Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits

Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves

Genetic variance (VG) in fitness related traits is often unexpectedly high, evoking the question how VG can be maintained in the face of selection. Sexually antagonistic (SA) selection favouring alternative alleles in the sexes is common and predicted to maintain VG, while directional selection should erode it. Both SA and sex-limited directional selection can lead to sex-specific adaptations but how each affect VG when sexual dimorphism evolves remain experimentally untested. Using replicated artificial selection on the seed beetle Callosobruchus maculatus body size we recently demonstrated an increase in size dimorphism under SA and male-limited (ML) selection by 50% and 32%, respectively. Here we test their consequences on genetic variation. We show that SA selection maintained significantly more ancestral, autosomal additive genetic variance than ML selection, while both eroded sex-linked additive variation equally. Ancestral female-specific dominance variance was completely lost under ML, while SA selection consistently sustained it. Further, both forms of selection preserved a high genetic correlation between the sexes (rm,f). These results demonstrate the potential for sexual antagonism to maintain more genetic variance while fuelling sex-specific adaptation in a short evolutionary time scale, and are in line with predicted importance of sex-specific dominance reducing sexual conflict over alternative alleles.

Identification of crucial factors involved in Cynoglossus semilaevis sexual size dimorphism by GWAS and demonstration of zbed1 regulatory network by DAP-seq

Sexual size dimorphism (SSD), whereby females and males exhibit different body sizes, are widely documented in animals. To explore crucial regulators implicated in female-biased SSD of Chinese tongue sole (Cynoglossus semilaevis), GWAS was conducted on 350 females and 59 males. Twenty SNPs and 25 genes including zbed1, nsd3, cdc45, klhl29, and smad4 with -log(p) > 7 were screened, mainly mapping to sex chromosome. The chromosome W-linked gene zbed1 attracted particular attention because it is a master key for cell proliferation. Thus, the regulatory network of zbed1 in C. semilaevis was explored by DAP-seq and 1352 peaks were discovered in the female brain. Moreover, zbed1 potentially regulated hippo signaling pathway, cell cycle, translation, and PI3k-Akt signaling pathway in C. semilaevis. These findings identify crucial SNPs and genes associated with female-biased SSD in C. semilaevis, also provide the first genome-wide survey for the zbed1 regulatory network in fish species.

Polygenic sex determination produces modular sex polymorphism in an African cichlid fish

For many vertebrates, a single genetic locus initiates a cascade of developmental sex differences in the gonad and throughout the organism, resulting in adults with two phenotypically distinct sexes. Species with polygenic sex determination (PSD) have multiple interacting sex determination alleles segregating within a single species, allowing for more than two genotypic sexes and scenarios where sex genotype at a given locus can be decoupled from gonadal sex. Here we investigate the effects of PSD on secondary sexual characteristics in the cichlid fish Metriaclima mbenjii, where one female (W) and one male (Y) sex determination allele interact to produce siblings with four possible sex classes: ZZXX females, ZWXX females, ZWXY females, and ZZXY males. We find that PSD in M. mbenjii produces an interplay of sex linkage and sex limitation resulting in modular variation in morphological and behavioral traits. Further, the evolution or introgression of a newly acquired sex determiner creates additional axes of phenotypic variation for varied traits, including genital morphology, craniofacial morphology, gastrointestinal morphology, and home tank behaviors. In contrast to single-locus sex determination, which broadly results in sexual dimorphism, polygenic sex determination can induce higher-order sexual polymorphism. The modularity of secondary sexual characteristics produced by PSD provides context for understanding the evolutionary causes and consequences of maintenance, gain, or loss of sex determination alleles in populations.

Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance

Sexual dimorphism is ubiquitous in nature but its evolution is puzzling given that the mostly shared genome constrains independent evolution in the sexes. Sex differences should result from asymmetries between the sexes in selection or genetic variation but studies investigating both simultaneously are lacking. Here, we combine a quantitative genetic analysis of body size variation, partitioned into autosomal and sex chromosome contributions and ten generations of experimental evolution to dissect the evolution of sexual body size dimorphism in seed beetles (Callosobruchus maculatus) subjected to sexually antagonistic or sex-limited selection. Female additive genetic variance (V_A) was primarily linked to autosomes, exhibiting a strong intersexual genetic correlation with males ([Formula: see text] = 0.926), while X- and Y-linked genes further contributed to the male V_A and X-linked genes contributed to female dominance variance. Consistent with these estimates, sexual body size dimorphism did not evolve in response to female-limited selection but evolved by 30-50% under male-limited and sexually antagonistic selection. Remarkably, Y-linked variance alone could change dimorphism by 30%, despite the C. maculatus Y chromosome being small and heterochromatic. Our results demonstrate how the potential for sexual dimorphism to evolve depends on both its underlying genetic basis and the nature of sex-specific selection.

Density-Dependent Adaptive Topography in a Small Passerine Bird, the Collared Flycatcher

AbstractAdaptive topography is a central concept in evolutionary biology, describing how the mean fitness of a population changes with gene frequencies or mean phenotypes. We use expected population size as a quantity to be maximized by natural selection to show that selection on pairwise combinations of reproductive traits of collared flycatchers caused by fluctuations in population size generated an adaptive topography with distinct peaks often located at intermediate phenotypes. This occurred because r- and K-selection made phenotypes favored at small densities different from those with higher fitness at population sizes close to the carrying capacity K. Fitness decreased rapidly with a delay in the timing of egg laying, with a density-dependent effect especially occurring among early-laying females. The number of fledglings maximizing fitness was larger at small population sizes than when close to K. Finally, there was directional selection for large fledglings independent of population size. We suggest that these patterns can be explained by increased competition for some limiting resources or access to favorable nest sites at high population densities. Thus, r- and K-selection based on expected population size as an evolutionary maximization criterion may influence life-history evolution and constrain the selective responses to changes in the environment.

Autosomal and sex-linked (co)variance components and genetic parameters for growth traits of Iranian Zandi sheep

Separation of autosomal and sex-linked direct additive genetic effects has significant role in sheep breeding programs. Hence, this study was conducted to determine the genetic parameters of autosomal and sex-linked effects for growth traits of Zandi sheep. The data set used in this study contained 7571 Zandi lambs, descendent of 220 sires and 1481 dams, which were collected from Zandi sheep breeding Station at Khojir, Tehran, Iran from 1992 to 2011. The fixed effects included of year (20 classes), season (winter and spring), sex (male or female), birth type (single or twin), and the age of dam (seven classes, 2-8 years old). The data were analyzed using REML methodology by WOMBAT software. In the most appropriate fitted model, based on Akaike's information criterion (AIC) and Bayesian information criterion (BIC), the values of direct autosomal heritabilities of birth weight (BW), kleiber ratio at weaning (KR), 6-month weight (6MW), and 9-month weight (9MW) were 0.12 ± 0.03, 0.29 ± 0.05, 0.14 ± 0.04, and 0.15 ± 0.04, respectively. Furthermore, weaning weight (WW), average daily gain from birth to weaning (ADG), and 12-month weight (12 MW) showed the values of 0.19 ± 0.03 and 0.22 ± 0.03, 0.13 ± 0.05 and 0.15 ± 0.03, and 0.15 ± 0.05 and 0.18 ± 0.05, respectively. Based on the best models through all traits, estimates of the direct sex-linked heritability ranged from 0.0 (WW, ADG, KR, and 6MW) to 0.02 ± 0.03 (12MW). The average of autosomal and sex-linked breeding values (BVs) of body growth traits except KR (for autosomal) and 9MW and 12MW (for sex-linked) were greater than zero. The Pearson's/Spearman's correlation coefficients varied between 0.344 and 0.599/0.30 and 0.61 for autosomal and sex-linked BVs. Direct autosomal and sex-linked additive correlations for growth traits were ranged from - 0.02 (BW-KR) to 0.98 (WW-ADG) and 0.04 (KR-9 MW) to 0.99 (WW-ADG), respectively. Our results revealed that the genetic parameters related to growth traits in Zandi sheep could be more useful in selection strategies.

Evolution of sex-specific pace-of-life syndromes: genetic architecture and physiological mechanisms

Sex differences in life history, physiology, and behavior are nearly ubiquitous across taxa, owing to sex-specific selection that arises from different reproductive strategies of the sexes. The pace-of-life syndrome (POLS) hypothesis predicts that most variation in such traits among individuals, populations, and species falls along a slow-fast pace-of-life continuum. As a result of their different reproductive roles and environment, the sexes also commonly differ in pace-of-life, with important consequences for the evolution of POLS. Here, we outline mechanisms for how males and females can evolve differences in POLS traits and in how such traits can covary differently despite constraints resulting from a shared genome. We review the current knowledge of the genetic basis of POLS traits and suggest candidate genes and pathways for future studies. Pleiotropic effects may govern many of the genetic correlations, but little is still known about the mechanisms involved in trade-offs between current and future reproduction and their integration with behavioral variation. We highlight the importance of metabolic and hormonal pathways in mediating sex differences in POLS traits; however, there is still a shortage of studies that test for sex specificity in molecular effects and their evolutionary causes. Considering whether and how sexual dimorphism evolves in POLS traits provides a more holistic framework to understand how behavioral variation is integrated with life histories and physiology, and we call for studies that focus on examining the sex-specific genetic architecture of this integration.

Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes

Although secondary sexual traits are commonly more developed in males than females, in many animal species females also display elaborate ornaments or weaponry. Indirect selection on correlated traits in males and/or direct sexual or social selection in females are hypothesized to drive the evolution and maintenance of female ornaments. Yet, the relative roles of these evolutionary processes remain unidentified, because little is known about the genetic correlation that might exist between the ornaments of both sexes, and few estimates of sex-specific autosomal or sex-linked genetic variances are available. In this study, we used two wild blue tit populations with 9 years of measurements on two colour ornaments: one structurally based (blue crown) and one carotenoid based (yellow chest). We found significant autosomal heritability for the chromatic part of the structurally based colouration in both sexes, whereas carotenoid chroma was heritable only in males, and the achromatic part of both colour patches was mostly non heritable. Power limitations, which are probably common among most data sets collected so far in wild populations, prevented estimation of sex-linked genetic variance. Bivariate analyses revealed very strong cross-sex genetic correlations in all heritable traits, although the strength of these correlations was not related to the level of sexual dimorphism. In total, our results suggest that males and females share a majority of their genetic variation underlying colour ornamentation, and hence the evolution of these sex-specific traits may depend greatly on correlated responses to selection in the opposite sex.

Gauging the Purported Costs of Public Data Archiving for Long-Term Population Studies

It was recently proposed that long-term population studies be exempted from the expectation that authors publicly archive the primary data underlying published articles. Such studies are valuable to many areas of ecological and evolutionary biological research, and multiple risks to their viability were anticipated as a result of public data archiving (PDA), ultimately all stemming from independent reuse of archived data. However, empirical assessment was missing, making it difficult to determine whether such fears are realistic. I addressed this by surveying data packages from long-term population studies archived in the Dryad Digital Repository. I found no evidence that PDA results in reuse of data by independent parties, suggesting the purported costs of PDA for long-term population studies have been overstated.

Mother-offspring and nest-mate resemblance but no heritability in early-life telomere length in white-throated dippers

Telomeres are protective DNA-protein complexes located at the ends of eukaryotic chromosomes, whose length has been shown to predict life-history parameters in various species. Although this suggests that telomere length is subject to natural selection, its evolutionary dynamics crucially depends on its heritability. Using pedigree data for a population of white-throated dippers (Cinclus cinclus), we test whether and how variation in early-life relative telomere length (RTL, measured as the number of telomeric repeats relative to a control gene using qPCR) is transmitted across generations. We disentangle the relative effects of genes and environment and test for sex-specific patterns of inheritance. There was strong and significant resemblance among offspring sharing the same nest and offspring of the same cohort. Furthermore, although offspring resemble their mother, and there is some indication for an effect of inbreeding, additive genetic variance and heritability are close to zero. We find no evidence for a role of either maternal imprinting or Z-linked inheritance in generating these patterns, suggesting they are due to non-genetic maternal and common environment effects instead. We conclude that in this wild bird population, environmental factors are the main drivers of variation in early-life RTL, which will severely bias estimates of heritability when not modelled explicitly.

Selection and inheritance of sexually dimorphic juvenile plumage coloration

Sexually dimorphic plumage coloration is widespread in birds and is generally thought to be a result of sexual selection for more ornamented males. Although many studies find an association between coloration and fitness related traits, few of these simultaneously examine selection and inheritance. Theory predicts that sex‐linked genetic variation can facilitate the evolution of dimorphism, and some empirical work supports this, but we still know very little about the extent of sex linkage of sexually dimorphic traits. We used a longitudinal study on juvenile Florida scrub‐jays (Aphelocoma coerulescens) to estimate strength of selection and autosomal and Z‐linked heritability of mean brightness, UV chroma, and hue. Although plumage coloration signals dominance in juveniles, there was no indication that plumage coloration was related to whether or not an individual bred or its lifetime reproductive success. While mean brightness and UV chroma are moderately heritable, hue is not. There was no evidence for sex‐linked inheritance of any trait with most of the variation explained by maternal effects. The genetic correlation between the sexes was high and not significantly different from unity. These results indicate that evolution of sexual dimorphism in this species is constrained by low sex‐linked heritability and high intersexual genetic correlation.

Tracing reinforcement through asymmetrical partner preference in the European common vole Microtus arvalis

Background

The mechanistic basis of speciation and in particular the contribution of behaviour to the completion of the speciation process is often contentious. Contact zones between related taxa provide a situation where selection against hybridization might reinforce separation by behavioural mechanisms, which could ultimately fully isolate the taxa. One of the most abundant European mammals, the common vole Microtus arvalis, forms multiple natural hybrid zones where rapidly diverging evolutionary lineages meet in secondary contact. Very narrow zones of hybridization spanning only a few kilometres and sex-specific gene flow patterns indicate reduced fitness of natural hybrids and incipient speciation between some of the evolutionary lineages. In this study, we examined the contribution of behavioural mechanisms to the speciation process in these rodents by fine-mapping allopatric and parapatric populations in the hybrid zone between the Western and Central lineages and experimental testing of the partner preferences of wild, pure-bred and hybrid female common voles.

Results

Genetic analysis based on microsatellite markers revealed the presence of multiple parapatric and largely non-admixed populations at distances of about 10 km at the edge of the area of natural hybridization between the Western and Central lineages. Wild females from Western parapatric populations and lab-born F1 hybrids preferred males from the Western lineage whereas wild females of Central parapatric origin showed no measurable preference. Furthermore, wild and lab-born females from allopatric populations of the Western or Central lineages showed no detectable preference for males from either lineage.

Conclusions

The detected partner preferences are consistent with asymmetrical reinforcement of pre-mating reproductive isolation mechanisms in the European common vole and with earlier results suggesting that hybridization is more detrimental to the Western lineage. As a consequence, these differences in behaviour might contribute to a further geographical stabilization of this moving hybrid zone. Such behavioural processes could also provide a mechanistic perspective for frequently-detected asymmetrical introgression patterns in the largely allopatrically diversifying Microtus genus and other rapidly speciating rodents.

Sex-linked inheritance, genetic correlations and sexual dimorphism in three melanin-based colour traits in the barn owl

Theory states that genes on the sex chromosomes have stronger effects on sexual dimorphism than genes on the autosomes. Although empirical data are not necessarily consistent with this theory, this situation may prevail because the relative role of sex-linked and autosomally inherited genes on sexual dimorphism has rarely been evaluated. We estimated the quantitative genetics of three sexually dimorphic melanin-based traits in the barn owl (Tyto alba), in which females are on average darker reddish pheomelanic and display more and larger black eumelanic feather spots than males. The plumage traits with higher sex-linked inheritance showed lower heritability and genetic correlations, but contrary to prediction, these traits showed less pronounced sexual dimorphism. Strong offspring sexual dimorphism primarily resulted from daughters not expressing malelike melanin-based traits and from sons expressing femalelike traits to similar degrees as their sisters. We conclude that in the barn owl, polymorphism at autosomal genes rather than at sex-linked genes generate variation in sexual dimorphism in melanin-based traits.

The role of sex chromosomes in sexual dimorphism: discordance between molecular and phenotypic data

In addition to initial sex determination, genes on the sex chromosomes are theorized to play a particularly important role in phenotypic differences between males and females. Sex chromosomes in many species display molecular signatures consistent with these theoretical predictions, particularly through sex-specific gene expression. However, the phenotypic implications of this molecular signature are unresolved, and the role of the sex chromosomes in quantitative genetic studies of phenotypic sex differences is largely equivocal. In this article, we examine molecular and phenotypic data in the light of theoretical predictions about masculinization and feminization of the sex chromosomes. Additionally, we discuss the role of genetic and regulatory complexities in the genome–phenotype relationship, and ultimately how these affect the overall role of the sex chromosomes in sex differences.

Bias in the heritability of preference and its potential impact on the evolution of mate choice

The evolution of mate choice is a function of the heritability of preference. Estimation in the laboratory is typically made by presenting a female with a limited number of males. We show that such an approach produces a downwardly biased estimate, which we term the heritability of choice. When preference is treated as a threshold trait then less biased estimates are obtained particularly for preferences based on the relative value of the preferred trait. Because females in the wild typically survey on average less than five males we argue that the heritability of choice may be more meaningful than the heritability of preference. The restricted number of males surveyed can lead to a reduction in the phenotypic variance of the preferred trait in the group of males selected by the females if the phenotypic variance in preference is equal to or less than the phenotypic variance in the referred trait. If the phenotypic variance in preference exceeds that of the preferred trait then the opposite occurs. A second effect of the restricted number of males sampled is that females are likely to mate initially with males that are not the most preferred. The failure to find the most preferred male may account for the common observation of multiple matings and extra-pair copulations. We suggest that current explanations for polyandry need to take this failure into account.

Conflict on the sex chromosomes: cause, effect, and complexity

Intralocus sexual conflict and intragenomic conflict both affect sex chromosome evolution and can in extreme cases even cause the complete turnover of sex chromosomes. Additionally, established sex chromosomes often become the focus of heightened conflict. This creates a tangled relationship between sex chromosomes and conflict with respect to cause and effect. To further complicate matters, sexual and intragenomic conflict may exacerbate one another and thereby further fuel sex chromosome change. Different magnitudes and foci of conflict offer potential explanations for lineage-specific variation in sex chromosome evolution and answer long-standing questions as to why some sex chromosomes are remarkably stable, whereas others show rapid rates of evolutionary change.

On estimation and identifiability issues of sex-linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba)

Genetic evaluation using animal models or pedigree-based models generally assume only autosomal inheritance. Bayesian animal models provide a flexible framework for genetic evaluation, and we show how the model readily can accommodate situations where the trait of interest is influenced by both autosomal and sex-linked inheritance. This allows for simultaneous calculation of autosomal and sex-chromosomal additive genetic effects. Inferences were performed using integrated nested Laplace approximations (INLA), a nonsampling-based Bayesian inference methodology. We provide a detailed description of how to calculate the inverse of the X- or Z-chromosomal additive genetic relationship matrix, needed for inference. The case study of eumelanic spot diameter in a Swiss barn owl (Tyto alba) population shows that this trait is substantially influenced by variation in genes on the Z-chromosome ( and ). Further, a simulation study for this study system shows that the animal model accounting for both autosomal and sex-chromosome-linked inheritance is identifiable, that is, the two effects can be distinguished, and provides accurate inference on the variance components.

The shared genome is a pervasive constraint on the evolution of sex-biased gene expression

Males and females share most of their genomes, and differences between the sexes can therefore not evolve through sequence divergence in protein coding genes. Sexual dimorphism is instead restricted to occur through sex-specific expression and splicing of gene products. Evolution of sexual dimorphism through these mechanisms should, however, also be constrained when the sexes share the genetic architecture for regulation of gene expression. Despite these obstacles, sexual dimorphism is prevalent in the animal kingdom and commonly evolves rapidly. Here, we ask whether the genetic architecture of gene expression is plastic and easily molded by sex-specific selection, or if sexual dimorphism evolves rapidly despite pervasive genetic constraint. To address this question, we explore the relationship between the intersexual genetic correlation for gene expression (rMF), which captures how independently genes are regulated in the sexes, and the evolution of sex-biased gene expression. Using transcriptome data from Drosophila melanogaster, we find that most genes have a high rMF and that genes currently exposed to sexually antagonistic selection have a higher average rMF than other genes. We further show that genes with a high rMF have less pronounced sex-biased gene expression than genes with a low rMF within D. melanogaster and that the strength of the rMF in D. melanogaster predicts the degree to which the sex bias of a gene's expression has changed between D. melanogaster and six other species in the Drosophila genus. In sum, our results show that a shared genome constrains both short- and long-term evolution of sexual dimorphism.