Widespread cryptic variation in genetic architecture between the sexes

Hiding in plain sight: the Y chromosome and its reinvigorated role in evolutionary processes

Recent methodological approaches have expanded our understanding of Y chromosome sequence, revealed unexpected Y diversity, and sparked a growing realization of its importance in evolutionary processes. To fully understand the diversity and importance of the Y chromosome, we suggest the need to move from a holotype Y chromosome sequence, based on a single individual and meant to represent the species, to a thorough understanding of Y chromosome haplotype diversity, its phenotypic implications, and its phylogeographic distribution. Additionally, the Y chromosome may play an important role in two key rules of speciation that have otherwise been attributed to the X, namely Haldane's Rule and the Large-X Effect. Emerging genomic tools and analytical approaches are just now giving us the means to ask how important this small, often forgotten region of the genome is in evolutionary processes.

On the resolution of sexual conflict over shared traits

Anisogamy, different-sized male and female gametes, sits at the heart of sexual selection and conflict between the sexes. Sperm producers (males) and egg producers (females) of the same species generally share most, if not all, of the same genome, but selection frequently favours different trait values in each sex for traits common to both. The extent to which this conflict might be resolved, and the potential mechanisms by which this can occur, have been widely debated. Here, we summarize recent findings and emphasize that once the sexes evolve, sexual selection is ongoing, and therefore new conflict is always possible. In addition, sexual conflict is largely a multivariate problem, involving trait combinations underpinned by networks of interconnected genes. Although these complexities can hinder conflict resolution, they also provide multiple possible routes to decouple male and female phenotypes and permit sex-specific evolution. Finally, we highlight difficulty in the study of sexual conflict over shared traits and promising directions for future research.

Sex-biased gene expression in mammals

Sex differences in gene expression start at puberty and vary across species and organs.

The Ancestral Modulation Hypothesis: Predicting Mechanistic Control of Sexually Heteromorphic Traits Using Evolutionary History

AbstractAcross the animal kingdom there are myriad forms within a sex across, and even within, species, rendering concepts of universal sex traits moot. The mechanisms that regulate the development of these trait differences are varied, although in vertebrates, common pathways involve gonadal steroid hormones. Gonadal steroids are often associated with heteromorphic trait development, where the steroid found at higher circulating levels is the one involved in trait development for that sex. Occasionally, there are situations in which a gonadal steroid associated with heteromorphic trait development in one sex is involved in heteromorphic or monomorphic trait development in another sex. We propose a verbal hypothesis, the ancestral modulation hypothesis (AMH), that uses the evolutionary history of the trait-particularly which sex ancestrally possessed higher trait values-to predict the regulatory pathway that governs trait expression. The AMH predicts that the genomic architecture appears first to resolve sexual conflict in an initially monomorphic trait. This architecture takes advantage of existing sex-biased signals, the gonadal steroid pathway, to generate trait heteromorphism. In cases where the other sex experiences evolutionary pressure for the new phenotype, that sex will co-opt the existing architecture by altering its signal to match that of the original high-trait-value sex. We describe the integrated levels needed to produce this pattern and what the expected outcomes will be given the evolutionary history of the trait. We present this framework as a testable hypothesis for the scientific community to investigate and to create further engagement and analysis of both ultimate and proximate approaches to sexual heteromorphism.

The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation

Sexual dimorphism is one of the most prevalent, and often the most extreme, examples of phenotypic variation within species, and arises primarily from genomic variation that is shared between females and males. Many sexual dimorphisms arise through sex differences in gene expression, and sex-biased expression is one way that a single, shared genome can generate multiple, distinct phenotypes. Although many sexual dimorphisms are expected to result from sexual selection, and many studies have invoked the possible role of sexual selection to explain sex-specific traits, the role of sexual selection in the evolution of sexually dimorphic gene expression remains difficult to differentiate from other forms of sex-specific selection. In this Review, we propose a holistic framework for the study of sex-specific selection and transcriptome evolution. We advocate for a comparative approach, across tissues, developmental stages and species, which incorporates an understanding of the molecular mechanisms, including genomic variation and structure, governing gene expression. Such an approach is expected to yield substantial insights into the evolution of genetic variation and have important applications in a variety of fields, including ecology, evolution and behaviour.

Tests for associations between sexual dimorphism and patterns of quantitative genetic variation in the water strider, Aquarius remigis

The evolution of sexual dimorphisms requires divergence between sexes in the evolutionary trajectories of the traits involved. Discerning how genetic architecture could facilitate such divergence has proven challenging because of the difficulty in estimating non-additive and sex-linked genetic variances using traditional quantitative genetic designs. Here we use a three-generation, double-first-cousin pedigree design to estimate additive, sex-linked and dominance (co)variances for 12 traits in the water strider, Aquarius remigis. Comparisons among these traits, which have size ratios ranging from 1 to 5 (larger/smaller), allow us to ask if sexual dimorphisms are associated with characteristic patterns of quantitative genetic variation. We frame our analysis around three main questions, derived from existing theory and empirical evidence: Are sexual dimorphisms associated with (1) lower additive inter-sex genetic correlations, (2) higher proportions of sex-linked variance, or (3) differences between sexes in autosomal additive and dominance genetic variances? For questions (1) and (2), we find weak and non-significant trends in the expected directions, which preclude definitive conclusions. However, in answer to question (3), we find strong evidence for a positive relationship between sexual dimorphism and differences between sexes in proportions of autosomal dominance variance. We also find strong interactions among the three genetic components indicating that their relative influence differs among traits and between sexes. These results highlight the need to include all three components of genetic (co)variance in both theoretical evolutionary models and empirical estimations of the genetic architecture of dimorphic traits.

Recent progress in understanding the genomic architecture of sexual conflict

Genomic conflict between the sexes over shared traits is widely assumed to be resolved through the evolution of sex-biased expression and the subsequent emergence of sexually dimorphic phenotypes. However, while there is support for a broad relationship between genome-wide patterns of expression level and sexual conflict, recent studies suggest that sex differences in the nature and strength of interactions between loci are instead key to conflict resolution. Furthermore, the advent of new technologies for measuring and perturbing expression means we now have much more power to detect genomic signatures of sexual conflict. Here, we review our current understanding of the genomic architecture of sexual conflict in the light of these new studies and highlight the potential for novel approaches to address outstanding knowledge gaps.

Intrinsic emergence and modulation of sex-specific dominance reversals in threshold traits

Sex-specific dominance reversals (SSDRs) in fitness-related traits, where heterozygotes' phenotypes resemble those of alternative homozygotes in females versus males, can simultaneously maintain genetic variation in fitness and resolve sexual conflict and thereby shape key evolutionary outcomes. However, the full implications of SSDRs will depend on how they arise and the resulting potential for evolutionary, ecological and environmental modulation. Recent field and laboratory studies have demonstrated SSDRs in threshold(-like) traits with dichotomous or competitive phenotypic outcomes, implying that such traits could promote the emergence of SSDRs. However, such possibilities have not been explicitly examined. I show how phenotypic SSDRs can readily emerge in threshold traits given genetic architectures involving large-effect loci alongside sexual dimorphism in the mean and variance in polygenic liability. I also show how multilocus SSDRs can arise in line-cross experiments, especially given competitive reproductive systems that generate nonlinear fitness outcomes. SSDRs can consequently emerge in threshold(-like) traits as functions of sexual antagonism, sexual dimorphism and reproductive systems, even with purely additive underlying genetic effects. Accordingly, I identify theoretical and empirical advances that are now required to discern the basis and occurrence of SSDRs in nature, probe forms of (co-)evolutionary, ecological and environmental modulation, and evaluate net impacts on sexual conflict.

The relationship between sexual dimorphism and androgen response element proliferation in primate genomes

In the males of many vertebrate species, sexual selection has led to the evolution of sexually dimorphic traits, which often are developmentally controlled by androgen signaling involving androgen response elements (AREs). Evolutionary changes in the number and genomic locations of AREs can modify patterns of receptor regulation and potentially alter gene expression. Here, we use recently sequenced primate genomes to evaluate the hypothesis that the strength of sexual selection is related to the genome-wide number of AREs in a diversifying lineage. In humans, we find a higher incidence of AREs near male-biased genes and androgen-responsive genes when compared to randomly selected genes from the genome. In a set of primates, we find that gains or losses of AREs proximal to genes are correlated with changes in male expression levels and the degree of sex-biased expression of those genes. In a larger set of primates, we find that increases in indicators of sexual selection are correlated with genome-wide ARE counts. Our results suggest that the responsiveness of the genome to androgens in humans and their close relatives has been shaped by sexual selection that arises from competition among males for mating access to females.

Sex differences in the intergenerational inheritance of metabolic traits

Strong evidence suggests that early-life exposures to suboptimal environmental factors, including those in utero, influence our long-term metabolic health. This has been termed developmental programming. Mounting evidence suggests that the growth and metabolism of male and female fetuses differ. Therefore, sexual dimorphism in response to pre-conception or early-life exposures could contribute to known sex differences in susceptibility to poor metabolic health in adulthood. However, until recently, many studies, especially those in animal models, focused on a single sex, or, often in the case of studies performed during intrauterine development, did not report the sex of the animal at all. In this review, we (a) summarize the evidence that male and females respond differently to a suboptimal pre-conceptional or in utero environment, (b) explore the potential biological mechanisms that underlie these differences and (c) review the consequences of these differences for long-term metabolic health, including that of subsequent generations.

High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms

Differences between males and females are usually more subtle in dioecious plants than animals, but strong sexual dimorphism has evolved convergently in the South African Cape plant genus Leucadendron. Such sexual dimorphism in leaf size is expected largely to be due to differential gene expression between the sexes. We compared patterns of gene expression in leaves among 10 Leucadendron species across the genus. Surprisingly, we found no positive association between sexual dimorphism in morphology and the number or the percentage of sex-biased genes (SBGs). Sex bias in most SBGs evolved recently and was species specific. We compared rates of evolutionary change in expression for genes that were sex biased in one species but unbiased in others and found that SBGs evolved faster in expression than unbiased genes. This greater rate of expression evolution of SBGs, also documented in animals, might suggest the possible role of sexual selection in the evolution of gene expression. However, our comparative analysis clearly indicates that the more rapid rate of expression evolution of SBGs predated the origin of bias, and shifts towards bias were depleted in signatures of adaptation. Our results are thus more consistent with the view that sex bias is simply freer to evolve in genes less subject to constraints in expression level.

Developmental mechanisms of sex differences: from cells to organisms

Male-female differences in many developmental mechanisms lead to the formation of two morphologically and physiologically distinct sexes. Although this is expected for traits with prominent differences between the sexes, such as the gonads, sex-specific processes also contribute to traits without obvious male-female differences, such as the intestine. Here, we review sex differences in developmental mechanisms that operate at several levels of biological complexity - molecular, cellular, organ and organismal - and discuss how these differences influence organ formation, function and whole-body physiology. Together, the examples we highlight show that one simple way to gain a more accurate and comprehensive understanding of animal development is to include both sexes.