Widespread adaptive evolution of Drosophila genes with sex-biased expression

Transcriptional Interference Promotes Rapid Expression Divergence of Drosophila Nested Genes

Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remains unclear. Here, I compare RNA-seq expression profiles of nested, proximal intra-chromosomal, intermediate intra-chromosomal, distant intra-chromosomal, and inter-chromosomal gene pairs in two Drosophila species. I find that expression profiles of nested genes are more divergent than those of any other class of genes, supporting the hypothesis that concurrent expression of nested genes is deleterious due to transcriptional interference. Further analysis reveals that expression profiles of derived nested genes are more divergent than those of their ancestral un-nested orthologs, which are more divergent than those of un-nested genes with similar genomic features. Thus, gene expression divergence between nested genes is likely caused by selection against nesting of genes with insufficiently divergent expression profiles, as well as by continued expression divergence after nesting. Moreover, expression divergence and sequence evolutionary rates are elevated in young nested genes and reduced in old nested genes, indicating that a burst of rapid evolution occurs after nesting. Together, these findings suggest that similarity between expression profiles of nested genes is deleterious due to transcriptional interference, and that natural selection addresses this problem both by eradicating highly deleterious nestings and by enabling rapid expression divergence of surviving nested genes, thereby quickly limiting or abolishing transcriptional interference.

Testis-specific RNA-Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male-biased gene inquiry in Coleoptera

We report the architecture of testis transcriptomes of four closely related species of Calligrapha (Chrysomelidae) beetles, which diverged during the last 3 million years. Five cDNA libraries were sequenced using Illumina HiSeq technology, retrieving 102 884-176 514 assembled contigs, of which ~33-45% of these longer than 499 nt were functionally annotated. Annotation and sequence similarity comparisons of these libraries revealed high homogeneity in gene composition and the presence of several functional candidates related to reproduction or reproductive processes (0.72-1.08% of annotated sequences). Stringent sequence similarity analyses of these transcriptomes against empirically demonstrated male-biased genes in Drosophila melanogaster and Tribolium castaneum allowed the identification of 77 homologues in Calligrapha, possible candidates of male-biased expression. Some of these genes - including CG9313, Tektin-A or tomboy40 - were confirmed as orthologs of these male-biased genes using phylogenetic inference and available model insect data, increasing our confidence that they represent functional homologues too. Our transcriptomes are a valuable transcriptomic resource for the analysis of male-biased genes in Calligrapha, which has the added interest of including several female-only species. But it simultaneously represents a landmark for similar studies in Coleoptera, broadening the taxonomic diversity currently represented by the model species T. castaneum, and incipient genomic data in other herbivorous lineages, including weevils, longhorn beetles and leaf beetles.

Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae)

Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni. Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni. This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.

Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets

In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK) and apolipoprotein A-1 binding protein (APBP). These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of conspecific males to induce oviposition in females.

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations

A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees.

Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila

Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect.

Parallel faster-X evolution of gene expression and protein sequences in Drosophila: beyond differences in expression properties and protein interactions

Population genetics models predict that the X (or Z) chromosome will evolve at faster rates than the autosomes in XY (or ZW) systems. Studies of molecular evolution using large datasets in multiple species have provided evidence supporting this faster-X effect in protein-coding sequences and, more recently, in transcriptomes. However, X-linked and autosomal genes differ significantly in important properties besides hemizygosity in males, including gene expression levels, tissue specificity in gene expression, and the number of interactions in which they are involved (i.e., protein-protein or DNA-protein interactions). Most important, these properties are known to correlate with rates of evolution, which raises the question of whether differences between the X chromosome and autosomes in gene properties, rather than hemizygosity, are sufficient to explain faster-X evolution. Here I investigate this possibility using whole genome sequences and transcriptomes of Drosophila yakuba and D. santomea and show that this is not the case. Additional factors are needed to account for faster-X evolution of both gene expression and protein-coding sequences beyond differences in gene properties, likely a higher incidence of positive selection in combination with the accumulation of weakly deleterious mutations.

Sex-biased gene expression and sexual conflict throughout development

Sex-biased gene expression is likely to account for most sexually dimorphic traits because males and females share much of their genome. When fitness optima differ between sexes for a shared trait, sexual dimorphism can allow each sex to express their optimum trait phenotype, and in this way, the evolution of sex-biased gene expression is one mechanism that could help to resolve intralocus sexual conflict. Genome-wide patterns of sex-biased gene expression have been identified in a number of studies, which we review here. However, very little is known about how sex-biased gene expression relates to sex-specific fitness and about how sex-biased gene expression and conflict vary throughout development or across different genotypes, populations, and environments. We discuss the importance of these neglected areas of research and use data from a small-scale experiment on sex-specific expression of genes throughout development to highlight potentially interesting avenues for future research.

Divergence of the gene aly in experimentally evolved cytoraces, the members of the nasuta-albomicans complex of Drosophila

We generated cytoraces by crossing the chromosomal races (Drosophila nasuta nasuta and Drosophila nasuta albomicans) of the nasuta subgroup of Drosophila and maintained the offspring over many generations through sibling mating. These cytoraces, along with their parents, are members of the nasuta-albomicans complex of Drosophila. The gene always early (aly) is one of the rapidly evolving genes in the genus Drosophila and plays a central role in regulating meiosis. Here we examined the rate of molecular evolution of aly in cytoraces of Drosophila and demonstrated that the rate of substitutions amongst cytoraces is around eight times greater than their parents and even amongst species of subgenera. Thus, the presence of positive selection in the laboratory-derived cytoraces based on the analysis of the synonymous and nonsynonymous substitution rates of aly suggests the rapid evolution in cytoraces.

The coevolutionary period of Wolbachia pipientis infecting Drosophila ananassae and its impact on the evolution of the host germline stem cell regulating genes

The endosymbiotic bacteria Wolbachia pipientis is known to infect a wide range of arthropod species yet less is known about the coevolutionary history it has with its hosts. Evidence of highly identical W. pipientis strains in evolutionary divergent hosts suggests horizontal transfer between hosts. For example, Drosophila ananassae is infected with a W. pipientis strain that is nearly identical in sequence to a strain that infects both D. simulans and D. suzukii, suggesting recent horizontal transfer among these three species. However, it is unknown whether the W. pipientis strain had recently invaded all three species or a more complex infectious dynamic underlies the horizontal transfers. Here, we have examined the coevolutionary history of D. ananassae and its resident W. pipientis to infer its period of infection. Phylogenetic analysis of D. ananassae mitochondrial DNA and W. pipientis DNA sequence diversity revealed the current W. pipientis infection is not recent. In addition, we examined the population genetics and molecular evolution of several germline stem cell (GSC) regulating genes of D. ananassae. These studies reveal significant evidence of recent and long-term positive selection at stonewall in D. ananassae, whereas pumillio showed patterns of variation consistent with only recent positive selection. Previous studies had found evidence for adaptive evolution of two key germline differentiation genes, bag of marbles (bam) and benign gonial cell neoplasm (bgcn), in D. melanogaster and D. simulans and proposed that the adaptive evolution at these two genes was driven by arms race between the host GSC and W. pipientis. However, we did not find any statistical departures from a neutral model of evolution for bam and bgcn in D. ananassae despite our new evidence that this species has been infected with W. pipientis for a period longer than the most recent infection in D. melanogaster. In the end, analyzing the GSC regulating genes individually showed two of the seven genes to have evidence of selection. However, combining the data set and fitting a specific population genetic model significant proportion of the nonsynonymous sites across the GSC regulating genes were driven to fixation by positive selection. Clearly the GSC system is under rapid evolution and potentially multiple drivers are causing the rapid evolution.

Positive selection drives faster-Z evolution in silkmoths

Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This "faster-X effect" can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size of the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to genetic drift. Empirical results to date suggest that, while the overall pattern across taxa is complicated, systems with male heterogamy show a faster-X effect attributable to more efficient selection, whereas the faster-Z effect in female-heterogametic taxa is attributable to increased drift. To test the generality of the faster-Z pattern seen in birds and snakes, we sequenced the genome of the lepidopteran silkmoth Bombyx huttoni. We show that silkmoths experience faster-Z evolution, but unlike in birds and snakes, the faster-Z effect appears to be attributable to more efficient positive selection. These results suggest that female heterogamy alone is unlikely to explain the reduced efficacy of selection on vertebrate Z chromosomes. It is likely that many factors, including differences in overall effective population size, influence Z chromosome evolution.

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata

BACKGROUND

Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild.

RESULTS

To gain insight into molecular mechanisms underlying the guppy's sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions.

CONCLUSIONS

Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues.

Accelerated evolution of morph-biased genes in pea aphids

Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors, results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed selection, the consequence of which is the buildup of slightly deleterious mutations at these genes. Over time, this is expected to result in increased protein divergence at these genes between species and a signature of relaxed purifying selection within species. Here we test these theoretical expectations using morph-biased genes in the pea aphid, a species that produces multiple morphs via polyphenism. We find that morph-biased genes exhibit faster rates of evolution (in terms of dN/dS) relative to unbiased genes and that divergence generally increases with increasing morph bias. Further, genes with expression biased toward rarer morphs (sexual females and males) show faster rates of evolution than genes expressed in the more common morph (asexual females), demonstrating that the amount of time a gene spends being expressed in a morph is associated with its rate of evolution. And finally, we show that genes expressed in the rarer morphs experience decreased purifying selection relative to unbiased genes, suggesting that it is a relaxation of purifying selection that contributes to their faster rates of evolution. Our results provide an important empirical look at the impact of phenotypic plasticity on gene evolution.

Sex-biased expression of microRNAs in Drosophila melanogaster

Most animals have separate sexes. The differential expression of gene products, in particular that of gene regulators, is underlying sexual dimorphism. Analyses of sex-biased expression have focused mostly on protein-coding genes. Several lines of evidence indicate that microRNAs, a class of major gene regulators, are likely to have a significant role in sexual dimorphism. This role has not been systematically explored so far. Here, I study the sex-biased expression pattern of microRNAs in the model species Drosophila melanogaster. As with protein-coding genes, sex-biased microRNAs are associated with the reproductive function. Strikingly, contrary to protein-coding genes, male-biased microRNAs are enriched in the X chromosome, whereas female microRNAs are mostly autosomal. I propose that the chromosomal distribution is a consequence of high rates of de novo emergence, and a preference for new microRNAs to be expressed in the testis. I also suggest that demasculinization of the X chromosome may not affect microRNAs. Interestingly, female-biased microRNAs are often encoded within protein-coding genes that are also expressed in females. MicroRNAs with sex-biased expression do not preferentially target sex-biased gene transcripts. These results strongly suggest that the sex-biased expression of microRNAs is mainly a consequence of high rates of microRNA emergence in the X chromosome (male bias) or hitchhiked expression by host genes (female bias).

The ontogeny and evolution of sex-biased gene expression in Drosophila melanogaster

Sexually dimorphic phenotypes are thought to largely result from sex differences in gene expression, and genes with sex-biased expression have been well characterized in adults of many species. Although most sexual dimorphisms manifest in adults, many result from sex-specific developmental trajectories, implying that juveniles may exhibit significant levels of sex-biased expression. However, it is unclear how much sex-biased expression occurs before reproductive maturity and whether preadult sex-biased genes should exhibit the same evolutionary dynamics observed for adult sex-biased genes. In order to understand the continuity, or lack thereof, and evolutionary dynamics of sex-biased expression throughout the life cycle, we examined sex-biased genes in pre-gonad tissue of two preadult stages and compared them with the adult gonad of Drosophila melanogaster. We found that the majority of the genome is sex-biased at some point in the life cycle, with some genes exhibiting conserved sex-biased expression and others displaying stage-specific sex bias. Our results also reveal a far more complex pattern of evolution for sex-biased genes throughout development. The most rapid evolutionary divergence occurred in genes expressed only in larvae within each sex, compared with continuously expressed genes. In females—but not males—this pattern appeared to be due to relaxed purifying selection in larva-limited genes. Furthermore, genes that retained male bias throughout life evolved more rapidly than stage-specific male-biased genes, due to stronger purifying selection in stage-specific genes. However, female-biased genes that were specific to larvae evolved most rapidly, a pattern that could not be definitively attributed to differences in adaptive evolution or purifying selection, suggesting that pleiotropic constraints on protein-coding sequences can arise when genes are broadly expressed across developmental stages. These results indicate that the signature of sex-specific selection can be detected well before reproductive maturity and is strongest during development.

Role of sexual selection in speciation in Drosophila

The power of sexual selection to drive changes in the mate recognition system through divergence in sexually selected traits gives it the potential to be a potent force in speciation. To know how sexual selection can bring such type of divergence in the genus Drosophila, comparative studies based on intra- and inter-sexual selection are documented in this review. The studies provide evidence that both mate choice and male-male competition can cause selection of trait and preference which thereby leads to divergence among species. In the case of intrasexual selection, various kinds of signals play significant role in affecting the species mate recognition system and hence causing divergence between the species. However, intrasexual selection can bring the intraspecific divergence at the level of pre- and post-copulatory stage. This has been better explained through Hawaiian Drosophila which has been suggested a wonderful model system in explaining the events of speciation via sexual selection. This is due to their elaborate mating displays and some kind of ethological isolation persisting among them. Similarly, the genetic basis of sexually selected variations can provide yet another path in understanding the speciation genetics via sexual selection more closely.

Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana

Sex-biased genes are genes with a preferential or specific expression in one sex and tend to show an accelerated rate of evolution in animals. Various hypotheses--which are not mutually exclusive--have been put forth to explain observed patterns of rapid evolution. One possible explanation is positive selection, but this has been shown only in few animal species and mostly for male-specific genes. Here, we present a large-scale study that investigates evolutionary patterns of sex-biased genes in the predominantly self-fertilizing plant Arabidopsis thaliana. Unlike most animal species, A. thaliana does not possess sex chromosomes, its flowers develop both male and female sexual organs, and it is characterized by low outcrossing rates. Using cell-specific gene expression data, we identified genes whose expression is enriched in comparison with all other tissues in the male and female gametes (sperm, egg, and central cell), as well as in synergids, pollen, and pollen tubes, which also play an important role in reproduction. Genes specifically expressed in gametes and synergids show higher rates of protein evolution compared with the genome-wide average and no evidence for positive selection. In contrast, pollen- and pollen tube-specific genes not only have lower rates of protein evolution but also exhibit a higher proportion of adaptive amino acid substitutions. We show that this is the result of increased levels of purifying and positive selection among genes with pollen- and pollen tube-specific expression. The increased proportion of adaptive substitutions cannot be explained by the fact that pollen- and pollen tube-expressed genes are enriched in segmental duplications, are on average older, or have a larger effective population size. Our observations are consistent with prezygotic sexual selection as a result of interactions during pollination and pollen tube growth such as pollen tube competition.

Two rapidly evolving genes contribute to male fitness in Drosophila

Purifying selection often results in conservation of gene sequence and function. The most functionally conserved genes are also thought to be among the most biologically essential. These observations have led to the use of sequence conservation as a proxy for functional conservation. Here we describe two genes that are exceptions to this pattern. We show that lack of sequence conservation among orthologs of CG15460 and CG15323-herein named jean-baptiste (jb) and karr, respectively-does not necessarily predict lack of functional conservation. These two Drosophila melanogaster genes are among the most rapidly evolving protein-coding genes in this species, being nearly as diverged from their D. yakuba orthologs as random sequences are. jb and karr are both expressed at an elevated level in larval males and adult testes, but they are not accessory gland proteins and their loss does not affect male fertility. Instead, knockdown of these genes in D. melanogaster via RNA interference caused male-biased viability defects. These viability effects occur prior to the third instar for jb and during late pupation for karr. We show that putative orthologs to jb and karr are also expressed strongly in the testes of other Drosophila species and have similar gene structure across species despite low levels of sequence conservation. While standard molecular evolution tests could not reject neutrality, other data hint at a role for natural selection. Together these data provide a clear case where a lack of sequence conservation does not imply a lack of conservation of expression or function.

Sex-specific recombination rates and allele frequencies affect the invasion of sexually antagonistic variation on autosomes

The introduction and persistence of novel, sexually antagonistic alleles can depend upon factors that differ between males and females. Understanding the conditions for invasion in a two-locus model can elucidate these processes. For instance, selection can act differently upon the sexes, or sex linkage can facilitate the invasion of genetic variation with opposing fitness effects between the sexes. Two factors that deserve further attention are recombination rates and allele frequencies - both of which can vary substantially between the sexes. We find that sex-specific recombination rates in a two-locus diploid model can affect the invasion outcome of sexually antagonistic alleles and that the sex-averaged recombination rate is not necessarily sufficient to predict invasion. We confirm that the range of permissible recombination rates is smaller in the sex benefitting from invasion and larger in the sex harmed by invasion. However, within the invasion space, male recombination rate can be greater than, equal to or less than female recombination rate in order for a male-benefit, female-detriment allele to invade (and similarly for a female-benefit, male-detriment allele). We further show that a novel, sexually antagonistic allele that is also associated with a lowered recombination rate can invade more easily when present in the double heterozygote genotype. Finally, we find that sexual dimorphism in resident allele frequencies can impact the invasion of new sexually antagonistic alleles at a second locus. Our results suggest that accounting for sex-specific recombination rates and allele frequencies can determine the difference between invasion and non-invasion of novel, sexually antagonistic alleles in a two-locus model.

Sex-biased expression of microRNAs in Schistosoma mansoni

Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma. Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system. MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differentiation in dioecious species. Here we characterize 112 microRNAs from adult Schistosoma mansoni individuals, including 84 novel microRNA families, and investigate the expression pattern in different sexes. By deep sequencing, we measured the relative expression levels of conserved and newly identified microRNAs between male and female samples. We observed that 13 microRNAs exhibited sex-biased expression, 10 of which are more abundant in females than in males. Sex chromosomes showed a paucity of female-biased genes, as predicted by theoretical evolutionary models. We propose that the recent emergence of separate sexes in Schistosoma had an effect on the chromosomal distribution and evolution of microRNAs, and that microRNAs are likely to participate in the sex differentiation/maintenance process.

Schistosomiasis is the second most common disease caused by a parasite, affecting over 200 million people. The parasites involved are flatworms of the genus Schistosoma. Unlike most non-parasitic flatworms, Schistosoma species have separate sexes, and the emergence of sex has been associated with the development of a parasitic lifestyle. The identification of gene products that are expressed in a sex-biased fashion permits the study of the origin of sexual dimorphism and, in the case of the schistosomes, the evolution of a human parasite. Here we investigated the differential expression of microRNAs in male and female individuals of the species Schistosoma mansoni. MicroRNAs are crucial gene regulators. We observed that many new microRNAs emerged in the evolutionary lineage leading to the schistosomes. However, many sex-biased microRNAs were present in the hermaphrodite ancestor of the flatworms, and therefore acquired sex-biased expression later on. Our results suggest that changes in microRNA expression patterns were associated with the emergence of separate sexes in the schistosomes.

'Escaping' the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster

Genomic analyses of Drosophila species suggest that the X chromosome presents an unfavourable environment for the expression of genes in the male germline. A previous study in D. melanogaster used a reporter gene driven by a testis-specific promoter to show that expression was greatly reduced when the gene was inserted onto the X chromosome as compared with the autosomes. However, a limitation of this study was that only the expression regulated by a single, autosomal-derived promoter was investigated. To test for an increase in expression associated with 'escaping' the X chromosome, we analysed reporter gene expression driven by the promoters of three X-linked, testis-expressed genes (CG10920, CG12681 and CG1314) that were inserted randomly throughout the D. melanogaster genome. In all cases, insertions on the autosomes showed significantly higher expression than those on the X chromosome. Thus, even genes whose regulation has adapted to the X-chromosomal environment show increased male germline expression when relocated to an autosome. Our results provide direct experimental evidence for the suppression of X-linked gene expression in the Drosophila male germline that is independent of gene dose.

Sex-biased transcriptome evolution in Drosophila

Sex-biased genes are thought to drive phenotypic differences between males and females. The recent availability of high-throughput gene expression data for many related species has led to a burst of investigations into the genomic and evolutionary properties of sex-biased genes. In Drosophila, a number of studies have found that X chromosomes are deficient in male-biased genes (demasculinized) and enriched for female-biased genes (feminized) and that male-biased genes evolve faster than female-biased genes. However, studies have yielded vastly different conclusions regarding the numbers of sex-biased genes and forces shaping their evolution. Here, we use RNA-seq data from multiple tissues of Drosophila melanogaster and D. pseudoobscura, a species with a recently evolved X chromosome, to explore the evolution of sex-biased genes in Drosophila. First, we compare several independent metrics for classifying sex-biased genes and find that the overlap of genes identified by different metrics is small, particularly for female-biased genes. Second, we investigate genome-wide expression patterns and uncover evidence of demasculinization and feminization of both ancestral and new X chromosomes, demonstrating that gene content on sex chromosomes evolves rapidly. Third, we examine the evolutionary rates of sex-biased genes and show that male-biased genes evolve much faster than female-biased genes, which evolve at similar rates to unbiased genes. Analysis of gene expression among tissues reveals that this trend may be partially due to pleiotropic effects of female-biased genes, which limits their evolutionary potential. Thus, our findings illustrate the importance of accurately identifying sex-biased genes and provide insight into their evolutionary dynamics in Drosophila.

Network analysis of functional genomics data: application to avian sex-biased gene expression

Gene expression analysis is often used to investigate the molecular and functional underpinnings of a phenotype. However, differential expression of individual genes is limited in that it does not consider how the genes interact with each other in networks. To address this shortcoming we propose a number of network-based analyses that give additional functional insights into the studied process. These were applied to a dataset of sex-specific gene expression in the chicken gonad and brain at different developmental stages. We first constructed a global chicken interaction network. Combining the network with the expression data showed that most sex-biased genes tend to have lower network connectivity, that is, act within local network environments, although some interesting exceptions were found. Genes of the same sex bias were generally more strongly connected with each other than expected. We further studied the fates of duplicated sex-biased genes and found that there is a significant trend to keep the same pattern of sex bias after duplication. We also identified sex-biased modules in the network, which reveal pathways or complexes involved in sex-specific processes. Altogether, this work integrates evolutionary genomics with systems biology in a novel way, offering new insights into the modular nature of sex-biased genes.

Sex and speciation: Drosophila reproductive tract proteins- twenty five years later

The protein electrophoresis revolution, nearly fifty years ago, provided the first glimpse into the nature of molecular genetic variation within and between species and showed that the amount of genetic differences between newly arisen species was minimal. Twenty years later, 2D electrophoresis showed that, in contrast to general gene-enzyme variation, reproductive tract proteins were less polymorphic within species but highly diverged between species. The 2D results were interesting and revolutionary, but somewhat uninterpretable because, at the time, rapid evolution and selective sweeps were not yet part of the common vocabulary of evolutionary biologists. Since then, genomic studies of sex and reproduction-related (SRR) genes have grown rapidly into a large area of research in evolutionary biology and are shedding light on a number of phenomena. Here we review some of the major and current fields of research that have greatly contributed to our understanding of the evolutionary dynamics and importance of SRR genes and genetic systems in understanding reproductive biology and speciation.

Sex-biased gene expression on the avian Z chromosome: highly expressed genes show higher male-biased expression

Dosage compensation, the process whereby expression of sex-linked genes remains similar between sexes (despite heterogamety) and balanced with autosomal expression, was long believed to be essential. However, recent research has shown that several lineages, including birds, butterflies, monotremes and sticklebacks, lack chromosome-wide dosage compensation mechanisms and do not completely balance the expression of sex-linked and autosomal genes. To obtain further understanding of avian sex-biased gene expression, we studied Z-linked gene expression in the brain of two songbirds of different genera (zebra finch, Taeniopygia guttata, and common whitethroat, Sylvia communis) using microarray technology. In both species, the male-bias in gene expression was significantly higher for Z than for autosomes, although the ratio of Z-linked to autosomal expression (Z:A) was relatively close to one in both sexes (range: 0.89-1.01). Interestingly, the Z-linked male-bias in gene expression increased with expression level, and genes with low expression showed the lowest degree of sex-bias. These results support the view that the heterogametic females have up-regulated their single Z-linked homologues to a high extent when the W-chromosome degraded and thereby managed to largely balance their Z:A expression with the exception of highly expressed genes. The male-bias in highly expressed genes points towards male-driven selection on Z-linked loci, and this and other possible hypotheses are discussed.

Why chromosome palindromes?

We look at sex-limited chromosome (Y or W) evolution with particular emphasis on the importance of palindromes. Y chromosome palindromes consist of inverted duplicates that allow for local recombination in an otherwise nonrecombining chromosome. Since palindromes enable intrachromosomal gene conversion that can help eliminate deleterious mutations, they are often highlighted as mechanisms to protect against Y degeneration. However, the adaptive significance of recombination resides in its ability to decouple the evolutionary fates of linked mutations, leading to both a decrease in degeneration rate and an increase in adaptation rate. Our paper emphasizes the latter, that palindromes may exist to accelerate adaptation by increasing the potential targets and fixation rates of incoming beneficial mutations. This hypothesis helps reconcile two enigmatic features of the “palindromes as protectors” view: (1) genes that are not located in palindromes have been retained under purifying selection for tens of millions of years, and (2) under models that only consider deleterious mutations, gene conversion benefits duplicate gene maintenance but not initial fixation. We conclude by looking at ways to test the hypothesis that palindromes enhance the rate of adaptive evolution of Y-linked genes and whether this effect can be extended to palindromes on other chromosomes.

Statistical inference of selection and divergence from a time-dependent Poisson random field model

We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time (or 1.68 million years, assuming the haploid effective population size years) and a mean selection coefficient per generation . Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.

Rate of amino acid substitution is influenced by the degree and conservation of male-biased transcription over 50 myr of Drosophila evolution

Sex-biased gene expression (i.e., the differential expression of genes between males and females) is common among sexually reproducing species. However, genes often differ in their sex-bias classification or degree of sex bias between species. There is also an unequal distribution of sex-biased genes (especially male-biased genes) between the X chromosome and the autosomes. We used whole-genome expression data and evolutionary rate estimates for two different Drosophilid lineages, melanogaster and obscura, spanning an evolutionary time scale of around 50 Myr to investigate the influence of sex-biased gene expression and chromosomal location on the rate of molecular evolution. In both lineages, the rate of protein evolution correlated positively with the male/female expression ratio. Genes with highly male-biased expression, genes expressed specifically in male reproductive tissues, and genes with conserved male-biased expression over long evolutionary time scales showed the fastest rates of evolution. An analysis of sex-biased gene evolution in both lineages revealed evidence for a "fast-X" effect in which the rate of evolution was greater for X-linked than for autosomal genes. This pattern was particularly pronounced for male-biased genes. Genes located on the obscura "neo-X" chromosome, which originated from a recent X-autosome fusion, showed rates of evolution that were intermediate between genes located on the ancestral X-chromosome and the autosomes. This suggests that the shift to X-linkage led to an increase in the rate of molecular evolution.

Inter- and intraspecific variation in Drosophila genes with sex-biased expression

Genes with sexually dimorphic expression (sex-biased genes) often evolve rapidly and are thought to make an important contribution to reproductive isolation between species. We examined the molecular evolution of sex-biased genes in Drosophila melanogaster and D. ananassae, which represent two independent lineages within the melanogaster group. We find that strong purifying selection limits protein sequence variation within species, but that a considerable fraction of divergence between species can be attributed to positive selection. In D. melanogaster, the proportion of adaptive substitutions between species is greatest for male-biased genes and is especially high for those on the X chromosome. In contrast, male-biased genes do not show unusually high variation within or between populations. A similar pattern is seen at the level of gene expression, where sex-biased genes show high expression divergence between species, but low divergence between populations. In D. ananassae, there is no increased rate of adaptation of male-biased genes, suggesting that the type or strength of selection acting on sex-biased genes differs between lineages.

Gene duplication in the evolution of sexual dimorphism

Males and females share most of the same genes, so selection in one sex will typically produce a correlated response in the other sex. Yet, the sexes have evolved to differ in a multitude of behavioral, morphological, and physiological traits. How did this sexual dimorphism evolve despite the presence of a common underlying genome? We investigated the potential role of gene duplication in the evolution of sexual dimorphism. Because duplication events provide extra genetic material, the sexes each might use this redundancy to facilitate sex-specific gene expression, permitting the evolution of dimorphism. We investigated this hypothesis at the genome-wide level in Drosophila melanogaster, using the presence of sex-biased expression as a proxy for the sex-specific specialization of gene function. We expected that if sexually antagonistic selection is a potent force acting upon individual genes, duplication will result in paralog families whose members differ in sex-biased expression. Gene members of the same duplicate family can have different expression patterns in males versus females. In particular, duplicate pairs containing a male-biased gene are found more frequently than expected, in agreement with previous studies. Furthermore, when the singleton ortholog is unbiased, duplication appears to allow one of the paralog copies to acquire male-biased expression. Conversely, female-biased expression is not common among duplicates; fewer duplicate genes are expressed in the female-soma and ovaries than in the male-soma and testes. Expression divergence exists more in older than in younger duplicates pairs, but expression divergence does not correlate with protein sequence divergence. Finally, genomic proximity may have an effect on whether paralogs differ in sex-biased expression. We conclude that the data are consistent with a role of gene duplication in fostering male-biased, but not female-biased, gene expression, thereby aiding the evolution of sexual dimorphism.

De Novo assembly of the Manila clam Ruditapes philippinarum transcriptome provides new insights into expression bias, mitochondrial doubly uniparental inheritance and sex determination

Males and females share the same genome, thus, phenotypic divergence requires differential gene expression and sex-specific regulation. Accordingly, the analysis of expression patterns is pivotal to the understanding of sex determination mechanisms. Many bivalves are stable gonochoric species, but the mechanism of gonad sexualization and the genes involved are still unknown. Moreover, during the period of sexual rest, a gonad is not present and sex cannot be determined. A mechanism associated with germ line differentiation in some bivalves, including the Manila clam Ruditapes philippinarum, is the doubly uniparental inheritance (DUI) of mitochondria, a variation of strict maternal inheritance. Two mitochondrial lineages are present, one transmitted through eggs and the other through sperm, as well as a mother-dependent sex bias of the progeny. We produced a de novo annotation of 17,186 transcripts from R. philippinarum and compared the transcriptomes of males and females and identified 1,575 genes with strong sex-specific expression and 166 sex-specific single nucleotide polymorphisms, obtaining preliminary information about genes that could be involved in sex determination. Then we compared the transcriptomes between a family producing predominantly females and a family producing predominantly males to identify candidate genes involved in regulation of sex-specific aspects of DUI system, finding a relationship between sex bias and differential expression of several ubiquitination genes. In mammalian embryos, sperm mitochondria are degraded by ubiquitination. A modification of this mechanism is hypothesized to be responsible for the retention of sperm mitochondria in male embryos of DUI species. Ubiquitination can additionally regulate gene expression, playing a role in sex determination of several animals. These data enable us to develop a model that incorporates both the DUI literature and our new findings.

Gene duplication and the genome distribution of sex-biased genes

In species that have two sexes, a single genome encodes two morphs, as each sex can be thought of as a distinct morph. This means that the same set of genes are differentially expressed in the different sexes. Many questions emanate from this statement. What proportion of genes contributes to sexual dimorphism? How do they contribute to sexual dimorphism? How is sex-biased expression achieved? Which sex and what tissues contribute the most to sex-biased expression? Do sex-biased genes have the same evolutionary patterns as nonbiased genes? We review the current data on sex-biased expression in species with heteromorphic sex chromosomes and comment on the most important hypotheses suggested to explain the origin, evolution, and distribution patterns of sex-biased genes. In this perspective we emphasize how gene duplication serves as an important molecular mechanism to resolve genomic clashes and genetic conflicts by generating sex-biased genes, often sex-specific genes, and contributes greatly to the underlying genetic basis of sexual dimorphism.

Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family

The tempo and mode of evolution of loci with a large effect on adaptation and reproductive isolation will influence the rate of evolutionary divergence and speciation. Desaturase loci are involved in key biochemical changes in long-chain fatty acids. In insects, these have been shown to influence adaptation to starvation or desiccation resistance and in some cases act as important pheromones. The desaturase gene family of Drosophila is known to have evolved by gene duplication and diversification, and at least one locus shows rapid evolution of sex-specific expression variation. Here, we examine the evolution of the gene family in species representing the Drosophila phylogeny. We find that the family includes more loci than have been previously described. Most are represented as single-copy loci, but we also find additional examples of duplications in loci which influence pheromone blends. Most loci show patterns of variation associated with purifying selection, but there are strong signatures of diversifying selection in new duplicates. In the case of a new duplicate of desat1 in the obscura group species, we show that strong selection on the coding sequence is associated with the evolution of sex-specific expression variation. It seems likely that both sexual selection and ecological adaptation have influenced the evolution of this gene family in Drosophila.

Genetic basis of wing morphogenesis in Drosophila: sexual dimorphism and non-allometric effects of shape variation

BACKGROUND

The Drosophila wing represents a particularly appropriate model to investigate the developmental control of phenotypic variation. Previous studies which aimed to identify candidate genes for wing morphology demonstrated that the genetic basis of wing shape variation in D. melanogaster is composed of numerous genetic factors causing small, additive effects. In this study, we analyzed wing shape in males and females from 191 lines of D. melanogaster, homozygous for a single P-element insertion, using geometric morphometrics techniques. The analysis allowed us to identify known and novel candidate genes that may contribute to the expression of wing shape in each sex separately and to compare them to candidate genes affecting wing size which have been identified previously using the same lines.

RESULTS

Our results indicate that more than 63% of induced mutations affected wing shape in one or both sexes, although only 33% showed significant differences in both males and females. The joint analysis of wing size and shape revealed that only 19% of the P-element insertions caused coincident effects on both components of wing form in one or both sexes. Further morphometrical analyses revealed that the intersection between veins showed the smallest displacements in the proximal region of the wing. Finally, we observed that mutations causing general deformations were more common than expected in both sexes whereas the opposite occurred with those generating local changes. For most of the 94 candidate genes identified, this seems to be the first record relating them with wing shape variation.

CONCLUSIONS

Our results support the idea that the genetic architecture of wing shape is complex with many different genes contributing to the trait in a sexually dimorphic manner. This polygenic basis, which is relatively independent from that of wing size, is composed of genes generally involved in development and/or metabolic functions, especially related to the regulation of different cellular processes such as motility, adhesion, communication and signal transduction. This study suggests that understanding the genetic basis of wing shape requires merging the regulation of vein patterning by signalling pathways with processes that occur during wing development at the cellular level.

Evolution of a tissue-specific splicing network

Alternative splicing of precursor mRNA (pre-mRNA) is a strategy employed by most eukaryotes to increase transcript and proteomic diversity. Many metazoan splicing factors are members of multigene families, with each member having different functions. How these highly related proteins evolve unique properties has been unclear. Here we characterize the evolution and function of a new Drosophila splicing factor, termed LS2 (Large Subunit 2), that arose from a gene duplication event of dU2AF(50), the large subunit of the highly conserved heterodimeric general splicing factor U2AF (U2-associated factor). The quickly evolving LS2 gene has diverged from the splicing-promoting, ubiquitously expressed dU2AF(50) such that it binds a markedly different RNA sequence, acts as a splicing repressor, and is preferentially expressed in testes. Target transcripts of LS2 are also enriched for performing testes-related functions. We therefore propose a path for the evolution of a new splicing factor in Drosophila that regulates specific pre-mRNAs and contributes to transcript diversity in a tissue-specific manner.

Intralocus sexual conflict resolved through gene duplication

Gene duplication is mainly recognized by its primary role in the origin of new genes and functions. However, the idea that gene duplication can be a central player in resolving sexual genetic conflicts through its potential to generate sex-biased and sex-specifically expressed genes, has been almost entirely overlooked. We review recent data and theory that support gene duplication as a theoretically predicted and experimentally supported means of resolving intralocus sexual antagonism. We believe that this role is probably the consequence of sexual conflict for housekeeping genes that are required in males and females, and which are expressed in sexually dimorphic tissues (i.e. where sexually antagonistic selection is exerted). We think that these genes cannot evolve tissue-specific expression unless they duplicate.

Association between sex-biased gene expression and mutations with sex-specific phenotypic consequences in Drosophila

Genome-wide mRNA transcription profiles reveal widespread molecular sexual dimorphism or “sex-biased” gene expression, yet the relationship between molecular and phenotypic sexual dimorphism remains unclear. A major unresolved question is whether sex-biased genes typically perform male- and female-specific functions (whether these genes have sex-biased phenotypic or fitness consequences) or have similar functional importance for both sexes. To elucidate the relationship between sex-biased transcription and sex-biased fitness consequences, we analyzed a large data set of lethal, visible, and sterile mutations that have been mapped to the Drosophila melanogaster genome. The data permitted us to classify genes according to their sex-specific mutational effects and to infer the relationship between sex-biased transcription level and sex-specific fitness consequences. We find that mutations in female-biased genes are (on average) more deleterious to females than to males and that mutations in male-biased genes tend to be more deleterious to males than to females. Nevertheless, mutations in most sex-biased genes have similar phenotypic consequences for both sexes, which suggests that sex-biased transcription is not necessarily associated with functional genetic differentiation between males and females. These results have interesting implications for the evolution of sexual dimorphism and sex-specific adaptation.

The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds

Background

Despite virtually identical DNA sequences between the sexes, sexual dimorphism is a widespread phenomenon in nature. To a large extent the systematic differences between the sexes must therefore arise from processes involving gene regulation. In accordance, sexual dimorphism in gene expression is common and extensive. Genes with sexually dimorphic regulation are known to evolve rapidly, both in DNA sequence and in gene expression profile. Studies of gene expression in related species can shed light on the flexibility, or degree of conservation, of the gene expression profiles underlying sexual dimorphism.

Results

We have studied the extent of sexual dimorphism in gene expression in the brain of two species of songbirds, the zebra finch (Taeniopygia guttata) and the common whitethroat (Sylvia communis), using large-scale microarray technology. Sexual dimorphism in gene expression was extensive in both species, and predominantly sex-linked: most genes identified were male-biased and Z-linked. Interestingly, approximately 50% of the male-biased Z-linked genes were sex-biased only in one of the study species.

Conclusion

Our results corroborate the results of recent studies in chicken and zebra finch which have been interpreted as caused by a low degree of dosage compensation in female birds (i.e. the heterogametic sex). Moreover, they suggest that zebra finches and common whitethroats dosage compensate partly different sets of genes on the Z chromosome. It is possible that this pattern reflects differences in either the essentiality or the level of sexual antagonism of these genes in the respective species. Such differences might correspond to genes with different rates of evolution related to sexual dimorphism in the avian brain, and might therefore be correlated with differences between the species in sex-specific behaviours.

Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution

Genes that are differentially expressed between the sexes (sex-biased genes) are among the fastest evolving genes in animal genomes. The majority of sex-biased expression is attributable to genes that are primarily expressed in sex-limited reproductive tissues, and these reproductive genes are often rapidly evolving because of intra- and intersexual selection pressures. Additionally, studies of multiple taxa have revealed that genes with sex-biased expression are also expressed in a limited number of tissues. This is worth noting because narrowly expressed genes are known to evolve faster than broadly expressed genes. Therefore, it is not clear whether sex-biased genes are rapidly evolving because they have sexually dimorphic expression, because they are expressed in sex-limited reproductive tissues, or because they are narrowly expressed. To determine the extend to which other confounding variables can explain the rapid evolution of sex-biased genes, I analyzed the rates of evolution of sex-biased genes in Drosophila melanogaster and Mus musculus in light of tissue-specific measures of expression. I find that genes with sex-biased expression in somatic tissues shared by both sexes are often evolving faster than non-sex-biased genes, but this is best explained by the narrow expression profiles of sex-biased genes. Sex-biased genes in sex-limited tissues in D. melanogaster, however, evolve faster than other narrowly expressed genes. Therefore, the rapid evolution of sex-biased genes is limited only to those genes primarily expressed in sex-limited reproductive tissues.

Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species

The prevalence of natural selection relative to genetic drift is of central interest in evolutionary biology. Depending on the distribution of fitness effects of new mutations, the importance of these evolutionary forces may differ in species with different effective population sizes. Here, we survey population genetic variation at 105 orthologous X-linked protein coding regions in Drosophila melanogaster and its sister species D. simulans, two closely related species with distinct demographic histories. We observe significantly higher levels of polymorphism and evidence for stronger selection on codon usage bias in D. simulans, consistent with a larger historical effective population size on average for this species. Despite these differences, we estimate that <10% of newly arising nonsynonymous mutations have deleterious fitness effects in the nearly neutral range (i.e., −10 < N_es < 0) in both species. The inferred distributions of fitness effects and demographic models translate into surprisingly high estimates of the fraction of “adaptive” protein divergence in both species (∼85–90%). Despite evidence for different demographic histories, differences in population size have apparently played little role in the dynamics of protein evolution in these two species, and estimates of the adaptive fraction (α) of protein divergence in both species remain high even if we account for recent 10-fold growth. Furthermore, although several recent studies have noted strong signatures of recurrent adaptive protein evolution at genes involved in immunity, reproduction, sexual conflict, and intragenomic conflict, our finding of high levels of adaptive protein divergence at randomly chosen proteins (with respect to function) suggests that many other factors likely contribute to the adaptive protein divergence signature in Drosophila.

Specialization of a Drosophila capping protein essential for the protection of sperm telomeres

BACKGROUND

A critical function of telomeres is to prevent fusion of chromosome ends by the DNA repair machinery. In Drosophila somatic cells, assembly of the protecting capping complex at telomeres notably involves the recruitment of HOAP, HP1, and their recently identified partner, HipHop. We previously showed that the hiphop gene was duplicated before the radiation of the melanogaster subgroup of species, giving birth to K81, a unique paternal effect gene specifically expressed in the male germline.

RESULTS

Here we show that K81 specifically associates with telomeres during spermiogenesis, along with HOAP and HP1, and is retained on paternal chromosomes until zygote formation. In K81 mutant testes, capping proteins are not maintained at telomeres in differentiating spermatids, resulting in the transmission of uncapped paternal chromosomes that fail to properly divide during the first zygotic mitosis. Despite the apparent similar capping roles of K81 and HipHop in their respective domain of expression, we demonstrate by in vivo reciprocal complementation analyses that they are not interchangeable. Strikingly, HipHop appeared to be unable to maintain capping proteins at telomeres during the global chromatin remodeling of spermatid nuclei.

CONCLUSIONS

Our data demonstrate that K81 is essential for the maintenance of capping proteins at telomeres in postmeiotic male germ cells. In species of the melanogaster subgroup, HipHop and K81 have not only acquired complementary expression domains, they have also functionally diverged following the gene duplication event. We propose that K81 specialized in the maintenance of telomere protection in the highly peculiar chromatin environment of differentiating male gametes.

Sex chromosomes and the evolution of sexual dimorphism: lessons from the genome

Females and males of many animals exhibit a striking array of sexual dimorphisms, ranging from the primary differences of the gametes and gonads to the somatic differences often seen in behavior, morphology, and physiology. These differences raise many questions regarding how such divergent phenotypes can arise from a genome that is largely shared between the sexes. Recent progress in genomics has revealed some of the actual genetic mechanisms that create separate sex-specific phenotypes, and the evidence indicates that thousands of genes across all portions of the genome contribute to male and female forms through sex-biased gene expression. Related work has begun to define the strength and influence of sex-specific evolutionary forces that shape these phenotypic dimorphisms and how they in turn affect the genome. Additionally, theory has long suggested that the evolution of sexual dimorphism is facilitated by sex chromosomes, as these are the only portions of the genome that differ between males and females. Genomic analysis indicates that there is indeed a relationship between sexual dimorphism and the sex chromosomes. However, the connection is far more complicated than current theory allows, and this may ultimately require a reexamination of the assumptions so that predictions match the accumulating empirical data.

Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species

How much does the intensity of purifying selection vary among populations and species? How uniform are the shifts in selective pressures across the genome? To address these questions, we took advantage of a recent, whole-genome polymorphism data set from two closely related species of yeast, Saccharomyces cerevisiae and S. paradoxus, paying close attention to the population structure within these species. We found that the average intensity of purifying selection on amino acid sites varies markedly among populations and between species. As expected in the presence of extensive weakly deleterious mutations, the effect of purifying selection is substantially weaker on single nucleotide polymorphisms (SNPs) segregating within populations than on SNPs fixed between population samples. Also in accordance with a Nearly Neutral model, the variation in the intensity of purifying selection across populations corresponds almost perfectly to simple measures of their effective size. As a first step toward understanding the processes generating these patterns, we sought to tease apart the relative importance of systematic, genome-wide changes in the efficacy of selection, such as those expected from demographic processes and of gene-specific changes, which may be expected after a shift in selective pressures. For that purpose, we developed a new model for the evolution of purifying selection between populations and inferred its parameters from the genome-wide data using a likelihood approach. We found that most, but not all changes seem to be explained by systematic shifts in the efficacy of selection. One population, the sake-derived strains of S. cerevisiae, however, also shows extensive gene-specific changes, plausibly associated with domestication. These findings have important implications for our understanding of purifying selection as well as for estimates of the rate of molecular adaptation in yeast and in other species.

Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila

Gene duplication is a major force driving genome evolution, and examples of this mode of evolution and of the functions of duplicated genes are needed to reveal general patterns. Here, our study focuses on a particular retrogene (i.e., CG9573) that originated about 5-13 million years ago that we have named Drcd-1 related. It originated in Drosophila through retroposition of the parental gene Required for cell differentiation 1 of Drosophila (Drcd-1; CG14213), which is a known transcription cofactor. Drcd-1r is only present in D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Drcd-1r is an X to autosome retroposition event. Many retrogenes are X to autosome copies and it has been shown that positive selection underlies this bias. We sought to understand Drcd-1r mode of evolution and function to contribute to the understanding of the selective pressures acting on X to autosome retrogenes. Drcd-1r overlaps with another gene, it is within the 3' UTR of the gene CG13102 and is encoded in the opposite orientation. We have studied the characteristics of the transcripts and quantified expression of CG13102 and Drcd-1r in wild-type flies. We found that Drcd-1r is transcribed specifically in testes. We also studied the molecular evolution of Drcd-1r and Drcd-1 and found that the parental gene has evolved under very strong purifying selection but the retrogene has evolved very rapidly (Ka/Ks ~1) under both positive and purifying selection, as revealed using divergence and polymorphism data. These results indicate that Drcd-1r has a novel function in the Drosophila testes. To further explore Drcd-1r function we used a strain containing a P element inserted in the region where CG13102 and Drcd-1r are located that shows recessive male sterility. Analysis of this strain reveals the difficulties that can be encountered in studying the functions of genes with overlapping transcripts. Avenues for studying of the function of this gene are proposed.

Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda

We present the results of surveys of diversity in sets of >40 X-linked and autosomal loci in samples from natural populations of Drosophila miranda and D. pseudoobscura, together with their sequence divergence from D. affinis. Mean silent site diversity in D. miranda is approximately one-quarter of that in D. pseudoobscura; mean X-linked silent diversity is about three-quarters of that for the autosomes in both species. Estimates of the distribution of selection coefficients against heterozygous, deleterious nonsynonymous mutations from two different methods suggest a wide distribution, with coefficients of variation greater than one, and with the average segregating amino acid mutation being subject to only very weak selection. Only a small fraction of new amino acid mutations behave as effectively neutral, however. A large fraction of amino acid differences between D. pseudoobscura and D. affinis appear to have been fixed by positive natural selection, using three different methods of estimation; estimates between D. miranda and D. affinis are more equivocal. Sources of bias in the estimates, especially those arising from selection on synonymous mutations and from the choice of genes, are discussed and corrections for these applied. Overall, the results show that both purifying selection and positive selection on nonsynonymous mutations are pervasive.

Male sex drive and the maintenance of sex: evidence from Drosophila

The resolution of the paradoxes surrounding the evolutionary origins and maintenance of sexual reproduction has been a major focus in biology. The operation of sexual selection-which is very common among multicellular organisms-has been proposed as an important factor in the maintenance of sex, though in order for this hypothesis to hold, the strength of sexual selection must be stronger in males than in females. Sexual selection poses its own series of evolutionary questions, including how genetic variability is maintained in the face of sustained directional selection (known as the "paradox of the lek"). In this short review, we present evidence obtained from recent comparative genomics projects arguing that 1) the genomic consequences of sexual selection clearly show that its effect is stronger in males and 2) this sustained selection over evolutionary timescales also has an effect of capturing de novo genes and expression patterns influencing male fitness, thus providing a mechanism via which new genetic variation can be input into to male traits. Furthermore, we argue that this latter process of genomic "masculinization" has an additional effect of making males difficult to purge from populations, as evidence from Drosophila indicates that, for example, many male sexually selected seminal fluid factors are required to ensure maximally efficient reproduction. Newly arising parthenogenic mutations would suffer an immediate reproductive rate disadvantage were these proteins lost. We show that recent studies confirm that genomic masculinization, as a result of "male sex drive," has important consequences for the evolution of sexually dimorphic species.

On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila

The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here, we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns <or=120 bp, 3) all sites of introns <or=65 bp, 4) bases 8-30 of introns <or=120 bp, and 5) bases 8-30 of introns <or=65 bp. The last class of sites shows the highest levels of both interspecific divergence and intraspecific polymorphism, suggesting that these sites are under the least selective constraint. Bases 8-30 of introns <or=65 bp also have the lowest ratio of divergence to polymorphism, which may indicate that a small proportion of substitutions in the other classes of sites are the result of adaptive evolution. Although there is little signal of selection on the primary sequence of short introns, patterns of insertion-deletion polymorphism and divergence suggest that both positive and negative selection act to maintain an optimal intron length.