Species-wide genetic variation and demographic history of Drosophila sechellia, a species lacking population structure

Gene Protein Sequence Evolution Can Predict the Rapid Divergence of Ovariole Numbers in the Drosophila melanogaster Subgroup

Ovaries play key roles in fitness and evolution: they are essential female reproductive structures that develop and house the eggs in sexually reproducing animals. In Drosophila, the mature ovary contains multiple tubular egg-producing structures known as ovarioles. Ovarioles arise from somatic cellular structures in the larval ovary called terminal filaments (TFs), formed by TF cells and subsequently enclosed by sheath (SH) cells. As in many other insects, ovariole number per female varies extensively in Drosophila. At present, however, there is a striking gap of information on genetic mechanisms and evolutionary forces that shape the well-documented rapid interspecies divergence of ovariole numbers. To address this gap, here we studied genes associated with Drosophila melanogaster ovariole number or functions based on recent experimental and transcriptional datasets from larval ovaries, including TFs and SH cells, and assessed their rates and patterns of molecular evolution in five closely related species of the melanogaster subgroup that exhibit species-specific differences in ovariole numbers. From comprehensive analyses of protein sequence evolution (dN/dS), branch-site positive selection, expression specificity (tau), and phylogenetic regressions (phylogenetic generalized least squares), we report evidence of 42 genes that showed signs of playing roles in the genetic basis of interspecies evolutionary change of Drosophila ovariole number. These included the signaling genes upd2 and Ilp5 and extracellular matrix genes vkg and Col4a1, whose dN/dS predicted ovariole numbers among species. Together, we propose a model whereby a set of ovariole-involved gene proteins have an enhanced evolvability, including adaptive evolution, facilitating rapid shifts in ovariole number among Drosophila species.

Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species

The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.

Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species

The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.

Taste adaptations associated with host specialization in the specialist Drosophila sechellia

Chemosensory-driven host plant specialization is a major force mediating insect ecological adaptation and speciation. Drosophila sechellia, a species endemic to the Seychelles islands, feeds and oviposits on Morinda citrifolia almost exclusively. This fruit is harmless to D. sechellia but toxic to other Drosophilidae, including the closely related generalists D. simulans and D. melanogaster, because of its high content of fatty acids. While several olfactory adaptations mediating D. sechellia's preference for its host have been uncovered, the role of taste has been much less examined. We found that D. sechellia has reduced taste and feeding aversion to bitter compounds and host fatty acids that are aversive to D. melanogaster and D. simulans. The loss of aversion to canavanine, coumarin and fatty acids arose in the D. sechellia lineage, as its sister species D. simulans showed responses akin to those of D. melanogaster. Drosophila sechellia has increased taste and feeding responses towards M. citrifolia. These results are in line with D. sechellia's loss of genes that encode bitter gustatory receptors (GRs) in D. melanogaster. We found that two GR genes which are lost in D. sechellia, GR39a.a and GR28b.a, influence the reduction of aversive responses to some bitter compounds. Also, D. sechellia has increased appetite for a prominent host fatty acid compound that is toxic to its relatives. Our results support the hypothesis that changes in the taste system, specifically a reduction of sensitivity to bitter compounds that deter generalist ancestors, contribute to the specialization of D. sechellia for its host.

Drosophila sechellia: A Genetic Model for Behavioral Evolution and Neuroecology

Defining the mechanisms by which animals adapt to their ecological niche is an important problem bridging evolution, genetics, and neurobiology. We review the establishment of a powerful genetic model for comparative behavioral analysis and neuroecology, Drosophila sechellia. This island-endemic fly species is closely related to several cosmopolitan generalists, including Drosophila melanogaster, but has evolved extreme specialism, feeding and reproducing exclusively on the noni fruit of the tropical shrub Morinda citrifolia. We first describe the development and use of genetic approaches to facilitate genotype/phenotype associations in these drosophilids. Next, we survey the behavioral, physiological, and morphological adaptations of D. sechellia throughout its life cycle and outline our current understanding of the genetic and cellular basis of these traits. Finally, we discuss the principles this knowledge begins to establish in the context of host specialization, speciation, and the neurobiology of behavioral evolution and consider open questions and challenges in the field.

Moderate Population Structure in Drosophila sturtevanti from the South American Atlantic Forest Biome

Drosophila sturtevanti is a widely distributed Neotropical species. In South America, it is abundant and adapted to different phytophysiognomies of the Atlantic Forest biome. Reproductive, chromosomal and enzymatic studies have indicated the existence of a differentiation among D. sturtevanti populations. In this work, the level of genetic diversity and the population genetic structure were analyzed using four population groupings. One hundred and twenty-six D. sturtevanti males collected from nine forest fragments were analyzed for 11 species-specific microsatellite loci. A total of 109 alleles, ranging from 2 to 16 alleles per locus, were detected. The highest mean observed heterozygosity -H _O was estimated in samples from the largest collection areas, and the lowest H _O was from a population where fire events are common. A low molecular variation, around 3% among populations and negative among groups, an absence of genetic and geographic correlations and a moderate genetic differentiation -F _ST = 0.0663 -indicated that D. sturtevanti is not strongly structured. Besides no overall genetic and geographic distance correlation, the pair of closest geographically populations Matão and Nova Granada showed the lower differentiation through F _ST, DC and a Neighbor Joining tree. Ribeirão da Ilha -RDI, an isolated insular population, was the most differentiated according to F _ST, DC and a cluster-based Bayesian analysis. The isolation of RDI that resulted in significant divergence could be ancient, because of sea level regressions/transgressions, or more recently via founder effect/genetic drift by anthropic action carrying D. sturtevanti hosts from continent to island. This work is important for understanding the genetic variability distribution of a Neotropical forest-dwelling Drosophila species using for the first time, a wide population distribution approach.

An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

Satyrization in Drosophila fruitflies

The satyr of Greek mythology was half‐man, half‐goat, with an animal persona signifying immoderate sexual appetites. In biology, satyrization is the disruption of reproduction in matings between closely related species. Interestingly, its effects are often reciprocally asymmetric, manifesting more strongly in one direction of heterospecific mating than the other. Heterospecific matings are well known to result in female fitness costs due to the production of sterile or inviable hybrid offspring and can also occur due to reduced female sexual receptivity, lowering the likelihood of any subsequent conspecific matings. Here we investigated the costs and mechanisms of satyrization in the Drosophila melanogaster species subgroup of fruitflies. The results showed that D. simulans females experienced higher fitness costs from a loss of remating opportunities due to significantly reduced post‐mating sexual receptivity than did D. melanogaster females, as a result of reciprocal heterospecific matings. Reciprocal tests of the effects of male reproductive accessory gland protein (Acp) injections on female receptivity in pairwise comparisons between D. melanogaster and five other species within the melanogaster species subgroup revealed significant post‐mating receptivity asymmetries. This was due to variation in the effects of heterospecific Acps within species with which D. melanogaster can mate, and significant but nonasymmetric Acp effects in species with which it cannot. We conclude that asymmetric satyrization due to post‐mating effects of Acps may be common among diverging and hybridising species. The findings are of interest in understanding the evolution of reproductive isolation and species divergence.

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Background

Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65–62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles.

Results

Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations.

Conclusions

Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.

Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade

Satellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here, we use high-quality genome assemblies to study the evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 g/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spread by inserting into existing clusters of the older, more abundant 1.688 satellite, in events likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.

Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process. Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression. In this report we develop a supervised machine learning approach for uncovering loci which have introgressed across species boundaries. We show that our method, FILET, has greater accuracy and power than competing methods in discovering introgression, and in addition can detect the directionality associated with the gene flow between species. Using whole genome sequences from Drosophila simulans and Drosophila sechellia we show that FILET discovers quite extensive introgression between these species that has occurred mostly from D. simulans to D. sechellia. Our work highlights the complex process of speciation even within a well-studied system and points to the growing importance of supervised machine learning in population genetics.

Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation

A full understanding of how ecological factors drive the fixation of genetic changes during speciation is obscured by the lack of appropriate models with clear natural history and powerful genetic toolkits. In a recent study, we described an early stage of ecological speciation in a population of the generalist species Drosophila yakuba (melanogaster subgroup) on the island of Mayotte (Indian Ocean). On this island, flies are strongly associated with the toxic fruits of noni (Morinda citrifolia) and show a partial degree of pre-zygotic reproductive isolation. Here, I mine the nuclear and mitochondrial genomes and provide a full morphological description of this population. Only 29 nuclear sites (< 4 × 10^-7 of the genome) are fixed in this population and absent from 3 mainland populations and the closest relative D. santomea, but no mitochondrial or morphological character distinguish Mayotte flies from the mainland. This result indicates that physiological and behavioral traits may evolve faster than morphology at the early stages of speciation. Based on these differences, the Mayotte population is designated as a new subspecies, Drosophila yakuba mayottensis subsp. nov., and its strong potential in understanding the genetics of speciation and plant-insect interactions is discussed.

A single amino-acid substitution toggles chloride dependence of the alpha-amylase paralog amyrel in Drosophila melanogaster and Drosophila virilis species

In animals, most α-amylases are chloride-dependent enzymes. A chloride ion is required for allosteric activation and is coordinated by one asparagine and two arginine side chains. Whereas the asparagine and one arginine are strictly conserved, the main chloride binding arginine is replaced by a glutamine in some rare instances, resulting in the loss of chloride binding and activation. Amyrel is a distant paralogue of α-amylase in Diptera, which was not characterized biochemically to date. Amyrel shows both substitutions depending on the species. In Drosophila melanogaster, an arginine is present in the sequence but in Drosophila virilis, a glutamine occurs at this position. We have investigated basic enzymological parameters and the dependence to chloride of Amyrel of both species, produced in yeast, and in mutants substituting arginine to glutamine or glutamine to arginine. We found that the amylolytic activity of Amyrel is about thirty times weaker than the classical Drosophila α-amylase, and that the substitution of the arginine by a glutamine in D. melanogaster suppressed the chloride-dependence but was detrimental to activity. In contrast, changing the glutamine into an arginine rendered D. virilis Amyrel chloride-dependent, and interestingly, significantly increased its catalytic efficiency. These results show that the chloride ion is not mandatory for Amyrel but stimulates the reaction rate. The possible phylogenetic origin of the arginine/glutamine substitution is also discussed.

Evolutionary Transitions of MicroRNA-Target Pairs

How newly generated microRNA (miRNA) genes are integrated into gene regulatory networks during evolution is fundamental in understanding the molecular and evolutionary bases of robustness and plasticity in gene regulation. A recent model proposed that after the birth of a miRNA, the miRNA is generally integrated into the network by decreasing the number of target genes during evolution. However, this decreasing model remains to be carefully examined by considering in vivo conditions. In this study, we therefore compared the number of target genes among miRNAs with different ages, combining experiments with bioinformatics predictions. First, we focused on three Drosophila miRNAs with different ages. As a result, we found that an older miRNA has a greater number of target genes than a younger miRNA, suggesting the increasing number of targets for each miRNA during evolution (increasing model). To further confirm our results, we also predicted all target genes for all miRNAs in D. melanogaster, considering co-expression of miRNAs and mRNAs in vivo. The results obtained also do not support the decreasing model but are reasonably consistent with the increasing model of miRNA-target pairs. Furthermore, our large-scale analyses of currently available experimental data of miRNA-target pairs also showed a weak but the same trend in humans. These results indicate that the current decreasing model of miRNA-target pairs should be reconsidered and the increasing model may be more appropriate to explain the evolutionary transitions of miRNA-target pairs in many organisms.

Chemical and morphological filters in a specialized floral mimicry system

Many plant species attract insect pollinators through chemical mimicry of their oviposition sites, often detaining them in a trap chamber that ensures pollen transfer. These plant mimics are considered to be unspecialized at the pollinator species level, yet field observations of a mycoheterotrophic rainforest orchid (Gastrodia similis), which emits an odour reminiscent of rotting fruit, indicate that it is pollinated by a single drosophilid fly species (Scaptodrosophila bangi). We investigated the roles of floral volatiles and the dimensions of the trap chamber in enforcing this specialization, using gas chromatography-mass spectrometry analyses, bioassays and scanning electron microscopy. We showed that G. similis flowers predominantly emit three fatty-acid esters (ethyl acetate, ethyl isobutyrate and methyl isobutyrate) that were shown in experiments to attract only Scaptodrosophila flies. We additionally showed that the trap chamber, which flies enter into via a touch-sensitive 'trapdoor', closely matches the body size of the pollinator species S. bangi and plays a key role in pollen transfer. Our study demonstrates that specialization in oviposition site mimicry is due primarily to volatile chemistry and is reflected in the dimensions of the trapping apparatus. It also indicates that mycoheterotrophic plants can be specialized both on mycorrhizal fungi and insect pollinators.

Conservation genetics of a threatened butterfly: comparison of allozymes, RAPDs and microsatellites

Background

Addressing genetic issues in the management of fragmented wild populations of threatened species is one of the most important challenges in conservation biology. Nowadays, a diverse array of molecular methods exists to assess genetic diversity and differentiation of wild populations such as allozymes, dominant markers and co-dominant markers. However it remains worthwhile i) to compare the genetic estimates obtained using those several markers in order to ii) test their relative utility, reliability and relevance and iii) the impact of these results for the design of species-specific conservation measures.

Results

Following the successful isolation of 15 microsatellites loci for the cranberry fritillary butterfly, Boloria aquilonaris, we analyzed the genetic diversity and structure of eight populations located in four different landscapes, at both the regional and the landscape scales. We confront results based on microsatellites to those obtained using allozymes and RAPDs on the same samples. Genetic population analyses using different molecular markers indicate that the B. aquilonaris populations are characterized by a weak genetic variation, likely due to low effective population size and low dispersal at the regional scale. This results in inbreeding in some populations, which may have detrimental consequences on their long term viability. However, gene flow within landscape is limited but not inexistent, with some long range movements resulting in low or no isolation by distance. Spatial structuring was detected among the most isolated populations.

Conclusions

The use of allozymes and RAPD are of very limited value to determine population structuring at small spatial (i.e. landscape) scales, microsatellites giving much higher estimate resolution. The use of RAPD data is also limited for evidencing inbreeding. However, coarse-grain spatial structure (i.e. regional scale), and gene flow estimates based on RAPD and microsatellites data gave congruent results. At a time with increasing development of new molecular methods and markers, dominant markers may still be worthwhile to consider in organisms for which no genomic information is available, and for which limited resources are available.

Enzymatic characterization of recombinant α-amylase in the Drosophila melanogaster species subgroup: is there an effect of specialization on digestive enzyme?

We performed a comparative study on the enzymological features of purified recombinant α-amylase of three species belonging to the Drosophila melanogaster species subgroup: D. melanogaster, D. erecta and D. sechellia. D. erecta and D. sechellia are specialist species, with host plant Pandanus candelabrum (Pandanaceae) and Morinda citrifolia (Rubiaceae), respectively. The temperature optima were around 57-60℃ for the three species. The pH optima were 7.2 for D. melanogaster, 8.2 for D. erecta and 8.5 for D. sechellia. The kcat and Km were also estimated for each species with different substrates. The specialist species D. erecta and D. sechellia display a higher affinity for starch than D. melanogaster. α-Amylase activity is higher on starch than on glycogen in all species. α-Amylases of D. erecta and D. sechellia have a higher activity on maltooligosaccharides (G6 and G7) than on starch, contrary to D. melanogaster. Such differences in the enzymological features between the species might reflect adaptation to different ecological niches and feeding habits.

Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex

BACKGROUND

Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes, or treated recombination as a nuisance parameter. However, genes with recombination contribute additional information for the detection of gene flow (i.e. through linkage disequilibrium).

METHODS

We present three summary statistics based on the spatial arrangement of fixed differences, and shared and exclusive polymorphisms that are sensitive to the presence and direction of gene flow. Power and false positive rate for tests based on these statistics are studied by simulation.

RESULTS

The application of these tests to populations from the Drosophila simulans species complex yielded results consistent with migration between D. simulans and its two endemic sister species D. mauritiana and D. sechellia, and between populations D. mauritiana on the islands of the Mauritius and Rodrigues.

CONCLUSIONS

We demonstrate the sensitivity of the developed statistics to the presence and direction of gene flow, and characterize their power as a function of differentiation level and recombination rate. The properties of these statistics make them especially suitable for analyzing high-throughput sequencing data or for their integration within the approximate Bayesian computation framework.

Insulin signalling underlies both plasticity and divergence of a reproductive trait in Drosophila

Phenotypic plasticity is the ability of a single genotype to yield distinct phenotypes in different environments. The molecular mechanisms linking phenotypic plasticity to the evolution of heritable diversification, however, are largely unknown. Here, we show that insulin/insulin-like growth factor signalling (IIS) underlies both phenotypic plasticity and evolutionary diversification of ovariole number, a quantitative reproductive trait, in Drosophila. IIS activity levels and sensitivity have diverged between species, leading to both species-specific ovariole number and species-specific nutritional plasticity in ovariole number. Plastic range of ovariole number correlates with ecological niche, suggesting that the degree of nutritional plasticity may be an adaptive trait. This demonstrates that a plastic response conserved across animals can underlie the evolution of morphological diversity, underscoring the potential pervasiveness of plasticity as an evolutionary mechanism.

Evolutionary origins and genetic variation of the Seychelles treefrog, Tachycnemis seychellensis (Duméril and Bibron, 1841) (Amphibia: Anura: Hyperoliidae)

The hyperoliid frog Tachycnemis seychellensis, the only species of its genus, is endemic to the four largest granitic islands of the Seychelles archipelago and is reliant on freshwater bodies for reproduction. Its presence in the Seychelles is thought to be the product of a transoceanic dispersal, diverging from the genus Heterixalus, its closest living relative (currently endemic to Madagascar), between approximately 10-35Ma. A previous study documented substantial intraspecific morphological variation among island populations and also among populations within the largest island (Mahé). To assess intraspecific genetic variation and to infer the closest living relative(s) of T. seychellensis, DNA sequence data were generated for three mitochondrial and four nuclear markers. These data support a sister-group relationship between T. seychellensis and Heterixalus, with the divergence between the two occurring between approximately 11-19Ma based on cytb p-distances. Low levels of genetic variation were found among major mitochondrial haplotype clades of T. seychellensis (maximum 0.7% p-distance concatenated mtDNA), and samples from each of the islands (except La Digue) comprised multiple mitochondrial haplotype clades. Two nuclear genes (rag1 and tyr) showed no variation, and the other two (rho and pomc) lacked any notable geographic structuring, counter to patterns observed within presumably more vagile Seychelles taxa such as lizards. The low levels of genetic variation and phylogeographic structure support an interpretation that there is a single but morphologically highly variable species of Seychelles treefrog. The contrasting genetic and morphological intraspecific variation may be attributable to relatively recent admixture during low sea-level stands, ecophenotypic plasticity, local adaptation to different environmental conditions, and/or current and previously small population sizes. Low genetic phylogeographic structure but substantial morphological variation is unusual within anurans.

Intra-specific regulatory variation in Drosophila pseudoobscura

It is generally accepted that gene regulation serves an important role in determining the phenotype. To shed light on the evolutionary forces operating on gene regulation, previous studies mainly focused on the expression differences between species and their inter-specific hybrids. Here, we use RNA-Seq to study the intra-specific distribution of cis- and trans-regulatory variation in Drosophila pseudoobscura. Consistent with previous results, we find almost twice as many genes (26%) with significant trans-effects than genes with significant cis-effects (18%). While this result supports the previous suggestion of a larger mutational target of trans-effects, we also show that trans-effects may be subjected to purifying selection. Our results underline the importance of intra-specific analyses for the understanding of the evolution of gene expression.

A selective sweep across species boundaries in Drosophila

Adaptive mutations that accumulate during species divergence are likely to contribute to reproductive incompatibilities and hinder gene flow; however, there may also be a class of mutations that are generally advantageous and can spread across species boundaries. In this study, we characterize a 15 kb region on chromosome 3R that has introgressed from the cosmopolitan generalist species Drosophila simulans into the island endemic D. sechellia, which is an ecological specialist. The introgressed haplotype is fixed in D. sechellia over almost the entirety of the resequenced region, whereas a core region of the introgressed haplotype occurs at high frequency in D. simulans. The observed patterns of nucleotide variation and linkage disequilibrium are consistent with a recently completed selective sweep in D. sechellia and an incomplete sweep in D. simulans. Independent estimates of both the time to the introgression and sweep events are all close to 10,000 years before the present. Interestingly, the most likely target of selection is a highly occupied transcription factor binding region. This work confirms that it is possible for mutations to be globally advantageous, despite their occurrence in divergent genomic and ecological backgrounds.

Host plant-driven sensory specialization in Drosophila erecta

Finding appropriate feeding and breeding sites is crucial for all insects. To fulfil this vital task, many insects rely on their sense of smell. Alterations in the habitat—or in lifestyle—should accordingly also be reflected in the olfactory system. Solid functional evidence for direct adaptations in the olfactory system is however scarce. We have, therefore, examined the sense of smell of Drosophila erecta, a close relative of Drosophila melanogaster and specialist on screw pine fruits (Pandanus spp.). In comparison with three sympatric sibling species, D. erecta shows specific alterations in its olfactory system towards detection and processing of a characteristic Pandanus volatile (3-methyl-2-butenyl acetate, 3M2BA). We show that D. erecta is more sensitive towards this substance, and that the increased sensitivity derives from a numerical increase of one olfactory sensory neuron (OSN) class. We also show that axons from these OSNs form a complex of enlarged glomeruli in the antennal lobe, the first olfactory brain centre, of D. erecta. Finally, we show that 3M2BA induces oviposition in D. erecta, but not in D. melanogaster. The presumed adaptations observed here follow to a remarkable degree those found in Drosophila sechellia, a specialist upon noni fruit, and suggest a general principle for how specialization affects the sense of smell.

Genome sequencing reveals complex speciation in the Drosophila simulans clade

The three species of the Drosophila simulans clade—the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia—are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. The order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. Here we report on the analysis of a whole-genome four-species sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster reference sequence. The alignment comprises novel, paired short-read sequence data from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia. We are unable to reject a species phylogeny with a basal polytomy; the estimated age of the polytomy is 242,000 yr before the present. However, we also find that up to 4.6% of autosomal and 2.2% of X-linked regions have evolutionary histories consistent with recent gene flow between the mainland species (D. simulans) and the two island endemic species (D. mauritiana and D. sechellia). Our findings thus show that gene flow has occurred throughout the genomes of the D. simulans clade species despite considerable geographic, ecological, and intrinsic reproductive isolation. Last, our analysis of lineage-specific changes confirms that the D. sechellia genome has experienced a significant excess of slightly deleterious changes and a dearth of presumed favorable changes. The relatively reduced efficacy of natural selection in D. sechellia is consistent with its derived, persistently reduced historical effective population size.

The repatterning of eukaryotic genomes by random genetic drift

Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces.

Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila

The Drosophila Y chromosome is a degenerated, heterochromatic chromosome with few functional genes. Nonetheless, natural variation on the Y chromosome in Drosophila melanogaster has substantial trans-acting effects on the regulation of X-linked and autosomal genes. However, the contribution of Y chromosome divergence to gene expression divergence between species is unknown. In this study, we constructed a series of Y chromosome introgression lines, in which Y chromosomes from either Drosophila sechellia or Drosophila simulans are introgressed into a common D. simulans genetic background. Using these lines, we compared genome-wide gene expression and male reproductive phenotypes between heterospecific and conspecific Y chromosomes. We find significant differences in expression for 122 genes, or 2.84% of all genes analyzed. Genes down-regulated in males with heterospecific Y chromosomes are significantly biased toward testis-specific expression patterns. These same lines show reduced fecundity and sperm competitive ability. Taken together, these results imply a significant role for Y/X and Y/autosome interactions in maintaining proper expression of male-specific genes, either directly or via indirect effects on male reproductive tissue development or function.

Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation

Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.

Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race

BACKGROUND

Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencing pathway also plays a crucial role in limiting TE proliferation. How these two forces jointly determine TE abundance is not well understood. To shed light on the nature of factors that predict TE success, we test three distinct hypotheses in the Drosophila genus. First, we determine whether TE abundance and relaxed genome-wide purifying selection on protein sequences are positively correlated. This serves to test the hypothesis that variation in TE abundance in the Drosophila genus can be explained by the strength of natural selection, relative to drift, acting in parallel against mildly deleterious non-synonymous mutations. Second, we test whether increasing TE abundance is correlated with an increased rate of amino-acid evolution in genes encoding the piRNA machinery, as might be predicted by an evolutionary arms race model. Third, we test whether increasing TE abundance is correlated with greater codon bias in genes of the piRNA machinery. This is predicted if increasing TE abundance selects for increased efficiency in the machinery of genome defense.

RESULTS

Surprisingly, we find neither of the first two hypotheses to be true. Specifically, we found that genome-wide levels of purifying selection, measured by the ratio of non-synonymous to synonymous substitution rates (ω), were greater in species with greater TE abundance. In addition, species with greater TE abundance have greater levels of purifying selection in the piRNA machinery. In contrast, it appears that increasing TE abundance has primarily driven adaptation in the piRNA machinery by increasing codon bias.

CONCLUSIONS

These results indicate that within the Drosophila genus, a historically reduced strength of selection relative to drift is unlikely to explain patterns of increased TE success across species. Other factors, such as ecological exposure, are likely to contribute to variation in TE abundances within species. Furthermore, constraints on the piRNA machinery may temper the evolutionary arms race that would drive increasing rates of evolution at the amino acid level. In the face of these constraints, selection may act primarily by improving the translational efficiency of the machinery of genome defense through efficient codon usage.

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago

Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

Morphology evolves often through changes in developmental genes, but the causal mutations, and their effects, remain largely unknown. The evolution of naked cuticle—rather than trichomes—on larvae of Drosophila sechellia resulted from changes in five transcriptional enhancers of shavenbaby, a gene encoding a transcription factor that governs trichome morphogenesis. Here we show that the function of one of these enhancers evolved through multiple single nucleotide substitutions that altered both the timing and level of shavenbaby expression. The consequences of these nucleotide substitutions on larval morphology were quantified with a novel functional assay. We found that each substitution had a relatively small phenotypic effect, and that many nucleotide changes account for this large morphological difference. In addition, we observed that the substitutions displayed non-additive effects to generate a large phenotypic change. These data provide unprecedented resolution of the phenotypic effects of substitutions and show how individual nucleotide changes in a transcriptional enhancer have caused morphological evolution.

Inter-island divergence within Drosophila mauritiana, a species of the D. simulans complex: Past history and/or speciation in progress?

Speciation with gene flow may be more common than generally thought, which makes detailed understanding of the extent and pattern of genetic divergence between geographically isolated populations useful. Species of the Drosophila simulans complex provide a good model for speciation and evolutionary studies, and hence understanding their population genetic structure will increase our understanding of the context in which speciation has occurred. Here, we describe genetic diversity and genetic differentiation of two distant populations of D. mauritiana (Mauritius and Rodrigues Islands) at mitochondrial and nuclear loci. We surveyed the two populations for their mitochondrial haplotypes, eight nuclear genes and 18 microsatellite loci. A new mitochondrial type is fixed in the Rodrigues population of D. mauritiana. The two populations are highly differentiated, their divergence appears relatively ancient (100,000 years) compared to the origin of the species, around 0.25MYA, and they exhibit very limited gene flow. However, they have similar levels of divergence from their sibling, D. simulans. Both nuclear genes and microsatellites revealed contrasting demographic histories between the two populations, expansion for the Mauritius population and stable population size for the Rodrigues Island population. The discovery of pronounced geographic structure within D. mauritiana combined to genetic structuring and low gene flow between the two island populations illuminates the evolutionary history of the species and clearly merits further attention in the broad context of speciation.

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness.

Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids

Sequence differentiation has been widely studied between populations and species, whereas interest in expression divergence is relatively recent. Using microarrays, we compared four geographically distinct populations of Drosophila simulans and a population of Drosophila sechellia, and interspecific hybrids. We observed few differences between populations, suggesting a slight population structure in D. simulans. This structure was observed in direct population comparisons, as well as in interspecific comparisons (hybrids vs. parents, D. sechellia vs. D. simulans). Expression variance is higher in the French and Zimbabwean populations than in the populations from the ancestral range of D. simulans (Kenya and Seychelles). This suggests a large scale phenomenon of decanalization following the invasion of a new environment. Comparing D. simulans and D. sechellia, we revealed 304 consistently differentially expressed genes, with striking overrepresentation of genes of the cytochrome P450 family, which could be related to their role in detoxification as well as in hormone regulation. We also revealed differences in genes involved in Juvenile hormone and Dopamine differentiation. We finally observed very few differentially expressed genes between hybrids and parental populations, with an overrepresentation of X-linked genes.

Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size

Changes in effective population size impinge on patterns of molecular evolution. Notably, slightly deleterious mutations are more likely to drift to fixation in smaller populations, which should typically also lead to an overall acceleration in the rates of evolution. This prediction has been validated empirically for several endosymbiont and island taxa. Here, we first show that rate accelerations are also evident in bacterial pathogens whose recent shifts in virulence make them prime candidates for reduced effective population size: Bacillus anthracis, Bordetella parapertussis, Mycobacterium leprae, Salmonella enterica typhi, Shigella spp., and Yersinia pestis. Using closely related genomes to analyze substitution rate dynamics across six phylogenetically independent bacterial clades, we demonstrate that relative rates of coding sequence evolution are biased according to gene functional category. Notably, genes that buffer against slightly deleterious mutations, such as chaperones, experience stronger rate accelerations than other functional classes at both nonsynonymous and synonymous sites. Although theory predicts altered evolutionary dynamics for buffer loci in the face of accumulating deleterious mutations, to observe even stronger rate accelerations is surprising. We suggest that buffer loci experience elevated substitution rates because the accumulation of deleterious mutations in the remainder of the genome favors compensatory substitutions in trans. Critically, the hyper-acceleration is evident across phylogenetically independent clades, supporting the hypothesis that reductions in effective population size predictably induce epistatic responses in genes that buffer against slightly deleterious mutations.

Alignment-free estimation of nucleotide diversity

MOTIVATION

Sequencing capacity is currently growing more rapidly than CPU speed, leading to an analysis bottleneck in many genome projects. Alignment-free sequence analysis methods tend to be more efficient than their alignment-based counterparts. They may, therefore, be important in the long run for keeping sequence analysis abreast with sequencing.

RESULTS

We derive and implement an alignment-free estimator of the number of pairwise mismatches, . Our implementation of , pim, is based on an enhanced suffix array and inherits the superior time and memory efficiency of this data structure. Simulations demonstrate that is accurate if mutations are distributed randomly along the chromosome. While real data often deviates from this ideal, remains useful for identifying regions of low genetic diversity using a sliding window approach. We demonstrate this by applying it to the complete genomes of 37 strains of Drosophila melanogaster, and to the genomes of two closely related Drosophila species, D.simulans and D.sechellia. In both cases, we detect the diversity minimum and discuss its biological implications.

Regulatory divergence in Drosophila revealed by mRNA-seq

The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F(1) hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis- and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis- and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid incompatibilities. In addition, cis-regulatory differences contributed more to divergent expression of genes that showed additive rather than nonadditive inheritance. A correlation between sequence similarity and the conservation of cis-regulatory activity was also observed that appears to be a general feature of regulatory evolution. Finally, we examined regulatory divergence that may have contributed to the evolution of a specific trait--divergent feeding behavior in D. sechellia. Overall, this study illustrates the power of mRNA sequencing for investigating regulatory evolution, provides novel insight into the evolution of gene expression in Drosophila, and reveals general trends that are likely to extend to other species.