Drosophila Serrata Research Articles

The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach.

This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.

Maintenance of quantitative genetic variance in complex, multitrait phenotypes: the contribution of rare, large effect variants in 2 Drosophila species.

The interaction of evolutionary processes to determine quantitative genetic variation has implications for contemporary and future phenotypic evolution, as well as for our ability to detect causal genetic variants. While theoretical studies have provided robust predictions to discriminate among competing models, empirical assessment of these has been limited. In particular, theory highlights the importance of pleiotropy in resolving observations of selection and mutation, but empirical investigations have typically been limited to few traits. Here, we applied high-dimensional Bayesian Sparse Factor Genetic modeling to gene expression datasets in 2 species, Drosophila melanogaster and Drosophila serrata, to explore the distributions of genetic variance across high-dimensional phenotypic space. Surprisingly, most of the heritable trait covariation was due to few lines (genotypes) with extreme [>3 interquartile ranges (IQR) from the median] values. Intriguingly, while genotypes extreme for a multivariate factor also tended to have a higher proportion of individual traits that were extreme, we also observed genotypes that were extreme for multivariate factors but not for any individual trait. We observed other consistent differences between heritable multivariate factors with outlier lines vs those factors without extreme values, including differences in gene functions. We use these observations to identify further data required to advance our understanding of the evolutionary dynamics and nature of standing genetic variation for quantitative traits.

Evolutionary genetics: Dissecting a sexually antagonistic polymorphism

Males and females experience divergent selection on many shared traits, which can lead to 'sexual antagonism'- opposing fitness effects of genetic variants in each sex. A new study in the fly Drosophila serrata links sexually antagonistic selection on cuticular hydrocarbons to a single major-effect gene.

Mating traits are phenotypically but not genetically correlated to fitness

AbstractMisalignment between male and female interests over mating creates interlocus sexual conflict that is known to drive the coevolution of reproductive traits. Males and females also share the majority of their genome, which may cause these traits to be genetically covary between the sexes and experience intralocus sexual conflict where beneficial alleles in one sex are costly when expressed in the other. Here, we use a quantitative genetic experiment to test whether intralocus sexual conflict is operating on mating latency and copulation duration in the polyandrous fruit-fly Drosophila serrata. We performed two paternal half-sibling breeding designs in different populations and measured mating latency and copulation duration in males and females, and components of pre- and postcopulatory fitness in both sexes. Our design enabled the estimation of selection on mating latency and copulation duration and the heritabilities, and within-sex and across-sex genetic covariances of these traits. Mating latency and copulation duration were both heritable in males but not in females, and within sex and across-sex genetic correlations among the traits were all small. Despite significant phenotypic correlations between these mating traits and some male and female fitness components, we found no significant genetic covariance between any measured mating behaviors and fitness components, nor between male and female fitness. Our study, therefore, finds little evidence of ongoing intralocus sexual conflict over these traits. One explanation for our result is that these mating traits have been under strong selection, which has exhausted their genetic variation, limiting their ability to respond to ongoing selection.

Quantifying male harm and its divergence.

Male harm arises when traits that increase reproductive success in competition with other males also harm females as a side effect. The extent of harm depends on male and female phenotypes, both of which can diverge between populations. Within a population, harm is inferred when increased exposure to males reduces female fitness, but studies of the divergence of male harm rarely manipulate male exposure. Here, we quantify male harm and compare its magnitude between two lab populations of Drosophila serrata that were derived from a common ancestor 7 years earlier and subsequently held under conditions that minimized environmental differences. We manipulated female exposure to males in a factorial design involving all four combinations of males and females from these populations, providing insight into divergence in both sexes. Our results reveal substantial harm to females and provide stronger evidence of divergence in males than in females. Using these and other published data, we discuss conceptual issues surrounding the quantification and comparison of harm that arise because it involves a comparison of multiple quantities (e.g., female fitness under varying male exposure), and we demonstrate the increased insight that is gained by manipulating male exposure to quantify these quantities.

The Transposable Elements of the Drosophila serrata Reference Panel.

Transposable elements (TEs) are an important component of the complex genomic ecosystem. Understanding the tempo and mode of TE proliferation, that is whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. Although TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of TEs, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the TE landscape in an important model Drosophila, Drosophila serrata using the D. serrata reference panel, which is comprised of 102 sequenced inbred genotypes. We annotate the families of TEs in the D. serrata genome and investigate variation in TE copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family and includes a single TE making up to 50% of the genome content of TEs. We find that some TEs proliferate in particular genotypes compared with population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step toward characterizing the origin of variation within and between species.

Mating has opposite effects on male and female sexually selected cuticular hydrocarbons

In Drosophila serrata flies, there is female choice for male cuticular hydrocarbon (CHC) profiles and male choice for female CHC profiles. Furthermore, both males and females can alter their CHCs: when there is more opportunity for mating, males express combinations of CHCs preferred by females; however, females appear to change CHC profiles to avoid male harassment. In this study, I investigate the effect of number of matings (0–4) on male and female sexually selected CHCs. Mating caused males to express CHCs associated with higher male mating success. Thus, successfully mating males are likely to have increased future mating success. Conversely, females that mated more times expressed CHC profiles that were associated with lower female mating success. Females maximized their offspring production by mating more than once, but additional matings did not provide additional benefits. Furthermore, number of matings did not affect female survival. In total, these results suggest that females alter CHC expression to discourage male courtship when additional matings are not beneficial. In conclusion, plasticity in male and female CHC expression can both increase variance in male mating success and decrease variance in female mating success, driving the evolution of sexually selected chemical signals.

Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression.

Variational modules, sets of pleiotropically covarying traits, affect phenotypic evolution, and therefore are predicted to reflect functional modules, such that traits within a variational module also share a common function. Such an alignment of function and pleiotropy is expected to facilitate adaptation by reducing the deleterious effects of mutations, and by allowing coordinated evolution of functionally related sets of traits. Here, we adopt a high-dimensional quantitative genetic approach using a large number of gene expression traits in Drosophila serrata to test whether functional grouping, defined by gene ontology (GO terms), predicts variational modules. Mutational or standing genetic covariance was significantly greater than among randomly grouped sets of genes for 38% of our functional groups, indicating that GO terms can predict variational modularity to some extent. We estimated stabilizing selection acting on mutational covariance to test the prediction that functional pleiotropy would result in reduced deleterious effects of mutations within functional modules. Stabilizing selection within functional modules was weaker than that acting on randomly grouped sets of genes in only 23% of functional groups, indicating that functional alignment can reduce deleterious effects of pleiotropic mutation but typically does not. Our analyses also revealed the presence of variational modules that spanned multiple functions.

Sexual selection on spontaneous mutations strengthens the between-sex genetic correlation for fitness.

A proposed benefit to sexual selection is that it promotes purging of deleterious mutations from populations. For this benefit to be realized, sexual selection, which is usually stronger on males, must purge mutations deleterious to both sexes. Here, we experimentally test the hypothesis that sexual selection on males purges deleterious mutations that affect both male and female fitness. We measured male and female fitness in two panels of spontaneous mutation-accumulation lines of the fly, Drosophila serrata, each established from a common ancestor. One panel of mutation accumulation lines limited both natural and sexual selection (LS lines), whereas the other panel limited natural selection, but allowed sexual selection to operate (SS lines). Although mutation accumulation caused a significant reduction in male and female fitness in both the LS and SS lines, sexual selection had no detectable effect on the extent of the fitness reduction. Similarly, despite evidence of mutational variance for fitness in males and females of both treatments, sexual selection had no significant impact on the amount of mutational genetic variance for fitness. However, sexual selection did reshape the between-sex correlation for fitness: significantly strengthening it in the SS lines. After 25 generations, the between-sex correlation for fitness was positive but considerably less than one in the LS lines, suggesting that, although most mutations had sexually concordant fitness effects, sex-limited, and/or sex-biased mutations contributed substantially to the mutational variance. In the SS lines this correlation was strong and could not be distinguished from unity. Individual-based simulations that mimick the experimental setup reveal two conditions that may drive our results: (1) a modest-to-large fraction of mutations have sex-limited (or highly sex-biased) fitness effects, and (2) the average fitness effect of sex-limited mutations is larger than the average fitness effect of mutations that affect both sexes similarly.

Crowd control: sex ratio affects sexually selected cuticular hydrocarbons in male Drosophila serrata.

Although it is advantageous for males to express costly sexually selected signals when females are present, they may also benefit from suppressing these signals to avoid costly interactions with rival males. Cuticular chemical profiles frequently function as insect sexual signals; however, few studies have asked whether males alter these signals in response to their social environment. In Drosophila serrata, an Australian fly, there is sexual selection for a multivariate combination of male cuticular hydrocarbons (CHCs). Here, we show that the ratio of females to males that an adult male experiences has a strong effect on his CHC expression, with female-biased adult sex ratios eliciting greater expression of CHC profiles associated with higher male mating success. Classical models predict that male reproductive investment should be highest when there is a small but nonzero number of rivals, but we found that males expressed the most attractive combination of CHCs when there were no rivals. We found that male CHCs were highly sensitive to adult sex ratio, with males expressing higher values of CHC profiles associated with greater mating success as the ratio of females to males increased. Moreover, sex ratio has a stronger effect on male CHC expression than adult density. Finally, we explore whether sex ratio affects the variance among a group of males in their CHC expression, as might be expected if individuals respond differently to a given social environment, but find little effect. Our results reveal that subtle differences in social environment can induce plasticity in male chemical signal expression.

Testing for a genetic response to sexual selection in a wild Drosophila population

In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)-5,9-C27:2 . Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response.

Genomic Evidence that Sexual Selection Impedes Adaptation to a Novel Environment

Sexual selection is widely appreciated for generating remarkable phenotypic diversity, but its contribution to adaptation and the purging of deleterious mutations is unresolved. To provide insight into the impact of sexual selection on naturally segregating polymorphisms across the genome, we previously evolved 12 populations of Drosophila serrata in a novel environment employing a factorial manipulation of the opportunities for natural and sexual selection. Here, we genotype more than 1,400 SNPs in the evolved populations and reveal that sexual selection affected many of the same genomic regions as natural selection, aligning with it as often as opposing it. Intriguingly, more than half of the 80 SNPs showing treatment effects revealed an interaction between natural and sexual selection. For these SNPs, while sexual selection alone often caused a change in allele frequency in the same direction as natural selection alone, when natural and sexual selection occurred together, changes in allele frequency were greatly reduced or even reversed. This suggests an antagonism between natural and sexual selection arising from male-induced harm to females. Behavioral experiments showed that males preferentially courted and mated with high-fitness females, and that the harm associated with this increased male attention eliminated the female fitness advantage. During our experiment, females carrying otherwise adaptive alleles may therefore have disproportionally suffered male-induced harm due to their increased sexual attractiveness. These results suggest that a class of otherwise adaptive mutations may not contribute to adaptation when mating systems involve sexual conflict and male mate preferences.

The phenome-wide distribution of genetic variance.

A general observation emerging from estimates of additive genetic variance in sets of functionally or developmentally related traits is that much of the genetic variance is restricted to few trait combinations as a consequence of genetic covariance among traits. While this biased distribution of genetic variance among functionally related traits is now well documented, how it translates to the broader phenome and therefore any trait combination under selection in a given environment is unknown. We show that 8,750 gene expression traits measured in adult male Drosophila serrata exhibit widespread genetic covariance among random sets of five traits, implying that pleiotropy is common. Ultimately, to understand the phenome-wide distribution of genetic variance, very large additive genetic variance-covariance matrices (G) are required to be estimated. We draw upon recent advances in matrix theory for completing high-dimensional matrices to estimate the 8,750-trait G and show that large numbers of gene expression traits genetically covary as a consequence of a single genetic factor. Using gene ontology term enrichment analysis, we show that the major axis of genetic variance among expression traits successfully identified genetic covariance among genes involved in multiple modes of transcriptional regulation. Our approach provides a practical empirical framework for the genetic analysis of high-dimensional phenome-wide trait sets and for the investigation of the extent of high-dimensional genetic constraint.

Connecting thermal performance curve variation to the genotype: a multivariate QTL approach.

Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. Although thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs - specifically, the loci involved and the directionality of their effects across different temperatures. To address this, we took a multivariate approach, mapping quantitative trait loci (QTL) for locomotor activity TPCs in the fly, Drosophila serrata, using a panel of 76 recombinant inbred lines. The distribution of additive genetic (co)variance in the mapping population was remarkably similar to the distribution of mutational (co)variance for these traits. We detected 11 TPC QTL in females and 4 in males. Multivariate QTL effects were closely aligned with the major axes genetic (co)variation between temperatures; most QTL effects corresponded to variation for either overall increases or decreases in activity with a smaller number indicating possible trade-offs between activity at high and low temperatures. QTL representing changes in curve shape such as the 'generalist-specialist' trade-off, thought key to thermal adaptation, were poorly represented in the data. We discuss these results in the light of genetic constraints on thermal adaptation.

Female mate choice predicts paternity success in the absence of additive genetic variance for other female paternity bias mechanisms in Drosophila serrata.

After choosing a first mate, polyandrous females have access to a range of opportunities to bias paternity, such as repeating matings with the preferred male, facilitating fertilization from the best sperm or differentially investing in offspring according to their sire. Female ability to bias paternity after a first mating has been demonstrated in a few species, but unambiguous evidence remains limited by the access to complex behaviours, sperm storage organs and fertilization processes within females. Even when found at the phenotypic level, the potential evolution of any mechanism allowing females to bias paternity other than mate choice remains little explored. Using a large population of pedigreed females, we developed a simple test to determine whether there is additive genetic variation in female ability to bias paternity after a first, chosen, mating. We applied this method in the highly polyandrous Drosophila serrata, giving females the opportunity to successively mate with two males ad libitum. We found that despite high levels of polyandry (females mated more than once per day), the first mate choice was a significant predictor of male total reproductive success. Importantly, there was no detectable genetic variance in female ability to bias paternity beyond mate choice. Therefore, whether or not females can bias paternity before or after copulation, their role on the evolution of sexual male traits is likely to be limited to their first mate choice in D.serrata.

Pleiotropic mutations are subject to strong stabilizing selection.

The assumption that pleiotropic mutations are more deleterious than mutations with more restricted phenotypic effects is an important premise in models of evolution. However, empirical evidence supporting this assumption is limited. Here, we estimated the strength of stabilizing selection on mutations affecting gene expression in male Drosophila serrata. We estimated the mutational variance (VM) and the standing genetic variance (VG) from two well-matched panels of inbred lines: a panel of mutation accumulation (MA) lines derived from a single inbred ancestral line and a panel of inbred lines derived from an outbred population. For 855 gene-expression traits, we estimated the strength of stabilizing selection as s = VM/VG. Selection was observed to be relatively strong, with 17% of traits having s > 0.02, a magnitude typically associated with life-history traits. Randomly assigning expression traits to five-trait sets, we used factor analytic mixed modeling in the MA data set to identify covarying traits that shared pleiotropic mutations. By assigning traits to the same trait sets in the outbred line data set, we then estimated s for the combination of traits affected by pleiotropic mutation. For these pleiotropic combinations, the median s was three times greater than s acting on the individual component traits, and 46% of the pleiotropic trait combinations had s > 0.02. Although our analytical approach was biased toward detecting mutations with relatively large effects, likely overestimating the average strength of selection, our results provide widespread support for the prediction that stronger selection can act against mutations with pleiotropic effects.

Sexual selection on Drosophila serrata male pheromones does not vary with female age or mating status.

Mate preferences are costly and are thought to evolve due to the direct and/or indirect benefits they provide. Such costs and benefits may vary in response to intrinsic and extrinsic factors with important evolutionary consequences. Limited attention has been given to quantifying such variation and understanding its causes, most notably with respect to the direction and strength of preferences for multivariate sexual displays. In Drosophila serrata, female preferences target a pheromone blend of long-chain cuticular hydrocarbons (CHCs). We used a factorial design to test whether female age and mating status generated variation in the strength and direction of sexual selection on male CHCs. Replicate choice mating trials were conducted using young and old females (4 or 10 days post-emergence) that were either virgin or previously mated. The outcome of such trials is known to capture variation in female mate preferences, although male-male interactions may also contribute. Directional sexual selection on male CHCs was highly significant within each treatment, but there was little evidence of any variation among treatments. The absence of treatment effects implies that the multivariate combination of male CHCs preferred by females was constant with respect to female age and mating status. To the extent that male-male interactions may also contribute, our results similarly imply that these did not vary among treatments groups. With respect to D. serrata mate preferences, our results suggest that either plasticity with respect to age and mating status is not beneficial to females, or preference expression is somehow constrained.

The Genomic Distribution of Sex-Biased Genes in Drosophila serrata: X Chromosome Demasculinization, Feminization, and Hyperexpression in Both Sexes

The chromosomal distribution of genes with sex-biased expression is often nonrandom, and in species with XY sex chromosome systems, it is common to observe a deficit of X-linked male-biased genes and an excess of X-linked female-biased genes. One explanation for this pattern is that sex-specific selection has shaped the gene content of the X. Alternatively, the deficit of male-biased and excess of female-biased genes could be an artifact of differences between the sexes in the global expression level of their X chromosome(s), perhaps brought about by a lack of dosage compensation in males and hyperexpression in females. In the montium fruit fly, Drosophila serrata, both these explanations can account for a deficit of male-biased and excess of female-biased X-linked genes. Using genome-wide expression data from multiple male and female tissues (n = 176 hybridizations), we found that testis- and accessory gland-specific genes are underrepresented whereas female ovary-specific genes are overrepresented on the X chromosome, suggesting that X-linkage is disfavored for male function genes but favored for female function genes. However, genes with such sex-specific functions did not fully account for the deficit of male-biased and excess of female-biased X-linked genes. We did, however, observe sex differences in the global expression level of the X chromosome and autosomes. Surprisingly, and in contrast to other species where a lack of dosage compensation in males is responsible, we found that hyperexpression of X-linked genes in both sexes leads to this imbalance in D. serrata. Our results highlight how common genomic distributions of sex-biased genes, even among closely related species, may arise via quite different evolutionary processes.

Comparing the intersex genetic correlation for fitness across novel environments in the fruit fly, Drosophila serrata

Sexually antagonistic genetic variation can pose limits to the independent evolution and adaptation of the sexes. The extent of sexually antagonistic variation is reflected in the intersex genetic correlation for fitness (rw(FM)). Previous estimates of this correlation have been mostly limited to populations in environments to which they are already well adapted, making it difficult to gauge the importance of sexually antagonistic genetic variance during the early stages of adaptation, such as that occurring following abrupt environmental change or upon the colonization of new habitat. Here we assayed male and female lifetime fitness in a population of Drosophila serrata in four novel laboratory environments. We found that rw(FM) varied significantly across environments, with point estimates ranging from positive to negative values of considerable magnitude. We also found that the variability among estimates was because, at least in part, of significant differences among environments in the genetic variances of both male and female fitness, with no evidence of any significant changes in the intersex covariance itself, although standard errors of these estimates were large. Our results illustrate the unpredictable nature of rw(FM) in novel environments and suggest that, although sexually antagonistic genetic variance can be pronounced in some novel environments, it may have little effect in constraining the early stages of adaptation in others.

HIGH-DIMENSIONAL VARIANCE PARTITIONING REVEALS THE MODULAR GENETIC BASIS OF ADAPTIVE DIVERGENCE IN GENE EXPRESSION DURING REPRODUCTIVE CHARACTER DISPLACEMENT

Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted on adaptations that involve sets of high-dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.