An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster

During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have identified network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster male terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the male terminalia are highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (https://flyterminalia.pitt.edu/) as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.

A Maladaptive Combination of Traits Contributes to the Maintenance of a Drosophila Hybrid Zone

Drosophila teissieri and D. yakuba diverged approximately 3 mya and are thought to share a large, ancestral, African range [1-3]. These species now co-occur in parts of continental Africa and in west Africa on the island of Bioko [1, 4]. While D. yakuba is a human commensal, D. teissieri seems to be associated with Parinari fruits, restricting its range to forests [4-6]. Genome data indicate introgression, despite no evidence of contemporary hybridization. Here we report the discovery of D. yakuba-D. teissieri hybrids at the interface of secondary forests and disturbed, open habitats on Bioko. We demonstrate that hybrids are the F₁ progeny of D. yakuba females and D. teissieri males. At high temperatures like those found on Bioko, D. teissieri females are generally less receptive to mating, and in combination with temperature effects on egg lay and egg-to-adult viability, this decreases the potential for gene flow between female D. teissieri and male D. yakuba relative to the reciprocal cross. Field and laboratory experiments demonstrate that F₁ hybrids have a maladaptive combination of D. yakuba behavior and D. teissieri physiology, generating additional barriers to gene flow. Nevertheless, analysis of introgressed and non-introgressed regions of the genome indicate that, while rare, gene flow is relatively recent. Our observations identify precise intrinsic and extrinsic factors that, along with hybrid male sterility, limit gene flow and maintain these species. These data contribute to a growing body of literature that suggests the Gulf of Guinea may be a hotspot for hybridization.

Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.

Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation

Three hybridizing species-the clade [(Drosophila yakuba, D. santomea), D. teissieri]-comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia-maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intraspecific and interspecific CI. In D teissieri, analyses of F1 and backcross genotypes show that both host genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected females seem largely protected from intraspecific and interspecific CI, irrespective of Wolbachia and host genotypes. Wolbachia do not affect host mating behavior or female fecundity, within or between species. The latter suggests little apparent effect of Wolbachia on premating or gametic reproductive isolation (RI) between host species. In nature, Wolbachia frequencies varied spatially for D. yakuba in 2009, with 76% (N = 155) infected on São Tomé, and only 3% (N = 36) infected on Bioko; frequencies also varied temporally in D. yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal frequency fluctuations could generate asymmetries in interspecific mating success, and contribute to postzygotic RI. However, the fluctuations in Wolbachia frequencies that we observe also suggest that asymmetries are unlikely to persist. Finally, we address theoretical questions that our empirical findings raise about Wolbachia persistence when conditions fluctuate, and about the stable coexistence of Wolbachia and host variants that modulate Wolbachia effects.

The evolution of reproductive isolation in the Drosophila yakuba complex of species

In the Drosophila melanogaster subgroup, the yakuba species complex, D. yakuba, D. santomea and D. teissieri have identical mitochondrial genomes in spite of nuclear differentiation. The first two species can be readily hybridized in the laboratory and produce fertile females and sterile males. They also form hybrids in natural conditions. Nonetheless, the third species, D. teissieri, was thought to be unable to produce hybrids with either D. yakuba or D. santomea. This in turn posed the conundrum of why the three species shared a single mitochondrial genome. In this report, we show that D. teissieri can indeed hybridize with both D. yakuba and D. santomea. The resulting female hybrids from both crosses are fertile, whereas the hybrid males are sterile. We also characterize six isolating mechanisms that might be involved in keeping the three species apart. Our results open the possibility of studying the history of introgression in the yakuba species complex and dissecting the genetic basis of interspecific differences between these three species by genetic mapping.

Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes, and anal plates exhibit striking differences between Drosophila mauritiana and D. simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

Coevolution between male and female genitalia in the Drosophila melanogaster species subgroup

In contrast to male genitalia that typically exhibit patterns of rapid and divergent evolution among internally fertilizing animals, female genitalia have been less well studied and are generally thought to evolve slowly among closely-related species. As a result, few cases of male-female genital coevolution have been documented. In Drosophila, female copulatory structures have been claimed to be mostly invariant compared to male structures. Here, we re-examined male and female genitalia in the nine species of the D. melanogaster subgroup. We describe several new species-specific female genital structures that appear to coevolve with male genital structures, and provide evidence that the coevolving structures contact each other during copulation. Several female structures might be defensive shields against apparently harmful male structures, such as cercal teeth, phallic hooks and spines. Evidence for male-female morphological coevolution in Drosophila has previously been shown at the post-copulatory level (e.g., sperm length and sperm storage organ size), and our results provide support for male-female coevolution at the copulatory level.

Male terminalia variation in the rainforest dwelling Drosophila teissieri contrasts with the sperm pattern and species stability

It is commonly recognized that speciation does not necessarily imply extensive variation between populations, and what the speciation process per se consists of still remains an unanswered question. We advocate here that the variation of male terminalia does not necessarily result in noticeable reproductive isolation. We report whether there is invariance or variance of traits central to sexual selection processes (i.e. male terminalia and sperm length) compared to traits which are generally assumed to vary more neutrally (i.e. allozymes) in the strictly Afrotropical forest-dwelling continental species Drosophila teissieri. Three geographic blocks can be recognized along the present range of the species. Our data suggest that the components of the species integrity do not obey the variance/invariance alternative consistently. Male terminalia and allozymes show extensive variation while sperm length distribution is strikingly similar between the geographic blocks. It is therefore inferred that sperm length might be one of the major targets of stabilizing selection. Finally, it is suggested that the striking fit between the extent of sperm heteromorphism (within male) and sperm polymorphism (between males) is instrumental in maintaining the species integrity.

Natural selection and genital variation: a role for the environment, parasites and sperm ageing?

Male genitalia are more variable between species (and populations) than other organs, and are more morphologically complex in polygamous compared to monogamous species. Therefore, sexual selection has been put forward as the major explanation of genital variation and complexity, in particular cryptic female choice for male copulatory courtship. As cryptic female choice is based on differences between males it is somewhat paradoxical that there is such low within-species variation in male genitalia that they are a prime morphological identification character for animal species. Processes other than sexual selection may also lead to genitalia variation but they have recently become neglected. Here I focus on pleiotropy and natural selection and provide examples how they link genitalia morphology with genital environments. Pleiotropy appears to be important because most studies that specifically tested for pleiotropic effects on genital morphology found them. Natural selection likely favours certain genital morphology over others in various environments, as well as by reducing re-infection with sexually transmitted diseases or reducing the likelihood of fertilisation with aged sperm. Both pleiotropy and natural selection differ locally and between species so may contribute to local variation in genitalia and sometimes variation between monogamous and polygamous species. Furthermore, the multitude of genital environments will lead to a multitude of genital functions via natural selection and pleiotropy, and may also contribute to explaining the complexity of genitalia.

Fragmented forests, evolving flies: molecular variation in African populations of Drosophila teissieri

Microsatellite variation from eight loci was studied in five populations of Drosophila teissieri, a fruit-fly found only in the rain forests of sub-Saharan Africa. Five noncontiguous rain forest sites (from Tanzania, Gabon and Ivory Coast) were sampled to measure the effects of historical forest fragmentation on population structure in an obligatory forest-dwelling species. The Ivory Coast and Gabon populations showed a wider range of alleles, different modal alleles and had a higher genetic diversity than the three East African populations. As could be expected, genetic differentiation (FST) was significantly correlated with physical distance, but the westernmost population (Ivory Coast) showed values that were intermediate between the central (Gabon) and Eastern (Tanzania) populations. A migration-drift equilibrium in a stable continuum of populations did not appear adequate to describe the observed distribution. It seems probable that the species has undergone abrupt changes involving isolation, merging and migration of populations, as a consequence of repeated waves of forest fragmentation and coalescence.

Differentiation of dialects and courtship strategies in allopatric populations of Drosophila teissieri

Intra-specific differentiation has been investigated between two geographically isolated populations of D. teissieri, one from Brazzaville (Congo) and the other from Silinda (Zimbabwe). Courtship songs were analyzed on 23 parameters. In addition, certain parameters related to sexual activity (five) and wing morphology (five) were also examined. As in other Drosophilidae, there are two types of courtship songs resulting from wing vibration: the love song, and the sine song. Love songs from Brazzaville are longer than those from Silinda (334ms vs. 216) with a tendency to smaller and more regular inter-pulse intervals (24.56ms vs. 25.5). The sine songs (SS) are about six times longer than the love songs in each population, with an adaptation of their duration according to the receptivity of the female in Brazzaville. All the LS temporal parameters, except the interpulse interval mean, are significantly different between the two populations. The Brazzaville flies show a greater acoustic activity and have higher mating success than the Silinda ones (53.3% vs. 27.7%). Their wings are slightly shorter and wider than those from Silinda. The role of acoustic parameters, sexual activity and wing physical constraints are discussed in the perspective of incipient speciation.