The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias.

The aesthetic preferences of potential mates have driven the evolution of a baffling diversity of elaborate ornaments. Which fitness benefit-if any-choosers gain from expressing such preferences is controversial, however. Here, we simulate the evolution of preferences for multiple ornament types (e.g., "Fisherian," "handicap," and "indicator" ornaments) that differ in their associations with genes for attractiveness and other components of fitness. We model the costs of preference expression in a biologically plausible way, which decouples costly mate search from cost-free preferences. Ornaments of all types evolved in our model, but their occurrence was far from random. Females typically preferred ornaments that carried information about a male's quality, defined here as his ability to acquire and metabolize resources. Highly salient ornaments, which key into preexisting perceptual biases, were also more likely to evolve. When males expressed quality-dependent ornaments, females invested readily in costly mate search to locate preferred males. In contrast, the genetic benefits associated with purely arbitrary ornaments were insufficient to sustain highly costly mate search. Arbitrary ornaments could nonetheless "piggyback" on mate-search effort favored by other, quality-dependent ornaments. We further show that the potential to produce attractive male offspring ("sexy sons") can be as important as producing offspring of high general quality ("good genes") in shaping female preferences, even when preferred ornaments are quality dependent. Our model highlights the importance of mate-search effort as a driver of aesthetic coevolution.

The population genomics of repeated freshwater colonizations by Gulf pipefish.

How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.

The Estrogen-Responsive Transcriptome of Female Secondary Sexual Traits in the Gulf Pipefish.

Sexual dimorphism often results from hormonally regulated trait differences between the sexes. In sex-role-reversed vertebrates, females often have ornaments used in mating competition that are expected to be under hormonal control. Males of the sex-role-reversed Gulf pipefish (Syngnathus scovelli) develop female-typical traits when they are exposed to estrogens. We aimed to identify genes whose expression levels changed during the development and maintenance of female-specific ornaments. We performed RNA-sequencing on skin and muscle tissue in male Gulf pipefish with and without exposure to estrogen to investigate the transcriptome of the sexually dimorphic ornament of vertical iridescent bands found in females and estrogen-exposed males. We further compared differential gene expression patterns between males and females to generate a list of genes putatively involved in the female secondary sex traits of bands and body depth. A detailed analysis of estrogen-receptor binding sites demonstrates that estrogen-regulated genes tend to have nearby cis-regulatory elements. Our results identified a number of genes that differed between the sexes and confirmed that many of these were estrogen-responsive. These estrogen-regulated genes may be involved in the arrangement of chromatophores for color patterning, as well as in the growth of muscles to achieve the greater body depth typical of females in this species. In addition, anaerobic respiration and adipose tissue could be involved in the rigors of female courtship and mating competition. Overall, this study generates a number of interesting hypotheses regarding the genetic basis of a female ornament in a sex-role-reversed pipefish.

Sex roles and the evolution of parental care specialization.

Males and females are defined by the relative size of their gametes (anisogamy), but secondary sexual dimorphism in fertilization, parental investment and mating competition is widespread and often remarkably stable over evolutionary timescales. Recent theory has clarified the causal connections between anisogamy and the most prevalent differences between the sexes, but deviations from these patterns remain poorly understood. Here, we study how sex differences in parental investment and mating competition coevolve with parental care specialization. Parental investment often consists of two or more distinct activities (e.g. provisioning and defence) and parents may care more efficiently by specializing in a subset of these activities. Our model predicts that efficient care specialization broadens the conditions under which biparental investment can evolve in lineages that historically had uniparental care. Major transitions in sex roles (e.g. from female-biased care with strong male mating competition to male-biased care with strong female competition) can arise following ecologically induced changes in the costs or benefits of different care types, or in the sex ratio at maturation. Our model provides a clear evolutionary mechanism for sex-role transitions, but also predicts that such transitions should be rare. It consequently contributes towards explaining widespread phylogenetic inertia in parenting and mating systems.

The future of parentage analysis: From microsatellites to SNPs and beyond.

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci.

With the advent of next-generation sequencing approaches, the search for individual loci underlying local adaptation has become a major enterprise in evolutionary biology. One promising method to identify such loci is to examine genome-wide patterns of differentiation, using an FST-outlier approach. The effects of pleiotropy and epistasis on this approach are not yet known. Here, we model 2 populations of a sexually reproducing, diploid organism with 2 quantitative traits, one of which is involved in local adaptation. We consider genetic architectures with and without pleiotropy and epistasis. We also model neutral marker loci on an explicit genetic map as the 2 populations diverge and apply FST outlier approaches to determine the extent to which quantitative trait loci (QTL) are detectable. Our results show, under a wide range of conditions, that only a small number of QTL are typically responsible for most of the trait divergence between populations, even when inheritance is highly polygenic. We find that the loci making the largest contributions to trait divergence tend to be detectable outliers. These loci also make the largest contributions to within-population genetic variance. The addition of pleiotropy reduces the extent to which quantitative traits can evolve independently but does not reduce the efficacy of outlier scans. The addition of epistasis, however, reduces the mean FST values for causative QTL, making these loci more difficult, but not impossible, to detect in outlier scans.

The G-matrix Simulator Family: Software for Research and Teaching.

Genetic variation plays a fundamental role in all models of evolution. For phenotypes composed of multiple quantitative traits, genetic variation is best quantified as additive genetic variances and covariances, as these values determine the rate and trajectory of evolution. Additive genetic variances and covariances are often summarized conveniently in the G-matrix, which has additive genetic variances for each trait on the diagonal and additive genetic covariances as its off-diagonal elements. The evolution of the G-matrix is an interesting topic in its own right, because the processes that affect trait means also affect the distribution of standing genetic variation, which, in turn, feeds back to affect the rate of change of trait means. Theoretical studies of the G-matrix have profitably employed simulation-based models because the topic is often too complex to yield meaningful analytical results. Here, we present a series of G-matrix simulation software packages, which have emerged from about 15 years of research on this topic. These simulation models are useful for research and for building intuition regarding the evolution of the G-matrix under a wide variety of circumstances. A tutorial and source code also provide a foundation upon which future models can be built. These tools will be useful to students as well as researchers.

Parabolic variation in sexual selection intensity across the range of a cold-water pipefish: implications for susceptibility to climate change.

While an understanding of evolutionary processes in shifting environments is vital in the context of rapid ecological change, one of the most potent selective forces, sexual selection, remains curiously unexplored. Variation in sexual selection across a species range, especially across a gradient of temperature regimes, has the potential to provide a window into the possible impacts of climate change on the evolution of mating patterns. Here, we investigated some of the links between temperature and indicators of sexual selection, using a cold-water pipefish as model. We found that populations differed with respect to body size, length of the breeding season, fecundity, and sexual dimorphism across a wide latitudinal gradient. We encountered two types of latitudinal patterns, either linear, when related to body size, or parabolic in shape when considering variables related to sexual selection intensity, such as sexual dimorphism and reproductive investment. Our results suggest that sexual selection intensity increases toward both edges of the distribution and that the large differences in temperature likely play a significant role. Shorter breeding seasons in the north and reduced periods for gamete production in the south certainly have the potential to alter mating systems, breeding synchrony, and mate monopolization rates. As latitude and water temperature are tightly coupled across the European coasts, the observed patterns in traits related to sexual selection can lead to predictions regarding how sexual selection should change in response to climate change. Based on data from extant populations, we can predict that as the worm pipefish moves northward, a wave of decreasing selection intensity will likely replace the strong sexual selection at the northern range margin. In contrast, the southern populations will be followed by heightened sexual selection, which may exacerbate the problem of local extinction at this retreating boundary.

Constraints on the FST-Heterozygosity Outlier Approach.

The FST-heterozygosity outlier approach has been a popular method for identifying loci under balancing and positive selection since Beaumont and Nichols first proposed it in 1996 and recommended its use for studies sampling a large number of independent populations (at least 10). Since then, their program FDIST2 and a user-friendly program optimized for large datasets, LOSITAN, have been used widely in the population genetics literature, often without the requisite number of samples. We observed empirical datasets whose distributions could not be reconciled with the confidence intervals generated by the null coalescent island model. Here, we use forward-in-time simulations to investigate circumstances under which the FST-heterozygosity outlier approach performs poorly for next-generation single nucleotide polymorphism (SNP) datasets. Our results show that samples involving few independent populations, particularly when migration rates are low, result in distributions of the FST-heterozygosity relationship that are not described by the null model implemented in LOSITAN. In addition, even under favorable conditions LOSITAN rarely provides confidence intervals that precisely fit SNP data, making the associated P-values only roughly valid at best. We present an alternative method, implemented in a new R package named fsthet, which uses the raw empirical data to generate smoothed outlier plots for the FST-heterozygosity relationship.

Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish.

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction-site-associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome-wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype-environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.

Post-copulatory sexual selection and sexual conflict in the evolution of male pregnancy.

Male pregnancy in seahorses, pipefishes and sea dragons (family Syngnathidae) represents a striking reproductive adaptation that has shaped the evolution of behaviour and morphology in this group of fishes. In many syngnathid species, males brood their offspring in a specialized pouch, which presumably evolved to facilitate male parental care. However, an unexplored possibility is that brood pouch evolution was partly shaped by parent-offspring or sexual conflict, processes that would result in trade-offs between current and future pregnancies. Here we report a controlled breeding experiment using the sexually dimorphic Gulf pipefish, Syngnathus scovelli, to test for post-copulatory sexual selection within broods and for trade-offs between successive male pregnancies as functions of female attractiveness. Offspring survivorship within a pregnancy was affected by the size of a male's mate, the number of eggs transferred and the male's sexual responsiveness. Significantly, we also found that embryo survivorship in a current pregnancy was negatively related to survivorship in the prior pregnancy, clearly demonstrating fitness trade-offs between broods. Overall, our data indicate that post-copulatory sexual selection and sexual conflict occur in Gulf pipefishes. The conflict seems to be mediated by a strategy of cryptic choice in which males increase rates of offspring abortion in pregnancies from unattractive mothers to retain resources for future reproductive opportunities. Hence, the male brood pouch of syngnathid fishes, which nurtures offspring, also seems to have an important role as an arbiter of conflict between the sexes.

A DNA-Based Assessment of the Phylogenetic Position of a Morphologically Distinct, Anchialine-Lake-Restricted Seahorse.

Isolated populations provide special opportunities to study local adaptation and incipient speciation. In some cases, however, morphological evolution can obscure the taxonomic status of recently founded populations. Here, we use molecular markers to show that an anchialine-lake-restricted population of seahorses, originally identified as Hippocampus reidi, appears on the basis of DNA data to be Hippocampus erectus We collected seahorses from Sweetings Pond, on Eleuthera Island, Bahamas, during the summer of 2014. We measured morphological traits and sequenced 2 genes, cytochrome b and ribosomal protein S7, from 19 seahorses in our sample. On the basis of morphology, Sweetings Pond seahorses could not be assigned definitively to either of the 2 species of seahorse, H. reidi and H. erectus, that occur in marine waters surrounding the Bahamas. However, our DNA-based phylogenetic analysis showed that the Sweetings Pond fish were firmly nested within the H. erectus clade with a Bayesian posterior probability greater than 0.99. Thus, Sweetings Pond seahorses most recently shared a common ancestor with H. erectus populations from the Western Atlantic. Interestingly, the seahorses from Sweetings Pond differ morphologically from other marine populations of H. erectus in having a more even torso to tail length ratio. The substantial habitat differences between Sweetings Pond and the surrounding coastal habitat make Sweetings Pond seahorses particularly interesting from the perspectives of conservation, local adaptation, and incipient speciation.

Multiple mating and reproductive skew in parental and introgressed females of the live-bearing fish Xiphophorus birchmanni.

Just as mating patterns can promote speciation or hybridization, the presence of hybridization can shape mating patterns within a population. In this study, we characterized patterns of multiple mating and reproductive skew in a naturally hybridizing swordtail fish species, Xiphophorus birchmanni. We quantified multiple mating using microsatellite markers to genotype embryos from 43 females collected from 2 wild populations. We also used a suite of single-nucleotide polymorphism markers to categorize females and their inferred mates as either parental X. birchmanni or as introgressed individuals, which carried alleles from a sister species, X. malinche. We found that parental and introgressed X. birchmanni females mated multiply with both parental and introgressed males. We found no difference in mating patterns or reproductive skew between parental and introgressed X. birchmanni females. However, nonintrogressed X. birchmanni males mated more often with large, fecund females. These females also had the greatest levels of skew in fertilization success of males. Thus, our results show that X. birchmanni has a polygynandrous mating system and that introgression of X. malinche alleles has only subtle effects on mating patterns in this species.

Genetic evidence for monogamy in the dwarf seahorse, Hippocampus zosterae.

Syngnathid fishes (pipefishes, seahorses, and seadragons) exhibit a wide array of mating systems ranging from monogamy with long-term pair bonds to more promiscuous mating systems, such as polyandry and polygynandry. Some seahorses, including the dwarf seahorse Hippocampus zosterae, have been found to be socially monogamous. Although several seahorse species have also been shown to be genetically monogamous, parentage analysis has not yet been applied to the dwarf seahorse. We developed 8 novel microsatellites for the dwarf seahorse to conduct genetic parentage analysis to confirm that this species is indeed monogamous. Using 4 selected loci and a total of 16 pregnant male seahorses, with 8 collected in Florida and 8 sampled in Texas, we genotyped all of the offspring within each male's brood to determine the maternal contributions to each brood. We found a maximum of 4 alleles per locus segregating within each pregnant male's brood, a pattern consistent with each brood having exactly 1 mother and 1 father. These results support previous laboratory-based behavioral studies and indicate that the dwarf seahorse, H. zosterae, is genetically monogamous.

The contributions of premating and postmating selection episodes to total selection in sex-role-reversed Gulf pipefish.

Empirical studies of sexual selection often focus on events occurring either before or after mating but rarely both and consequently may fail to discern the relative magnitudes and interactions of premating and postmating episodes of selection. Here, we simultaneously quantify premating and postmating selection in the sex-role-reversed Gulf pipefish by using a microsatellite-based analysis of parentage in experimental populations. Female pipefish exhibited an opportunity for selection (I) of 1.64, which was higher than that of males (0.35). Decompositions of I and the selection differential on body size showed that over 95% of the selection on females arose from the premating phase. We also found evidence for a trade-off between selection phases, where multiply mating females had significantly lower offspring survivorship compared to singly mated females. In males, variance in relative fitness arose mainly from the number of eggs received per copulation and a small number of males who failed to mate. Overall, our study exemplifies a general approach for the decomposition of total selection into premating and postmating phases to understand the interplay among components of natural and sexual selection that conspire to shape sexually selected traits.

The effects of stochastic and episodic movement of the optimum on the evolution of the G-matrix and the response of the trait mean to selection.

Theoretical and empirical results demonstrate that the G-matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G-matrix could potentially have wide-ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G-matrix stability and evolution when movement of an intermediate optimum includes large, episodic jumps or stochasticity. Here, we investigate such scenarios by using simulation-based models of G-matrix evolution. These analyses yield four important insights regarding the evolution and stability of the G-matrix. (i) Regardless of the model of peak movement, a moving optimum causes the G-matrix to orient towards the direction of net peak movement, so that genetic variance is enhanced in that direction (the variance enhancement effect). (ii) Peak movement skews the distribution of breeding values in the direction of movement, which impedes the response to selection. (iii) The stability of the G-matrix is affected by the overall magnitude and direction of peak movement, but modes and rates of peak movement have surprisingly small effects (the invariance principle). (iv) Both episodic and stochastic peak movement increase the probability that a population will fall below its carrying capacity and go extinct. We also present novel equations for the response of the trait mean to multivariate selection, which take into account the higher moments of the distribution of breeding values.

Population structure of the Gulf pipefish in and around Mobile Bay and the northern Gulf of Mexico.

The genetic structure of inshore aquatic populations can be influenced by a number of factors, including coastal configurations, flow rates, and local adaptation. Properties such as salinity and temperature can differ significantly along the coasts and into the bays and rivers that contribute to these systems. Within these environments, low migratory euryhaline species provide a unique system to examine how these factors influence population structure, even when these populations are continuously distributed. In this study, we utilized microsatellite data to assess the population structure of 7 Gulf pipefish populations located in and around Mobile Bay and the northern Gulf of Mexico. Global F (ST) values (F (ST) = 0.025) suggest moderate levels of genetic structure among the populations. Local genetic structure was present among all coastal pipefish populations. Significant levels of genetic structure were also observed between coastal and estuarine populations (P < 0.05), with bay populations being distinct from their coastal counterparts. Cluster analysis suggests 2 parental populations, with one consisting mainly of estuarine individuals and the other comprising mainly coastal individuals. However, although these populations were genetically distinct, the genetic data also suggested moderate levels of migration between coastal and estuarine areas. We suggest that the differentiation between these populations is likely due to the colonization of individuals from coastal populations followed by limited dispersal out of the bay. It is also possible that different selective pressures between coastal and estuarine habitats may be contributing to the genetic differences between these populations.

Mate choice and sexual selection: what have we learned since Darwin?

Charles Darwin laid the foundation for all modern work on sexual selection in his seminal book The Descent of Man, and Selection in Relation to Sex. In this work, Darwin fleshed out the mechanism of sexual selection, a hypothesis that he had proposed in The Origin of Species. He went well beyond a simple description of the phenomenon by providing extensive evidence and considering the far-reaching implications of the idea. Here we consider the contributions of Darwin to sexual selection with a particular eye on how far we have progressed in the last 150 years. We focus on 2 key questions in sexual selection. First, why does mate choice evolve at all? And second, what factors determine the strength of mate choice (or intensity of sexual selection) in each sex? Darwin provided partial answers to these questions, and the progress that has been made on both of these topics since his time should be seen as one of the great triumphs of modern evolutionary biology. However, a review of the literature shows that key aspects of sexual selection are still plagued by confusion and disagreement. Many of these areas are complex and will require new theory and empirical data for complete resolution. Overall, Darwin's contributions are still surprisingly relevant to the modern study of sexual selection, so students of evolutionary biology would be well advised to revisit his works. Although we have made significant progress in some areas of sexual selection research, we still have much to accomplish.

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.

The evolution of the testis transcriptome in pregnant male pipefishes and seahorses.

In many animals, sperm competition and sexual conflict are thought to drive the rapid evolution of male-specific genes, especially those expressed in the testes. A potential exception occurs in the male pregnant pipefishes, where females transfer eggs to the males, eliminating testes from participating in these processes. Here, we show that testis-related genes differ dramatically in their rates of molecular evolution and expression patterns in pipefishes and seahorses (Syngnathidae) compared to other fish. Genes involved in testis or sperm function within syngnathids experience weaker selection in comparison to their orthologs in spawning and livebearing fishes. An assessment of gene turnover and expression in the testis transcriptome suggests that syngnathids have lost (or significantly reduced expression of) important classes of genes from their testis transcriptomes compared to other fish. Our results indicate that more than 50 million years of male pregnancy have removed syngnathid testes from the molecular arms race that drives the rapid evolution of male reproductive genes in other taxa.