Historicity and the Population Genetics of Drosophila Melanogaster and D. Simulans

We summarize data showing that there is population structure in African populations of Drosophila from the melanogaster-simulans complex. In D. melanogaster, population structuring is found at individual loci, but is obscured by population structuring for large inversions that simultaneously affect several loci. In D. simulans, molecular polymorphism at the X-linked vermilion locus suggests that different groups of populations have been geographically isolated for some time. Invading populations are probably derived from different areas in Africa. European populations originate from an east African population that was probably not at a demographic equilibrium. The origin of the Antilles population is apparently different and is as yet unknown. In south-western France, populations from these two species undergo different population structuring at the scale of a few kilometres: D. melanogaster makes up a large panmictic population, whereas D. simulans forms a metapopulation that is divided into smaller demes.     

Population structure among African and derived populations of Drosophila simulans: evidence for ancient subdivision and recent admixture.

Previous studies based on allozyme variation have found little evidence for genetic differentiation in Drosophila simulans. On the basis of DNA sequence variation at two nuclear loci in four African populations of D. simulans, we show that there is significant structure to D. simulans populations within Africa. Variation at one of the loci, vermilion, appears to be neutral and supports an eastern African origin for European and American populations. Samples from the West Indies, Europe, and North America had a nucleotide diversity lower than that of African populations at vermilion and show nonequilibrium haplotype distributions at both vermilion and G6pd, consistent with a hypothesis of recent bottleneck and possibly also admixture in the history of these populations. Directional selection, previously documented at G6pd, appears to have occurred within the coalescence time of the species, obscuring deep population history.     

Genetic variation and differentiation at microsatellite loci in Drosophila simulans. Evidence for founder effects in new world populations.

Drosophila simulans isofemale lines from Africa, South America, and two locations in North America were surveyed for variation at 16 microsatellite loci on the X, second, and third chromosomes, and 18 microsatellites, which are unmapped. D. simulans is thought to have colonized New World habitats only relatively recently (within the last few hundred years). Consistent with a founder effect occurring as colonizers moved into these New World habitats, we find less microsatellite variability in North and South American D. simulans populations than for an African population. Population subdivision as measured at microsatellites is moderate when averaged across all loci (FST = 0.136), but contrasts sharply with previous studies of allozyme variation, which have showed significantly less differentiation in D. simulans than in D. melanogaster. There are substantially fewer private alleles observed in New World populations of D. simulans than seen in a similar survey of D. melanogaster. In addition to possible differences in population size during their evolutionary histories, varying colonization histories or other demographic events may be necessary to explain discrepancies in the patterns of variation observed at various genetic markers between these closely related species.     

Microsatellite variation and differentiation in African and non-African populations of Drosophila simulans

Drosophila simulans originated in sub-Saharan Africa or Madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic history, sub-Saharan African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, only limited information is available on the population structure of D. simulans. Here, we analysed X-linked and autosomal microsatellite loci in four sub-Saharan African, one North African, one Israeli, and two European D. simulans populations. Bayesian clustering algorithms combined the North African, Israeli, and European populations into a single cosmopolitan group. The four sub-Saharan populations were split into two separate groups. Pairwise F(ST) analysis, however, indicated significant population differentiation between all eight populations surveyed. A significant signal for population reduction in cosmopolitan populations was found only for X-linked loci.     

Unusual pattern of nucleotide sequence variation at the OS-E and OS-F genomic regions of Drosophila simulans

Nucleotide variation at the genomic region encompassing the odorant-binding protein genes OS-E and OS-F (OS region) was surveyed in two populations of Drosophila simulans, one from Europe and the other from Africa. We found that the European population shows an atypical and large haplotype structure, which extends throughout the approximately 5-kb surveyed genomic region. This structure is depicted by two major haplotype groups segregating at intermediate frequency in the sample, one haplogroup with nearly no variation, and the other at levels more typical for this species. This pattern of variation was incompatible with neutral predictions for a population at a stationary equilibrium. Nevertheless, neutrality tests contrasting polymorphism and divergence data fail to detect any departure from the standard neutral model in this species, whereas they confirm the non-neutral behavior previously observed at the OS-E gene in D. melanogaster. Although positive Darwinian selection may have been responsible for the observed unusual nucleotide variation structure, coalescent simulation results do not allow rejecting the hypothesis that the pattern was generated by a recent bottleneck in the history of European populations of D. simulans.     

Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans

We analyzed microsatellite variability at 42 X-linked and 39 autosomal loci from African and European populations of Drosophila simulans. The African D. simulans harbored significantly more microsatellite variability than the European flies. In the European population, X-linked polymorphism was more reduced than autosomal variation, whereas there was no significant difference between chromosomes in the African population. Previous studies also observed a similar pattern but failed to distinguish between a demographic event and a selection scenario. We performed extensive computer simulations using a wide range of demographic scenarios to distinguish between the two hypotheses. Approximate summary likelihood estimates differed dramatically among X chromosomes and autosomes. Furthermore, our experimental data showed a surplus of X-linked microsatellites with a significantly reduced variability in non-African D. simulans. We conclude that our data are not compatible with a neutral scenario. Thus, the reduced variability at X-linked loci is most likely caused by selective sweeps associated with the out-of-Africa habitat expansion of D. simulans.     

Molecular Variation at the Vermilion Locus in Geographically Diverse Populations of Drosophila Melanogaster and D. Simulans

We surveyed nucleotide variation at vermilion in population samples of Drosophila melanogaster from Africa, Asia and the Americas to test the hypothesis that the vermilion gene was a target of balancing selection and to improve our understanding of geographic differentiation. Patterns of polymorphism and divergence showed no evidence for non-neutral evolution. However, the frequency spectrum of polymorphic sites in some non-African samples departed from the neutral equilibrium expectation. Furthermore, there were high levels of linkage disequilibrium in non-African samples, despite apparently high rates of crossing over in the vermilion region. In the absence of comparable data from other loci in these same population samples, we cannot determine whether the unusual patterns of variation at vermilion reflect demographic as opposed to locus-specific events. We found surprisingly high levels of differentiation at vermilion between U.S. and Congo samples of D. simulans. In light of previously published allozyme and mtDNA data that provided no evidence for significant differentiation between African and non-African D. simulans populations, the vermilion data raise the possibility that both mtDNA and allozymes have been influenced by selection.     

A Reanalysis of Protein Polymorphism in Drosophila Melanogaster, D. Simulans, D. Sechellia and D. Mauritiana: Effects of Population Size and Selection

Comparison of synonymous and nonsynonymous variation/substitution within and between species at individual genes has become a widely used general approach to detect the effect of selection versus drift. The sibling species group comprised of two cosmopolitan (Drosophila melanogaster and Drosophila simulans) and two island (Drosophila mauritiana and Drosophila sechellia) species has become a model system for such studies. In the present study we reanalyzed the pattern of protein variation in these species, and the results were compared against the patterns of nucleotide variation obtained from the literature, mostly available for melanogaster and simulans. We have mainly focused on the contrasting patterns of variation between the cosmopolitan pair. The results can be summarized as follows: (1) As expected the island species D. mauritiana and D. sechellia showed much less variation than the cosmopolitan species D. melanogaster and D. simulans. (2) The chromosome 2 showed significantly less variation than chromosome 3 and X in all four species which may indicate effects of past selective sweeps. (3) In contrast to its overall low variation, D. mauritiana showed highest variation for X-linked loci which may indicate introgression from its sibling, D. simulans. (4) An average population of D. simulans was as heterozygous as that of D. melanogaster (14.4% v.s. 13.9%) but the difference was large and significant when considering only polymorphic loci (37.2% v.s. 26.1%). (5) The species-wise pooled populations of these two species showed similar results (all loci = 18.3% v.s. 20.0%, polymorphic loci = 47.2% v.s. 37.6%). (6) An average population of D. simulans had more low-frequency alleles than D. melanogaster, and the D. simulans alleles were found widely distributed in all populations whereas the D. melanogaster alleles were limited to local populations. As a results of this, pooled populations of D. melanogaster showed more polymorphic loci than those of D. simulans (48.0% v.s. 32.0%) but the difference was reduced when the comparison was made on the basis of an average population (29.1% v.s. 21.4%). (7) While the allele frequency distributions within populations were nonsignificant in both D. melanogaster and D. simulans, melanogaster had fewer than simulans, but more than expected from the neutral theory, low frequency alleles. (8) Diallelic loci with the second allele with a frequency less than 20% had similar frequencies in all four species but those with the second allele with a frequency higher than 20% were limited to only melanogaster the latter group of loci have clinal (latitudinal) patterns of variation indicative of balancing selection. (9) The comparison of D. simulans/D. melanogaster protein variation gave a ratio of 1.04 for all loci and 1.42 for polymorphic loci, against a ratio of approximately 2-fold difference for silent nucleotide sites. This suggests that the species ratios of protein and silent nucleotide polymorphism are too close to call for selective difference between silent and allozyme variation in D. simulans. In conclusion, the contrasting levels of allozyme polymorphism, distribution of rare alleles, number of diallelic loci and the patterns of geographic differentiation between the two species suggest the role of natural selection in D. melanogaster, and of possibly ancient population structure and recent worldwide migration in D. simulans. Population size differences alone are insufficient as an explanation for the patterns of variation between these two species.     

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.     

African Drosophila melanogaster and D. simulans populations have similar levels of sequence variability, suggesting comparable effective population sizes

Drosophila melanogaster and D. simulans are two closely related species with a similar distribution range. Many studies suggested that D. melanogaster has a smaller effective population size than D. simulans. As most evidence was derived from non-African populations, we readdressed this question by sequencing 10 X-linked loci in five African D. simulans and six African D. melanogaster populations. Contrary to previous results, we found no evidence for higher variability, and thus larger effective population size, in D. simulans. Our observation of similar levels of variability of both species will have important implications for the interpretation of patterns of molecular evolution.     

Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans

Surveys of molecular variation in Drosophila melanogaster and Drosophila simulans have suggested that diversity outside of Africa is a subset of that within Africa. It has been argued that reduced levels of diversity in non-African populations reflect a population bottleneck, adaptation to temperate climates, or both. Here, I summarize the available single-nucleotide polymorphism data for both species. A simple "out of Africa" bottleneck scenario is consistent with geographic patterns for loci on the X chromosome but not with loci on the autosomes. Interestingly, there is a trend toward lower nucleotide diversity on the X chromosome relative to autosomes in non-African populations of D. melanogaster, but the opposite trend is seen in African populations. In African populations, autosomal inversion polymorphisms in D. melanogaster may contribute to reduced autosome diversity relative to the X chromosome. To elucidate the role that selection might play in shaping patterns of variability, I present a summary of within- and between-species patterns of synonymous and replacement variation in both species. Overall, D. melanogaster autosomes harbor an excess of amino acid replacement polymorphisms relative to D. simulans. Interestingly, range expansion from Africa appears to have had little effect on synonymous-to-replacement polymorphism ratios.     

Molecular variation at the In(2L)t proximal breakpoint site in natural populations of Drosophila melanogaster and D. simulans

A previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the number of haplotypes near the proximal breakpoint of In(2L)t, a common inversion polymorphism in this species. Another striking feature of the data was a window of unusually high nucleotide diversity spanning the breakpoint site. To distinguish between selective and neutral demographic explanations for the observed patterns in the data, we sample alleles from three additional populations of D. melanogaster and one population of D. simulans. We find that the strength of associations among sites found at the breakpoint varies between populations of D. melanogaster. In D. simulans, analysis of the homologous region reveals unusually elevated levels of nucleotide polymorphism spanning the breakpoint site. As with American populations of D. melanogaster, our D. simulans sample shows a marked reduction in the number of haplotypes but not in nucleotide diversity. Haplotype tests reveal a significant deficiency in the number of haplotypes relative to the neutral expectation in the D. simulans sample and some populations of D. melanogaster. At the breakpoint site, the level of divergence between haplotype classes is comparable to interspecific divergence. The observation of interspecific polymorphisms that differentiate major haplotype classes in both species suggests that haplotype classes at this locus are considerably old. When considered in the context of other studies on patterns of variation within and between populations of D. melanogaster and D. simulans, our data appear more consistent with the operation of selection than with simple demographic explanations.     

Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila.

Nucleotide sequence variation at the Acp29AB gene region has been surveyed in Drosophila melanogaster from Spain (12 lines), Ivory Coast (14 lines), and Malawi (13 lines) and in one line of D. simulans. The approximately 1.7-kb region studied encompasses the Acp29AB gene that codes for a male accessory gland protein and its flanking regions. Seventy-seven nucleotide and 8 length polymorphisms were detected. Nonsynonymous polymorphism was an order of magnitude lower than synonymous polymorphism, but still high relative to other non-sex-related genes. In D. melanogaster variation at this region revealed no major genetic differentiation between East and West African populations, while differentiation was highly significant between the European and the two African populations. Comparison of polymorphism and divergence at synonymous and nonsynonymous sites showed an excess of fixed nonsynonymous changes, which indicates that the evolution of the Acp29AB protein has been driven by directional selection at least after the split of the D. melanogaster and D. simulans lineages. The pattern of variation in extant populations of D. melanogaster favors a scenario where the fixation of advantageous replacement substitutions occurred in the early stages of speciation and balancing selection is maintaining variation in this species.     

History and structure of sub-Saharan populations of Drosophila melanogaster

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.     

Inferences of Demography and Selection in an African Population of Drosophila melanogaster

It remains a central problem in population genetics to infer the past action of natural selection, and these inferences pose a challenge because demographic events will also substantially affect patterns of polymorphism and divergence. Thus it is imperative to explicitly model the underlying demographic history of the population whenever making inferences about natural selection. In light of the considerable interest in adaptation in African populations of Drosophila melanogaster, which are considered ancestral to the species, we generated a large polymorphism data set representing 2.1 Mb from each of 20 individuals from a Ugandan population of D. melanogaster. In contrast to previous inferences of a simple population expansion in eastern Africa, our demographic modeling of this ancestral population reveals a strong signature of a population bottleneck followed by population expansion, which has significant implications for future demographic modeling of derived populations of this species. Taking this more complex underlying demographic history into account, we also estimate a mean X-linked region-wide rate of adaptation of 6 × 10⁻¹¹/site/generation and a mean selection coefficient of beneficial mutations of 0.0009. These inferences regarding the rate and strength of selection are largely consistent with most other estimates from D. melanogaster and indicate a relatively high rate of adaptation driven by weakly beneficial mutations.     

The phylogeographical clade trade: tracing the impact of human-mediated dispersal on the colonization of northern Europe by the oak gallwasp Andricus kollari

Human dispersal of organisms is an important process modifying natural patterns of biodiversity. Such dispersal generates new patterns of genetic diversity that overlie natural phylogeographical signatures, allowing discrimination between alternative dispersal mechanisms. Here we use allele frequency and DNA sequence data to distinguish between alternative scenarios (unassisted range expansion and long range introduction) for the colonization of northern Europe by an oak-feeding gallwasp, Andricus kollari. Native to Mediterranean latitudes from Portugal to Iran, this species became established in northern Europe following human introduction of a host plant, the Turkey oak Quercus cerris. Colonization of northern Europe is possible through three alternative routes: (i) unassisted range expansion from natural populations in the Iberian Peninsula; (ii) unassisted range expansion from natural populations in Italy and Hungary; or (iii) descent from populations imported to the UK as trade goods from the eastern Mediterranean in the 1830s. We show that while populations in France were colonized from sources in Italy and Hungary, populations in the UK and neighbouring parts of coastal northern Europe encompass allozyme and sequence variation absent from the known native range. Further, these populations show demographic signatures expected for large stable populations, rather than signatures of rapid population growth from small numbers of founders. The extent and spatial distribution of genetic diversity in the UK suggests that these A. kollari populations are derived from introductions of large numbers of individuals from each of two genetically divergent centres of diversity in the eastern Mediterranean. The strong spatial patterning in genetic diversity observed between different regions of northern Europe, and between sites in the UK, is compatible with leptokurtic models of population establishment.     

Population structure in African Drosophila melanogaster revealed by microsatellite analysis

Tropical sub-Saharan regions are considered to be the geographical origin of Drosophila melanogaster. Starting from there, the species colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic scenario, African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, limited information is available on the genetic structure of African populations. We used X chromosomal microsatellite variation to study the population structure of D. melanogaster populations using 13 sampling sites in North, West and East Africa. These populations were compared to six European and one North American population. Significant population structure was found among African D. melanogaster populations. Using a Bayesian method for inferring population structure we detected two distinct groups of populations among African D. melanogaster. Interestingly, the comparison to cosmopolitan D. melanogaster populations indicated that one of the divergent African groups is closely related to cosmopolitan flies. Low, but significant levels of differentiation were observed for sub-Saharan D. melanogaster populations from West and East Africa.     

Molecular polymorphism in Drosophila melanogaster and D. simulans: what have we learned from recent studies?

We present a review of recent studies of molecular polymorphism in Drosophila melanogaster and D. simulans. The availability of African and non-African samples for these species makes it possible to compare microsatellite and DNA sequence polymorphism between these species, both inside and outside their native regions. There are four main results: (i) variability is larger in African populations; (ii) variation is usually higher on the autosomes, except for African D. melanogaster; (iii) DNA sequence variation is higher on D. simulans than on D. melanogaster autosomes; (iv) the ratio of replacement to silent polymorphisms is higher for D. melanogaster autosomal loci. We summarize the main hypotheses put forward to explain these results.