Sequence Analysis of Active Mariner Elements in Natural Populations of Drosophila Simulans

Active and inactive mariner elements from natural and laboratory populations of Drosophila simulans were isolated and sequenced in order to assess their nucleotide variability and to compare them with previously isolated mariner elements from the sibling species Drosophila mauritiana and Drosophila sechellia. The active elements of D. simulans are very similar among themselves (average 99.7% nucleotide identity), suggesting that the level of mariner expression in different natural populations is largely determined by position effects, dosage effects and perhaps other factors. Furthermore, the D. simulans elements exhibit nucleotide identities of 98% or greater when compared with mariner elements from the sibling species. Parsimony analysis of mariner elements places active elements from the three species into separate groups and suggests that D. simulans is the species from which mariner elements in D. mauritiana and D. sechellia are most likely derived. This result strongly suggests that the ancestral form of mariner among these species was an active element. The two inactive mariner elements sequenced from D. simulans are very similar to the inactive peach element from D. mauritiana. The similarity may result from introgression between D. simulans and D. mauritiana or from selective constraints imposed by regulatory effects of inactive elements.     

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.     

Worldwide distribution of transposable element copy number in natural populations of Drosophila simulans

Abstract.— Transposable elements (TEs), which promote various kinds of mutations, constitute a large fraction of the genome. How they invade natural populations and species is therefore of fundamental importance for understanding the dynamics of genetic diversity and genome composition. On the basis of 85 samples of natural populations of Drosophila simulans , we report the distributions of the genome insertion site numbers of nine TEs that were chosen because they have a low average number of sites. Most populations were found to have 0–3 insertion sites, but some of them had a significantly higher number of sites for a given TE. The populations located in regions outside Africa had the highest number of sites for all elements except HMS Beagle and Coral , suggesting a recent increase in the activity of some TEs associated with the colonization patterns of Drosophila simulans . The element Tirant had a very distinctive pattern of distribution: it was identified mainly in populations from East Africa and some islands in the Indian Ocean, and its insertion site number was low in all these populations. The data suggest that the genome of the entire species of Drosophila simulans may be being invaded by TEs from populations in which they are present in high copy number.     

Active mariner transposable elements are widespread in natural populations of Drosophila simulans

The occurrence of active, or autonomous, mariner elements was investigated by crossing white-peach mutant Drosophila simulans females with wild-type males from various geographic origins. From a total of 194 experimental crosses only 17 failed to produce progeny with eye mosaicism (MOS, i.e. pigmented spots in otherwise white-peach eyes). Therefore, active mariner elements inducing somatic excision of the copy inserted at the white locus are abundant in all populations sampled. In the experimental crosses the frequency of mosaic offspring ranged from 0 to 100%, showing that the phenotypic expression is highly variable. The MOS phenotype, measured by the number of spots on the eyes, is quite variable within the progeny of single crosses. Although a difference was observed in the average MOS score (percentage of mosaic flies) between northern and southern populations of France, there was no indication of long range variation between geographic populations. Neither was there a systematic difference between recently collected populations and samples kept several years as isofemale lines.     

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.     

The genetics and evolution of the mariner transposable element in Drosophila simulans: worldwide distribution and experimental population dynamics

We have studied both the frequency and biogeographical distribution of the transposable DNA element mariner in natural populations of Drosophila simulans and the short-term evolutionary characteristics of mariner in experimental populations. The mariner element has been identified in natural populations of D. simulans from Africa, Europe, the Middle East, Japan, Australia, several Pacific islands, North America, and South America. Only four lines out of 296 were devoid of active mariner elements, as measured by the presence of functional mariner transposase. A slight correlation was found between the latitudinal coordinate of the collection sites and the level of mariner activity in the population; this correlation became highly significant in Australia where a cline in mariner activity was observed along the eastern coast of the continent. We also observed that wild-type laboratory strains kept for several years as small populations might lose mariner activity over time. Using experimental populations, we modeled what might happen when naturally occurring populations exhibiting high and low levels of mariner activity encounter one another. We found that active mariner elements either will tend to lose their activity over time and gradually become inactive or possibly will be lost from the population; in either case, this will lead to the pattern seen in this experiment of a significant loss of mariner activity over time. This revised version was published online in July 2006 with corrections to the Cover Date.     

Is genome size influenced by colonization of new environments in dipteran species?

Genome size differences are usually attributed to the amplification and deletion of various repeated DNA sequences, including transposable elements (TEs). Because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. We tested this hypothesis by estimating the genome size of geographically distinct populations of Drosophila ananassae, Drosophila malerkotliana, Drosophila melanogaster, Drosophila simulans, Drosophila subobscura, and Zaprionus indianus, all of which have known colonization capacities. There was no strong statistical differences between continents for most species. However, we found that populations of D. melanogaster from east Africa have smaller genomes than more recent populations. For species in which colonization is a recent event, the differences between genome sizes do not thus seem to be related to colonization history. These findings suggest either that genome size is seldom modified in a significant way during colonization or that it takes time for genome size of invading species to change significantly.     

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.     

Nucleotide variation in Quercus crispula Blume

Quercus is attractive for evolutionary studies, primarily for developing the concepts of the species, speciation and adaptation; however, remarkably little is known about levels of nucleotide polymorphism in the nuclear functional genes of this genus. This article provides the first characterization of levels of nucleotide polymorphism in 11 gene fragments in natural populations of a Quercus species, Quercus crispula Blume. Results show that the level of nucleotide variation in this oak is generally higher than that in conifers, as high as that in a European oak, but lower than that in an aspen. The level of population recombination is relatively high. Within-population inbreeding is negligible and between-population differentiation is modest. The decay of linkage disequilibrium is significantly faster in the species-wide samples and the three northernmost populations than in the other populations. Statistical tests support the hypothesis of a recent bottleneck for several populations in the southern part of Japan. The amounts and patterns of nucleotide variation, recombination and linkage disequilibrium, and genetic differentiation observed among populations of this species are contradictory to our expectations, given the recent colonization history of the northern Japan populations.     

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.     

Genetic screens for factors involved in the notum bristle loss of interspecific hybrids between Drosophila melanogaster and D. simulans

Interspecific cross is a powerful means to uncover hidden within- and between-species variation in populations. One example is a bristle loss phenotype of hybrids between Drosophila melanogaster and D. simulans, although both the pure species have exactly the same pattern of bristle formation on the notum. There exists a large amount of genetic variability in the simulans populations with respect to the number of missing bristles in hybrids, and the variation is largely attributable to simulans X chromosomes. Using nine molecular markers, I screened the simulans X chromosome for genetic factors that were responsible for the differences between a pair of simulans lines with high (H) and low (L) missing bristle numbers. Together with duplication-rescue experiments, a single major quantitative locus was mapped to a 13F-14F region. Importantly, this region accounted for most of the differences between H and L lines in three other independent pairs, suggesting segregation of H and L alleles at the single locus in different populations. Moreover, a deficiency screening uncovered several regions with factors that potentially cause the hybrid bristle loss due to epistatic interactions with the other factors.     

Genetic structure and phylogeography of a temperate-boreal herb, Cardamine scutata (Brassicaceae), in northeast Asia inferred from AFLPs and cpDNA haplotypes

? Premise of the study: Studies on genetic structure of plant populations help us understand the history of local flora and vegetation. In this study, we focus on the temperate-boreal herb Cardamine scutata from northeast Asia, an area with scarce phylogeographic studies. We explore patterns of genetic variation within this species, with an aim to infer its (post-) glacial history with reference to colonization routes and migrations via land bridges. ? Methods: We analyzed 46 populations sampled in Japan, Kamchatka, and Korea using AFLP and cpDNA sequence data. ? Key results: Two intraspecific genetic groups were resolved, distributed in the northeastern and southwestern part of the study area, most likely reflecting lineages isolated from each other during (at least) the last glaciation. A zone of secondary contacts was found in central/northern Honshu, and a few cases of long-distance dispersal were observed. We detected efficient gene flow across the marine straits, supporting the role of land bridges created by sea level decline during the last glacial period. The cpDNA data indicated extensive recent expansion and diversification within both lineages. We inferred recent colonization of Kamchatka from Hokkaido, associated with genetic impoverishment. ? Conclusions: The pattern of north-south genetic differentiation found in C. scutata is rather common among several other plant species studied in Japan, despite their distinct biological features. We assume that different processes and factors may have brought about this similarity. Overall, this study contributes to better understanding of the biogeography of northeast Asia.     

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.     

The Y chromosomes of Drosophila simulans are highly polymorphic for their ability to suppress sex-ratio drive

The sex-ratio trait, known in several species of Drosophila including D. simulans, results from meiotic drive of the X chromosome against the Y. Males that carry a sex-ratio X chromosome produce strongly female-biased progeny. In D. simulans, drive suppressors have evolved on the Y chromosome and on the autosomes. Both the frequency of sex-ratio X and the strength of the total drive suppression (Y-linked and autosomal) vary widely among geographic populations of this worldwide species. We have investigated the pattern of Y-linked drive suppression in six natural populations representative of this variability. Y-linked suppressors were found to be a regular component of the suppression, with large differences between populations in the mean level of suppression. These variations did not correspond to differences in frequency of discrete types of Y chromosomes, but to a more or less wide continuum of phenotypes, from nonsuppressor to partial or total suppressor. We concluded that a large diversity of Y-linked suppressor alleles exists in D. simulans and that some populations are highly polymorphic. Our results support the hypothesis that a Y-chromosome polymorphism can be easily maintained by a balance between meiotic drive and the cost of drive suppression.     

Polymorphism in structure of the retrotransposable element 412 in Drosophila simulans and D. melanogaster populations.

The structure of the 412 retrotransposable element was investigated in various natural populations of D. melanogaster and D. simulans by a restriction enzyme analysis. We show that although the canonical structure of the 412 element was the same in both species, a high structural polymorphism existed with various rearranged elements. A 412 family was thus composed of heterogeneous copies of different sizes, with a large proportion of full-size copies. D. simulans had more rearranged copies than D. melanogaster, with some specific copies, such as a 5.6-kb BsrBI fragment, present in all populations of D. simulans. Full-size and rearranged copies were detected in both the euchromatin and the heterochromatin, with many rearranged copies in D. simulans, suggesting a recent mobilization of the 412 element in this species.     

Do species’ traits predict recent shifts at expanding range edges?

Although some organisms have moved to higher elevations and latitudes in response to recent climate change, there is little consensus regarding the capacity of different species to track rapid climate change via range shifts. Understanding species' abilities to shift ranges has important implications for assessing extinction risk and predicting future community structure. At an expanding front, colonization rates are determined jointly by rates of reproduction and dispersal. In addition, establishment of viable populations requires that individuals find suitable resources in novel habitats. Thus, species with greater dispersal ability, reproductive rate and ecological generalization should be more likely to expand into new regions under climate change. Here, we assess current evidence for the relationship between leading-edge range shifts and species' traits. We found expected relationships for several datasets, including diet breadth in North American Passeriformes and egg-laying habitat in British Odonata. However, models generally had low explanatory power. Thus, even statistically and biologically meaningful relationships are unlikely to be of predictive utility for conservation and management. Trait-based range shift forecasts face several challenges, including quantifying relevant natural history variation across large numbers of species and coupling these data with extrinsic factors such as habitat fragmentation and availability.     

Effect of breeding structure on population genetic parameters in Drosophila

The breeding structure of populations has been neglected in studies of Drosophila, even though Wright and Dobzhansky's pioneering work on the genetics of natural populations was an attempt to tackle what they regarded as an essential factor in evolution. We compared the breeding structure of sympatric populations of D. melanogaster and D. simulans, two sibling species that are widely used in evolutionary studies. We recorded changes in population density and microsatellite variation patterns for 3 years in a temperate environment of southwestern France. Results were distinctively different in the two species. Maximum population levels in summer and in autumn were similar and fluctuated greatly over years, each species being in turn the most abundant. However, genetic data showed that D. melanogaster made up a continuous breeding population in time and space of practically infinite effective size. D. simulans was fragmented into isolates with a local effective size of between 50 and 350 individuals. A consequence of this was that, while a local sample provided a reliable estimate of regional genetic variability in D. melanogaster, a sample from the same area provided an underestimate of this parameter in D. simulans. In practical terms, this means that variations in breeding structure should be accounted for in sampling schemes and in designing evolutionary genetic models. More generally, this suggests the existence of differential reactions to local environments that might contribute to several genomic differences observed between these species.     

The genetic structure of Drosophila ananassae populations from Asia, Australia and Samoa

Information about genetic structure and historical demography of natural populations is central to understanding how natural selection changes genomes. Drosophila ananassae is a widespread species occurring in geographically isolated or partially isolated populations and provides a unique opportunity to investigate population structure and molecular variation. We assayed microsatellite repeat-length variation among 13 populations of D. ananassae to assess the level of structure among the populations and to make inferences about their ancestry and historic biogeography. High levels of genetic structure are apparent among all populations, particularly in Australasia and the South Pacific, and patterns are consistent with the hypothesis that the ancestral populations are from Southeast Asia. Analysis of population structure and use of F-statistics and Bayesian analysis suggest that the range expansion of the species into the Pacific is complex, with multiple colonization events evident in some populations represented by lineages that show no evidence of recent admixture. The demographic patterns show isolation by distance among populations and population expansion within all populations. A morphologically distinct sister species, D. pallidosa, collected in Malololelei, Samoa, appears to be more closely related to some of the D. ananassae populations than many of the D. ananassae populations are to one another. The patterns of genotypic diversity suggest that many of the individuals that we sampled may be morphologically indistinguishable nascent species.