Drosophila Persimilis Research Articles

The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.

Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.

Inversions shape the divergence of Drosophila pseudoobscura and Drosophila persimilis on multiple timescales.

By shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage disequilibrium prespeciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and Drosophila persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between D. pseudoobscura and D. persimilis over three distinct timescales: (1) segregation of ancestral polymorphism early in the speciation process, (2) gene flow after the split of D. pseudoobscura and D. persimilis, but prior to the split of D. pseudoobscura subspecies, and (3) recent gene flow between sympatric D. pseudoobscura and D. persimilis, after the split of D. pseudoobscura subspecies. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in other systems.

The spontaneous mutation rate of Drosophila pseudoobscura.

The spontaneous mutation rate is a very variable trait that is subject to drift, selection and is sometimes highly plastic. Consequently, its variation between close species, or even between populations from the same species, can be very large. Here, I estimated the spontaneous mutation rate of Drosophila pseudoobscura and Drosophila persimilis crosses to explore the mutation rate variation within the Drosophila genus. All mutation rate estimations in Drosophila varied fourfold, probably explained by the sensitivity of the mutation rate to environmental and experimental conditions. Moreover, I found a very high mutation rate in the hybrid cross between D. pseudoobscura and D. persimilis, in agreement with known elevated mutation rate in hybrids. This mutation rate increase can be explained by heterozygosity and fitness decrease effects in hybrids.

Ancestral polymorphisms explain the role of chromosomal inversions in speciation.

Understanding the role of chromosomal inversions in speciation is a fundamental problem in evolutionary genetics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in Drosophila persimilis and D. pseudoobscura. We provide a solution to the puzzling origins of the selfish Sex-Ratio arrangement in D. persimilis and uncover surprising patterns of phylogenetic discordance on this chromosome. These patterns show that, contrary to widely held views, all fixed chromosomal inversions between D. persimilis and D. pseudoobscura were already present in their ancestral population long before the species split. Our results suggest that patterns of higher genomic divergence and an association of reproductive isolation genes with chromosomal inversions may be a direct consequence of incomplete lineage sorting of ancestral polymorphisms. These findings force a reconsideration of the role of chromosomal inversions in speciation, not as protectors of existing hybrid incompatibilities, but as fertile grounds for their formation.

Triggers of the Postural Display of Courtship in Drosophila persimilis Flies

D. persimilis courtship shows some flexibility and courting males sometimes perform an elaborate postural display in addition to the standard courtship behaviours shared by most Drosophila species. This postural display includes the acrobatic contortion and tremulation of their abdomen, accompanied by the generation of substrate-borne vibrations, and they proffer a nutritional droplet to the female. Here, we use courtship and choice assays to ask what triggers this display and what advantages males may gain from it during courtship. In pair assays, we found no differences in the courtship duration and copulation success between displaying and non-displaying males. In trio assays, however, the female always mated with the male who performed the display. To investigate what promotes the male display, we varied the level of receptivity of the female and studied the impact of a second male. We found that rejection by the female does not induce the male to display, contrary to what was previously suggested. We present evidence that the male display is in fact promoted by the presence of an attentive and sexually receptive female and the absence of male competition, with the greatest exhibition rate obtained if the courted female is starved. These findings provide valuable information about the social ecology of flies, and how internal and external cues influence sexual behaviours and mate choice.

Remating responses are consistent with male postcopulatory manipulation but not reinforcement in D.pseudoobscura.

Reinforcement occurs when hybridization between closely related lineages produces low‐fitness offspring, prompting selection for elevated reproductive isolation specifically in areas of sympatry. Both premating and postmating prezygotic behaviors have been shown to be the target of reinforcing selection, but it remains unclear whether remating behaviors experience reinforcement, although they can also influence offspring identity and limit formation of hybrids. Here, we evaluated evidence for reinforcing selection on remating behaviors in Drosophila pseudoobscura, by comparing remating traits in females from populations historically allopatric and sympatric with Drosophila persimilis. We found that the propensity to remate was not higher in sympatric females, compared to allopatric females, regardless of whether the first mated male was heterospecific or conspecific. Moreover, remating behavior did not contribute to interspecific reproductive isolation among any population; that is, females showed no higher propensity to remate following a heterospecific first mating than following a conspecific first mating. Instead, we found that females are less likely to remate after initial matings with unfamiliar males, regardless of species identity. This is consistent with one scenario of postmating sexual conflict in which females are poorly defended against postcopulatory manipulation by males with whom they have not coevolved. Our results are generally inconsistent with reinforcement on remating traits and suggest that this behavior might be more strongly shaped by the consequences of local antagonistic male–female interactions than interactions with heterospecifics.

The Elaborate Postural Display of Courting Drosophila persimilis Flies Produces Substrate-Borne Vibratory Signals.

Sexual selection has led to the evolution of extraordinary and elaborate male courtship behaviors across taxa, including mammals and birds, as well as some species of flies. Drosophila persimilis flies perform complex courtship behaviors found in most Drosophila species, which consist of visual, air-borne, gustatory and olfactory cues. In addition, Drosophila persimilis courting males also perform an elaborate postural display that is not found in most other Drosophila species. This postural display includes an upwards contortion of their abdomen, specialized movements of the head and forelegs, raising both wings into a “wing-posture” and, most remarkably, the males proffer the female a regurgitated droplet. Here, we use high-resolution imaging, laser vibrometry and air-borne acoustic recordings to analyse this postural display to ask which signals may promote copulation. Surprisingly, we find that no air-borne signals are generated during the display. We show, however, that the abdomen tremulates to generate substrate-borne vibratory signals, which correlate with the female’s immobility before she feeds onto the droplet and accepts copulation.Electronic supplementary materialThe online version of this article (doi:10.1007/s10905-016-9579-8) contains supplementary material, which is available to authorized users.

Temporal Stability of Molecular Diversity Measures in Natural Populations of Drosophila pseudoobscura and Drosophila persimilis.

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, but that data represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and Drosophila pseudoobscura collected 16 years apart at the same time of year and same site at 4 X-linked and 2 mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima's D between D. pseudoobscura timepoints at 1 locus associated with increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.

Temporal stability of molecular diversity measures in natural populations of Drosophila pseudoobscura and Drosophila persimilis

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, but that data represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and Drosophila pseudoobscura collected 16 years apart at the same time of year and same site at 4 X-linked and 2 mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima’s D between D. pseudoobscura timepoints at 1 locus associated with increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.

Chromosomal localization and partial sequencing of the 18S and 28S ribosomal genes from Bradysia hygida (Diptera: Sciaridae).

In insects, ribosomal genes are usually detected in sex chromosomes, but have also or only been detected in autosomal chromosomes in some cases. Previous results from our research group indicated that in Bradysia hygida, nucleolus organizer regions were associated with heterochromatic regions of the autosomal C chromosome, using the silver impregnation technique. The present study confirmed this location of the ribosomal genes using fluorescence in situ hybridization analysis. This analysis also revealed the partial sequences of the 18S and 28S genes for this sciarid. The sequence alignment showed that the 18S gene has 98% identity to Corydalus armatus and 91% identity to Drosophila persimilis and Drosophila melanogaster. The partial sequence analysis of the 28S gene showed 95% identity with Bradysia amoena and 93% identity with Schwenckfeldina sp. These results confirmed the location of ribosomal genes of B. hygida in an autosomal chromosome, and the partial sequence analysis of the 18S and 28S genes demonstrated a high percentage of identity among several insect ribosomal genes.

Mapping of within‐species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D.persimilis and D.pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system.

Alignment-free population genomics: an efficient estimator of sequence diversity.

Comparative sequencing contributes critically to the functional annotation of genomes. One prerequisite for successful analysis of the increasingly abundant comparative sequencing data is the availability of efficient computational tools. We present here a strategy for comparing unaligned genomes based on a coalescent approach combined with advanced algorithms for indexing sequences. These algorithms are particularly efficient when analyzing large genomes, as their run time ideally grows only linearly with sequence length. Using this approach, we have derived and implemented a maximum-likelihood estimator of the average number of mismatches per site between two closely related sequences, π. By allowing for fluctuating coalescent times, we are able to improve a previously published alignment-free estimator of π. We show through simulation that our new estimator is fast and accurate even with moderate recombination (ρ ≤ π). To demonstrate its applicability to real data, we compare the unaligned genomes of Drosophila persimilis and D. pseudoobscura. In agreement with previous studies, our sliding window analysis locates the global divergence minimum between these two genomes to the pericentromeric region of chromosome 3.

New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies

Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.

Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group.

Taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. Additionally, hybridization may spread alleles that confer barrier traits to other taxa. Historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. Here, we test for allelic variation within Drosophila persimilis and within the Bogota subspecies of D. pseudoobscura at regions previously shown to contribute to hybrid male sterility. We also test whether D. persimilis and the USA subspecies of D. pseudoobscura share an allele conferring hybrid sterility in a D. pseudoobscura bogotana genetic background. All loci conferred similar hybrid sterility effects across all strains studied, although we detected some statistically significant quantitative effect variation among D. persimilis alleles of some hybrid incompatibility QTLs. We also detected allelism between D. persimilis and D. pseudoobscura USA at a second chromosome hybrid sterility QTL. We hypothesize that either the QTL is ancestral in D. persimilis and D. pseudoobscura USA and lost in D. pseudoobscura bogotana, or gene flow transferred the QTL from D. persimilis to D. pseudoobscura USA. We discuss our findings in the context of population features that may contribute to variation in hybrid incompatibilities.

Effects of Inversions on Within- and Between-Species Recombination and Divergence

Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing-over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and Drosophila persimilis, we detected one double recombinant among 9,739 progeny from F1 hybrids screened, consistent with published double-crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species versus within species. Moreover, we observed strong “interchromosomal effect” (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within versus between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously.

Genetic and Evolutionary Correlates of Fine-Scale Recombination Rate Variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed "recombinational neighborhoods," where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5-7Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D.persimilis are strongly correlated with those obtained from a comparable study of its sister species, D.pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.

Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed “recombinational neighborhoods,” where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5–7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.

EPISTASIS MODIFIES THE DOMINANCE OF LOCI CAUSING HYBRID MALE STERILITY IN THEDROSOPHILA PSEUDOOBSCURASPECIES GROUP

Speciation, the evolution of reproductive isolation between populations, serves as the driving force for generating biodiversity. Postzygotic barriers to gene flow, such as F(1) hybrid sterility and inviability, play important roles in the establishment and maintenance of biological species. F(1) hybrid incompatibilities in taxa that obey Haldane's rule, the observation that the heterogametic sex suffers greater hybrid fitness problems than the homogametic sex, are thought to often result from interactions between recessive-acting X-linked loci and dominant-acting autosomal loci. Because they play such prominent roles in producing hybrid incompatibilities, we examine the dominance and nature of epistasis between alleles derived from Drosophila persimilis that confer hybrid male sterility in the genetic background of its sister species, D. pseudoobscura bogotana. We show that epistasis elevates the apparent dominance of individually recessive-acting QTL such that they can contribute to F(1) hybrid sterility. These results have important implications for assumptions underlying theoretical models of hybrid incompatibilities and may offer a possible explanation for why, to date, identification of dominant-acting autosomal "speciation genes" has been challenging.

Learning magnifies individual variation in heterospecific mating propensity

Recent research indicating learning in the context of sexual behaviour in fruit flies suggests that learning could increase levels of assortative mating between partially diverged populations. We present a graphic model examining the role of learning and a series of experiments evaluating assumptions and predictions of the model. We found that male Drosophila persimilis that previously succeeded in mating with females of the sibling species, D. pseudoobscura, did not have a higher heterospecific mating success than males that were either virgin or previously mated with conspecific females. On the other hand, female D. pseudoobscura with apparently strict mating criteria, which rejected heterospecific males, were also more likely to reject conspecific males than were females inexperienced with males. Finally, D. persimilis males previously rejected by heterospecific females courted significantly less and had half as much heterospecific mating success as males previously accepted by heterospecific females. These results, combined with previous evidence demonstrating that males rejected by heterospecific females learn to avoid courting such females, indicate that learning can increase phenotypic divergence between populations with partial pre-mating isolation.

Encapsulation ability: Are all Drosophila species equally armed? An investigation in the obscura group

Unable to form cellular capsules around large foreign bodies, the species Drosophila subobscura Collin in Gordon, 1936 was previously shown devoid of lamellocytes, the capsule-forming hemocytes in Drosophila melanogaster Meigen, 1830. This unusual case of deficiency in encapsulation ability was remarkable enough to motivate further investigations in phylogenetically related species of the obscura group. Like D. subobscura, the species Drosophila azteca Sturtevant and Dobzhansky, 1936, Drosophila bifasciata Pomini, 1940, Drosophila guanche Monclus, 1976, Drosophila miranda Dobzhansky, 1935, Drosophila persimilis Dobzhansky and Epling, 1944, and Drosophila pseudoobcura Frovola and Astaurov, 1929 were found to be unable to encapsulate large foreign bodies and also to lack lamellocytes. Surprisingly, Drosophila affinis Sturtevant, 1916, Drosophila tolteca Patterson and Mainland, 1944, and Drosophila obscura Fallen, 1823 were capable of mounting cellular capsules, although their encapsulation abilities remained weak. These three species were free of lamellocytes but possessed small pools of never before described “atypical hemocytes” present in the hemolymph when capsules were formed.