major transition arose via incremental or step-wise modes of evolution. We suggest that examination of the molecular processes underpinning different levels of social complexity represented across the major transition from solitary to complex sociality can help address this question. We present a framework for using molecular data to assess to what extent the mechanistic processes that take place in the major transition to complex sociality and superorganismality involve nonlinear (implying step-wise evolution) or linear (implying incremental evolution) changes in the underlying molecular mechanisms. We assess the evidence for these two modes using data from social insects and discuss how this framework can be used to test the generality of molecular patterns and processes across other major transitions. This article is part of a discussion meeting issue 'Collective behaviour through time'.

Clustering drives cooperation on reputation networks, all else fixed

Reputation-based cooperation on social networks offers a causal mechanism between graph properties and social trust. Using a simple model, this paper demonstrates the underlying mechanism in a way that is accessible to scientists not specializing in networks or mathematics. The paper shows that when the size and degree of the network is fixed (i.e. all graphs have the same number of agents, who all have the same number of connections), it is the clustering coefficient that drives differences in how cooperative social networks are.

On Nonstationary Gaussian Process Model for Solving Data-Driven Optimization Problems

In data-driven evolutionary optimization, most existing Gaussian processes (GPs)-assisted evolutionary algorithms (EAs) adopt stationary GPs (SGPs) as surrogate models, which might be insufficient for solving most optimization problems. This article finds that GPs in the optimization problems are nonstationary with great probability. We propose to employ a nonstationary GP (NSGP) surrogate model for data-driven evolutionary optimization, where the mean of the NSGP is allowed to vary with the decision variables, while its residue variance follows an SGP. In this article, the nonstationarity of GPs in the tested functions is theoretically analyzed. In addition, this article constructs an NSGP where the SGP is a degenerate case. Performance comparisons of the NSGP with the SGP and the NSGP-assisted EA (NSGP-MAEA) with the SGP-assisted EA (SGP-MAEA) are carried out on a set of benchmark problems and an antenna design problem. These comparison results demonstrate the competitiveness of the NSGP model.

Proportional processing of a visual mate choice signal in the green swordtail, Xiphophorus hellerii

During mate choice, receivers often assess the magnitude (duration, size, etc.) of signals that vary along a continuum and reflect variation in signaller quality. It is generally assumed that receivers assess this variation linearly, meaning each difference in signalling trait between signallers results in a commensurate change in receiver response. However, increasing evidence shows receivers can respond to signals non-linearly, for example through Weber's Law of proportional processing, where discrimination between stimuli is based on proportional, rather than absolute, differences in magnitude. We quantified mate preferences of female green swordtail fish, Xiphophorus hellerii, for pairs of males differing in body size. Preferences for larger males were better predicted by the proportional difference between males (proportional processing) than the absolute difference (linear processing). This demonstration of proportional processing of a visual signal implies that receiver perception may be an important mechanism selecting against the evolution of ever-larger signalling traits.

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.

Heritability Estimation Approaches Utilizing Genome-Wide Data

Prior to the development of genome-wide arrays and whole genome sequencing technologies, heritability estimation mainly relied on the study of related individuals. Over the past decade, various approaches have been developed to estimate SNP-based narrow-sense heritability (h SNP 2 ${\rm{h}}_{{\rm{SNP}}}^2$ ) in unrelated individuals. These latter approaches use either individual-level genetic variations or summary results from genome-wide association studies (GWAS). Recently, several studies compared these approaches using extensive simulations and empirical datasets. However, sparse information on hands-on training necessitates revisiting these approaches from the perspective of a stepwise guide for practical applications. Here, we provide an overview of the commonly used SNP-heritability estimation approaches utilizing genome-wide array, imputed or whole genome data from unrelated individuals, or summary results. We not only discuss these approaches based on their statistical concepts, utility, advantages, and limitations, but also provide step-by-step protocols to apply these approaches. For illustration purposes, we estimateh SNP 2 ${\rm{h}}_{{\rm{SNP}}}^2$ of height and BMI utilizing individual-level data from The Northern Finland Birth Cohort (NFBC) and summary results from the Genetic Investigation of ANthropometric Traits (GIANT;) consortium. We present this review as a template for the researchers who estimate and use heritability in their studies and as a reference for geneticists who develop or extend heritability estimation approaches. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: GREML (GCTA) Alternate Protocol 1: Stratified GREML Basic Protocol 2: LDAK Alternate Protocol 2: Stratified LDAK Basic Protocol 3: Threshold GREML Basic Protocol 4: LD score (LDSC) regression Basic Protocol 5: SumHer.

Indiscriminate Mating and the Coevolution of Sex Discrimination and Sexual Signals

AbstractThe presence of same-sex sexual behavior across the animal kingdom is often viewed as unexpected. One explanation for its prevalence in some taxa is indiscriminate mating-a strategy wherein an individual does not attempt to determine the sex of its potential partner before attempting copulation. Indiscriminate mating has been argued to be the ancestral mode of sexual reproduction and can also be an optimal strategy given search costs of choosiness. Less attention has been paid to the fact that sex discrimination requires not just the attempt to differentiate between the sexes but also some discernible difference (a signal or cue) that can be detected. To address this, we extend models of mating behavior to consider the coevolution of sex discrimination and sexual signals. We find that under a wide range of parameters, including some with relatively minor costs, indiscriminate mating and the absence of sexual signals will be an evolutionary end point. Furthermore, the absence of both sex discrimination and sexual signals is always evolutionarily stable. These results suggest that an observable difference between the sexes likely arose as a by-product of the evolution of different sexes, allowing discrimination to evolve.

Disruptive selection and the evolution of discrete color morphs in Timema stick insects

A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here, we show that Timema stick insects exhibit genetically determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.

Post-marital residence patterns and the timing of reproduction: evidence from a matrilineal society

Humans exhibit a broad range of post-marital residence patterns and there is growing recognition that post-marital residence predicts women's reproductive success; however, the nature of the relationship is probably dependent on whether co-resident kin are cooperators or competitors. Here, we explore this relationship in a Tibetan population, where couples practice a mixture of post-marital residence patterns, co-residing in the same village with the wife's parents, the husband's parents or endogamously with both sets of parents. Using detailed demographic data from 17 villages we find that women who live with only their own parents have an earlier age at first birth (AFB) and age at last birth (ALB) than women who live with only their parents-in-law. Women who co-reside with both sets of parents have the earliest AFB and ALB. However, those with co-resident older siblings postponed reproduction, suggestive of competition-related delay. Shifts to earlier reproductive timing were also observed in relation to the imposition of family planning policies, in line with Fisherian expectations. Our study provides evidence of the costs and benefits to women's direct fitness of co-residing with different kin, against a backdrop of adaptive responses to cultural constraints on completed fertility.

Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia

Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.

Assessment of population, habitat, and threats to Cycas pectinata Buch.-Ham. (Cycadaceae), a vulnerable cycad in Bhutan

Cycas pectinata Buch.-Ham. is an ancient gymnosperm that is now confined to pockets of habitats in the Indian subcontinent but was once widely distributed. Its decline is attributable to habitat loss, and has reached the point where C. pectinata is listed as ‘Vulnerable’ in the IUCN Red List. C. pectinata is the only species of Cycas found in Bhutan, and in this biodiversity-rich area it is present as a relic of great scientific and conservation value because of its rarity and long evolutionary history. Although it is well known in India, it has not been studied in detail in Bhutan. This study assessed populations and threats to C. pectinata in two places in Bhutan. Field visits were made to document the distribution, habitats, and associated threats to the populations. Plants were observed growing in steep rugged terrain in the open Chir Pine forest. Populations are significantly threatened due to human activities such as habitat destruction and over collection as ornamental plant. Possible expansion of populations is naturally threatened by low seed production and by predators. 

Origins of life: first came evolutionary dynamics

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking a molecule type, we seek a dynamical process. Biology required an ability to evolve before it could choose and optimise materials. We hypothesise that the evolution process was rooted in the peptide folding process. Modelling shows how short random peptides can collapse in water and catalyse the elongation of others, powering both increased folding stability and emergent autocatalysis through a disorder-to-order process.

Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis

In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.

Entropic Dynamics in a Theoretical Framework for Biosystems

Central to an understanding of the physical nature of biosystems is an apprehension of their ability to control entropy dynamics in their environment. To achieve ongoing stability and survival, living systems must adaptively respond to incoming information signals concerning matter and energy perturbations in their biological continuum (biocontinuum). Entropy dynamics for the living system are then determined by the natural drive for reconciliation of these information divergences in the context of the constraints formed by the geometry of the biocontinuum information space. The configuration of this information geometry is determined by the inherent biological structure, processes and adaptive controls that are necessary for the stable functioning of the organism. The trajectory of this adaptive reconciliation process can be described by an information-theoretic formulation of the living system's procedure for actionable knowledge acquisition that incorporates the axiomatic inference of the Kullback principle of minimum information discrimination (a derivative of Jaynes' principle of maximal entropy). Utilizing relative information for entropic inference provides for the incorporation of a background of the adaptive constraints in biosystems within the operations of Fisher biologic replicator dynamics. This mathematical expression for entropic dynamics within the biocontinuum may then serve as a theoretical framework for the general analysis of biological phenomena.

Temporal and spatial variations in local sex ratios in a suburban population of the European green toad Bufotes viridis

BACKGROUND

Sex ratios of animal populations are important factors of population demographics. In pond-breeding amphibians, the operational sex ratio (OSR) among the breeding population is usually male-biased. Also, in European green toads (Bufotes viridis), males usually outnumber females at breeding sites, while the sex ratio of the total adult population (ASR) is assumed to be balanced. It has been suggested that sex-specific breeding behavior causes male-predominance at the breeding sites. We used a dataset of 5 years of street patrols to test this hypothesis. For this we analyzed local sex ratios of green toads in terrestrial habitats and at two artificial breeding ponds. We expected temporal and/or spatial changes of local sex ratios which would indicate sex dependent differences in breeding behavior.

RESULTS

Overall observed ASR among 2111 green toads, counted in the course of street patrols from 2016 to 2020, was slightly male-biased (ASR = 0.56, annual ASRs = 0.49-0.63). Based on the data of 1631 toads (920 males, 711 females) captured within a radius of 300 m around nine main breeding sites, temporal and spatial variations in local ASRs were evaluated. Resulting values were compared to the calculated OSR at two artificial breeding ponds in 2021 (645 adult: 553 males, 92 females). Estimates predict more equally distributed females and males prior to the main breeding season. During breeding season, males predominated at both breeding sites (B1: 0.83, B2: 0.89), whereas females are estimated to outnumber males in terrestrial habitats. Proportions of females highly significantly increased with advancing time of the year and increasing distance to the breeding sites. While males tended to accumulate in proximity to water bodies, females dispersed soon after breeding to more distant areas.

CONCLUSIONS

Observed sex ratios in the studied green toad population changed with time and sampling site, deviating from the population-wide sex ratio. Expanding sampling effort in amphibian conservation assessments in time and space, i.e., outside the main breeding season and away from the breeding sites, would be important to encompass such variations.

Evolutionary transitions from camouflage to aposematism: Hidden signals play a pivotal role

The initial evolution of warning signals in unprofitable prey, termed aposematism, is often seen as a paradox because any new conspicuous mutant would be easier to detect than its cryptic conspecifics and not readily recognized by naïve predators as defended. One possibility is that permanent aposematism first evolved through species using hidden warning signals, which are only exposed to would-be predators on encounter. Here, we present a large-scale analysis of evolutionary transitions in amphibian antipredation coloration and demonstrate that the evolutionary transition from camouflage to aposematism is rarely direct but tends to involve an intermediary stage, namely cryptic species that facultatively reveal conspicuous coloration. Accounting for this intermediate step can resolve the paradox and thereby advance our understanding of the evolution of aposematism.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

LAY SUMMARY

- What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity?- 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity.- Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá.

RESUMEN

Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas.

The lack of genetic variation underlying thermal transcriptomic plasticity suggests limited adaptability of the Northern shrimp, Pandalus borealis

Introduction

Genetic variation underlies the populations’ potential to adapt to and persist in a changing environment, while phenotypic plasticity can play a key role in buffering the negative impacts of such change at the individual level.

Methods

We investigated the role of genetic variation in the thermal response of the northern shrimp Pandalus borealis, an ectotherm species distributed in the Arctic and North Atlantic Oceans. More specifically, we estimated the proportion transcriptomic responses explained by genetic variance of female shrimp from three origins after 30 days of exposure to three temperature treatments.

Results

We characterized the P. borealis transcriptome (170,377 transcripts, of which 27.48% were functionally annotated) and then detected a total of 1,607 and 907 differentially expressed transcripts between temperatures and origins, respectively. Shrimp from different origins displayed high but similar level of transcriptomic plasticity in response to elevated temperatures. Differences in transcript expression among origins were not correlated to population genetic differentiation or diversity but to environmental conditions at origin during sampling.

Discussion

The lack of genetic variation explaining thermal plasticity suggests limited adaptability in this species’ response to future environmental changes. These results together with higher mortality observed at the highest temperature indicate that the thermal niche of P. borealis will likely be restricted to higher latitudes in the future. This prediction concurs with current decreases in abundance observed at the southern edge of this species geographical distribution, as it is for other cold-adapted crustaceans.

The presence of a guard vicariously drives split sex ratios in a facultatively social bee

Split sex ratios provide broad insights into how reproductive strategies evolve, and historically have special relevance to the evolution of eusociality. Yet almost no attention has been directed to situations where split sex ratios may potentially decrease the payoffs for worker-like behaviour, increasing selective thresholds for eusociality. We examined sex ratios in a facultatively social colletid bee, Amphylaeus morosus. Sex ratios in this bee vary strongly with the presence of a nest guard and in a pattern that does not conform to assumptions of previous models in which split sex ratios facilitate altruism. While the production of daughters was constant across social and solitary nests, mothers produced more brood when a non-reproductive guard was present, but these extra brood were all male. This leads to split sex ratios, vicariously driven by guards that are unable to manipulate sex ratios in their favour. Importantly, if guarding becomes more common in a population this would lead to an excess of males and lower the genetic value of these extra males to guards, effectively putting a brake on selection for worker-like behaviour.

Widespread sex ratio polymorphism in Caenorhabditis nematodes

Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis, including 19 for which we tested multiple strains. For the species with multiple strains, five species had female-biased and two had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared with unlimited mating experiments, except that one C. becei strain showed significantly reduced female bias compared with unlimited mating. Our study shows frequent polymorphism in sex ratios within Caenorhabditis species and that sperm competition alone cannot explain the sex ratio bias.

Evo-devo beyond development: Generalizing evo-devo to all levels of the phenotypic evolution

A foundational idea of evo-devo is that morphological variation is not isotropic, that is, it does not occur in all directions. Instead, some directions of morphological variation are more likely than others from DNA-level variation and these largely depend on development. We argue that this evo-devo perspective should apply not only to morphology but to evolution at all phenotypic levels. At other phenotypic levels there is no development, but there are processes that can be seen, in analogy to development, as constructing the phenotype (e.g., protein folding, learning for behavior, etc.). We argue that to explain the direction of evolution two types of arguments need to be combined: generative arguments about which phenotypic variation arises in each generation and selective arguments about which of it passes to the next generation. We explain how a full consideration of the two types of arguments improves the explanatory power of evolutionary theory. Also see the video abstract here: https://youtu.be/Egbvma_uaKc.

Neutral and adaptive genetic diversity in plants: An overview

Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.

Learning by Population Genetics and Matrix Riccati Equation

A model of learning as a generalization of the Eigen's quasispecies model in population genetics is introduced. Eigen's model is considered as a matrix Riccati equation. The error catastrophe in the Eigen's model (when the purifying selection becomes ineffective) is discussed as the divergence of the Perron-Frobenius eigenvalue of the Riccati model in the limit of large matrices. A known estimate for the Perron-Frobenius eigenvalue provides an explanation for observed patterns of genomic evolution. We propose to consider the error catastrophe in Eigen's model as an analog of overfitting in learning theory; this gives a criterion for the presence of overfitting in learning.

Articulatory effects on perceptions of men's status and attractiveness

Research on heterosexual mating has demonstrated that acoustic parameters (e.g., pitch) of men's voices influence their attractiveness to women and appearance of status and formidability to other men. However, little is known about how men's tendency to clearly articulate their speech influences these important social perceptions. In the current study, we used a repeated-measures design to investigate how men's articulatory clarity or conformity influenced women's (N = 45) evaluations of men's attractiveness for both short- and long-term relationships, and men's (N = 46) evaluations of physical formidability and prestige. Results largely supported our hypotheses: men who enunciated phonemes more distinctly were more attractive to women for long-term relationships than short-term relationships and were perceived by other men to have higher prestige than physical dominance. These findings suggest that aspects of articulatory behavior that influence perceptions of prestige and long-term mating attractiveness may indicate an early social history characterized by high socioeconomic status, likely owing to crystallization of articulatory patterns during the critical period of language development. These articulatory patterns may also be honest signals of condition or disposition owing to the nature of complex, multicomponent traits, which deserve further empirical attention.

Candidate genes for mastitis resistance in dairy cattle: a data integration approach

BACKGROUND

Inflammation of the mammary tissue (mastitis) is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector. Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes. However, mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult. Currently, the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.

METHODS

To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci. Mastitis-associated candidate genes reported in association, expression, and mouse model studies were collected by searching the relevant literature and databases. The collected data were integrated into a single database, screened for overlaps, and used for gene set enrichment analysis.

RESULTS

The database contains candidate genes from association and expression studies and relevant transgenic mouse models. The 2448 collected candidate loci are evenly distributed across bovine chromosomes. Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL, revealing promising candidate genes for mastitis resistance.

CONCLUSION

Mastitis resistance is a complex trait influenced by numerous alleles. Based on the number of independent studies, we were able to prioritise candidate genes and propose a list of the 22 most promising. To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.

The geometry of evolutionary conflict

Conflicts of interest abound not only in human affairs but also in the biological realm. Evolutionary conflict occurs over multiple scales of biological organization, from genetic outlawry within genomes, to sibling rivalry within nuclear families, to collective-action disputes within societies. However, achieving a general understanding of the dynamics and consequences of evolutionary conflict remains an outstanding challenge. Here, we show that a development of R. A. Fisher's classic 'geometric model' of adaptation yields novel and surprising insights into the dynamics of evolutionary conflict and resulting maladaptation, including the discoveries that: (i) conflict can drive evolving traits arbitrarily far away from all parties' optima and, indeed, if all mutations are equally likely then contested traits are more often than not driven outwith the zone of actual conflict (hyper-maladaptation); (ii) evolutionary conflicts drive persistent maladaptation of orthogonal, non-contested traits (para-maladaptation); and (iii) modular design greatly ameliorates conflict-driven maladaptation, thereby facilitating major transitions in individuality.

Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma

Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with additional tumor suppressor mutations. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations required for the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.

A Call For More Ecologically And Evolutionarily Relevant Studies of Immune Costs

What are the relative costs and benefits of mounting immune responses? Practitioners of ecoimmunology have grappled with this central question since the field's inception with the main tension being how to make tractable methodological choices that maintain the ecological relevance of induced and measured immune costs. Here, we point out two methodological approaches that we feel are underrepresented in the field, describe risks associated with neglecting these methods, and suggest modern techniques that maximize both the diversity and ecological relevance of collected data. First, it is commonly assumed that frequently used and experimentally convenient immune stimulants will induce ecologically relevant immune responses in study organisms. This can be a dangerous assumption. Even if a stimulant's general immune response properties are well characterized, it is critical to also measure the type and scale of immune responses induced by live pathogens. Second, patterns of immune defenses evolve like other traits, thus a comparative approach is essential to understand what forces shape immune variation. Finally, we describe modern genetic and immunological approaches that will soon become essential tools for ecoimmunologists, and present case studies that exemplify the utility of our recommendations.

A Markov Chain Model for the Evolution of Sex Ratio

A model in the form of a Markov chain is constructed to mimic variations in the human sex ratio. It is illustrated by simulation. The equilibrium distribution is shown to be a simple modification of the binomial distribution. This enables an easy calculation of the variation in sex ratio which could be expected in small populations.

Wartime forced sex as a male mating strategy

The aim of this study was an analytical justification of the emergence and presence of the phenomenon of war among hominins, taking into account males' genetic benefits gained through war in the natural environment. Based on chimpanzee behavior, the analytical model of the primary warrior balance was explored, comparing the risk of a war expedition with the genetic profits from war rape-"life and death balance". On the profits side, genetic gains possible to obtain in terms of permanent attractiveness of females (warrior status and abductions of females) were also included. Kin cooperation, parochial altruism, and "partisan strategy" have been defined as psychological mechanisms that enable effective group violence. Male genetic benefit from a war rape could exceed the risk of a warrior's death in the chimpanzee-human LCA species; transition from the herd to the patriarchal tribal social system could increase warrior's genetic gains from war. At the root of war lie sexual limitations of cooperating males, induced by female sexual preferences and lack of the permanent female sexual drive. War rape allows reproductive success for dominated and thus sexually restricted males. Tendencies for group aggression to gain access to out-group females (the war gene) are common among sexually restricted men. Resource-rich areas favor increase in human population density, this affects group territoriality and promotes intergroup conflicts, and thus patriarchy. Roots of conventional patriarchal marriage are strongly combined with war-"the right to land entails the right to a female".

Individual- and group-level sex ratios under local mate competition: consequences of infanticide and reproductive dominance

Extremely female-biased sex ratios of parasitoid wasps in multiple-foundress groups challenges evolutionary theory which predicts diminishing bias as foundress numbers increase. Recent theory based on foundress cooperation has achieved qualitative rather than quantitative success in explaining bias among parasitoids in the genus Sclerodermus. Here, we develop an explanation, expanding the theory of local mate competition, based on the observation that male production seems dominated by some foundresses within groups. Two sex ratio effects arise from such reproductive dominance: an immediate effect via suppression of male production, and a long-term evolutionary response to reproductive skew. We analyze the outcome of these effects at the individual and group level, the latter being more readily observable. Three model scenarios are analyzed: (1) random killing of developing sons in a group by all foundresses, without reproductive skew, (2) the development of reproductive dominance by some foundresses after sex allocation decisions by all foundresses have been implemented, and (3) reproductive dominance within foundress groups before sex allocation decisions are implemented. The 3 scenarios have subtly different implications for sex ratio evolution, with Models 2 and 3 being novel additions to theory, showing how reproductive dominance can alter the outcome of sex ratio evolution. All models match observations in their outcomes better than other recently proposed theory, but Models 2 and 3 are closest to observations in their underlying assumptions. Further, Model 2 shows that differential offspring mortality after parental investment can influence the primary sex ratio even when random with respect to parental and offspring characters, but targeted at entire clutches. The novel models are solved for both diploid and haplodiploid genetic systems, and confirmed with simulations. Overall, these models provide a feasible explanation for the extremely female-biased sex ratios produced by multi-foundress groups and expand the scope of local mate competition theory to consider reproductive dominance.

Conformity in mate choice, the overlooked social component of animal and human culture

Although conformity as a major driver for human cultural evolution is a well-accepted and intensely studied phenomenon, its importance for non-human animal culture has been largely overlooked until recently. This limited for decades the possibility of studying the roots of human culture. Here, we provide a historical review of the study of conformity in both humans and non-human animals. We identify gaps in knowledge and propose an evolutionary route towards the sophisticated cultural processes that characterize humanity. A landmark in the study of conformity is Solomon Asch's famous experiment on humans in 1955. By contrast, interest in conformity among evolutionary biologists has only become salient since the turn of the new millennium. A striking result of our review is that, although studies of conformity have examined many biological contexts, only one looked at mate choice. This is surprising because mate choice is probably the only context in which conformity has self-reinforcing advantages across generations. Within a metapopulation, i.e. a group of subpopulations connected by dispersing individuals, dispersers able to conform to the local preference for a given type of mate have a strong and multigenerational fitness advantage. This is because once females within one subpopulation locally show a bias for one type of males, immigrant females who do not conform to the local trend have sons, grandsons, etc. of the non-preferred phenotype, which negatively and cumulatively affects fitness over generations in a process reminiscent of the Fisher runaway process. This led us to suggest a sex-driven origin of conformity, indicating a possible evolutionary route towards animal and human culture that is rooted in the basic, and thus ancient, social constraints acting on mating preferences within a metapopulation. In a generic model, we show that dispersal among subpopulations within a metapopulation can effectively maintain independent Fisher runaway processes within subpopulations, while favouring the evolution of social learning and conformity at the metapopulation scale; both being essential for the evolution of long-lasting local traditions. The proposed evolutionary route to social learning and conformity casts surprising light on one of the major processes that much later participated in making us human. We further highlight several research avenues to define the spectrum of conformity better, and to account for its complexity. Future studies of conformity should incorporate experimental manipulation of group majority. We also encourage the study of potential links between conformity and mate copying, animal aggregations, and collective actions. Moreover, validation of the sex-driven origin of conformity will rest on the capacity of human and evolutionary sciences to investigate jointly the origin of social learning and conformity. This constitutes a stimulating common agenda and militates for a rapprochement between these two currently largely independent research areas.

Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2

Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines.

Nesting Biology of the Potter Wasp Ancistrocerus flavomarginatus (Hymenoptera, Vespidae, Eumeninae) Revealed by Trap-Nest Experiments in Southern Brazil

This paper provides the first description of the nesting biology of Ancistrocerus flavomarginatus (Brèthes) (Hymenoptera, Vespidae, Eumeninae), the only species of the genus found in Brazil. Our trap-nest experiments were conducted in two Mixed Ombrophilous Forest fragments and two adjacent matrices in Guarapuava (Paraná state, Brazil) from August 2017 to July 2018. In each area, we set 192 trap nests divided into six groups of 32 units, totalling 768 trap nests. We obtained a total of 47 nests of A. flavomarginatus, the vast majority of them (43, 91.5%) founded in the forest fragments. Most nests were built in wooden traps with a bore diameter of either 5 or 7 mm (19 nests in each type, 80.8%). Nests comprised 1-12 subcylindrical brood cells arranged linearly and separated from one another by transverse partitions of soil mastic. Larvae consumed 6-10 lepidopteran caterpillars before spinning the cocoon. Ancistrocerus flavomarginatus produced up to 6 annual generations (multivoltinism) and its immature forms were parasitized by chrysidid and ichneumonid wasps. The calculated sex ratio (1.78:1) was statistically biased towards males, but since they (21.3 ± 2.0 mg) were significantly lighter than females (50.9 ± 4.0 mg), the resulting investment ratio (1.34:1) was female biased. Males emerged from more external cells and developed significantly faster (27.2 ± 0.46 days) than females (30.1 ± 0.66 days), hence a case of protandry. We demonstrated that A. flavomarginatus is largely dependent on the Atlantic Rainforest and thus that deforestation poses a critical threat to this important species.

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.

Sex-specific changes in autosomal methylation rate in ageing common terns

Senescence, an age-related decline in survival and/or reproductive performance, occurs in species across the tree of life. Molecular mechanisms underlying this within-individual phenomenon are still largely unknown, but DNA methylation changes with age are among the candidates. Using a longitudinal approach, we investigated age-specific changes in autosomal methylation of common terns, relatively long-lived migratory seabirds known to show senescence. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome. We found autosomal methylation levels to decrease with age within females, but not males, and no evidence for selective (dis)appearance of birds of either sex in relation to their methylation level. Moreover, although we found positions in the genome to consistently vary in their methylation levels, individuals did not show such strong consistent variance. These results pave the way for studies at the level of genome features or specific positions, which should elucidate the functional consequences of the patterns observed, and how they translate to the ageing phenotype.