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.     

Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. II. The Om(1D) locus

Restriction-site and sequence-length polymorphism in the Om(1D) locus region on the X chromosome in Drosophila ananassae was investigated for three natural populations (from Burma, India, and Brazil), by using hexanucleotide-recognizing restriction enzymes. The estimates of average heterozygosity per nucleotide (pi) were 0.0085, 0.0043, and 0.0004 for the Burma, India, and Brazil populations, respectively, and the average frequencies of insertions/deletions were 0.078, 0.054, and 0.007/chromosome/kb. While the pi values at this locus are similar to the estimates obtained from other euchromatic loci in D. ananassae or in other Drosophila species, the frequencies of insertions/deletions are much higher than those previously reported from Drosophila. The exceptionally high frequencies of length polymorphisms in the Burmese sample and, to a lesser extent, in the Indian sample indicate that the hypermutability of Om(1D), caused by the frequent insertion of the transposable element tom, may be due to locus-specific rather than to tom element-specific properties. The low level of nucleotide variation in the Brazilian population seems to be due to a recent bottleneck of population size. This population was apparently founded in recent years by a small number of individuals and has been relatively isolated ever since.     

Potential gene flow in natural populations of the Drosophila ananassae species cluster inferred from a nuclear mitochondrial pseudogene

A pseudogene with 94% similarity to mitochondrial cytochrome c oxidase subunit I (COI) was identified and localized to chromosome 4 of Drosophila ananassae. Because this chromosome is believed to have reduced recombination, its history can be traced using the pseudo-COI sequence. Pseudo-COI sequences were obtained from 27 iso-female lines of six taxa belonging to the D. ananassae species cluster in which reproductive isolation is incomplete. The phylogenetic network constructed from seven recognized haplotypes (#0-#6) indicated that different taxa inhabiting the same geographic area share the haplotypes: #1 from Papua New Guinean populations of D. ananassae and pallidosa-like-Wau; #2 from Papua New Guinean populations of D. ananassae, pallidosa-like, and papuensis-like; and #4 from South Pacific populations of D. ananassae and D. pallidosa. Taxon-K has a unique haplotype (#6), and 18 mutation steps separate it from the closest haplotype, #2. We discuss the possibility of chromosome 4 introgression beyond taxon boundaries.     

Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae

Drosophila ananassae is a cosmopolitan species with a geographic range throughout most of the tropical and subtropical regions of the world. Previous studies of DNA sequence polymorphism in three genes has shown evidence of selection affecting broad expanses of the genome in regions with low rates of recombination in geographically local populations in and around India. The studies suggest that extensive physical and genetic maps based on molecular markers, and detailed studies of population structure may provide insight into the degree to which natural selection affects DNA sequence polymorphism across broad regions of chromosomes. We have isolated 85 dinucleotide repeat microsatellite sequences and developed assay conditions for genotyping using PCR. The dinucleotide repeats we isolated are shorter, on average, than those isolated in many other Drosophila species. Levels of genetic variation are high, comparable to Drosophila melanogaster. The levels of variation indicate the effective population size of an Indonesian population of D. ananassae is 58,692 (infinite allele model) and 217,284 (stepwise mutation model), similar to estimates of effective population size for D. melanogaster calculated using dinucleotide repeat microsatellites. The data also show that the Indonesian population is in a rapid expansion phase. Cross-species amplification of the microsatellites in 11 species from the Ananassae, Elegans, Eugracilis and Ficusphila subgroups indicates that the loci may be useful for studies of the sister species, D. pallidosa, but will have limited use for more distantly related species.     

Genetic diversity and structuring across the range of a widely distributed ladybird: focus on rear‐edge populations phenotypically divergent

Population genetics and phenotypic structures are often predicted to vary along the geographic range of a species. This phenomenon would be accentuated for species with large range areas, with discontinuities and marginal populations. We herein compare the genetic patterns of central populations of Coccinella septempunctata L. with those of two phenotypically differentiated populations considered as rear‐edge populations and subspecies based on phenotype (Algeria and Japan). According to the central‐marginal model and expected characteristics of rear‐edge populations, we hypothesize that these rear‐edge populations have (1) a reduced genetic diversity, resulting from their relative isolation over long periods of time, (2) a higher population genetic differentiation, explained by low contemporary gene flow levels, and (3) a relationship between genetic diversity characteristics and phenotypes, due to historical isolation and/or local adaptation. Based on genotyping of 28 populations for 18 microsatellite markers, several levels of regional genetic diversity and differentiation are observed between and within populations, according to their localization: low within‐population genetic diversity and higher genetic differentiation of rear‐edge populations. The genetic structuring clearly dissociates the Algerian and Eastern Asia populations from the others. Geographical patterns of genetic diversity and differentiation support the hypothesis of the central‐marginal model. The pattern observed is in agreement with the phenotypic structure across species range. A clear genetic break between populations of Algeria, the Eastern Asia, and the remaining populations is a dominant feature of the data. Differential local adaptations, absence of gene flow between marginal and central populations, and/or incapacity to mate after colonization, have contributed to their distinct genotypic and phenotypic characteristics.     

Population genetics of Drosophila ananassae: genetic differentiation among Indian natural populations at the level of inversion polymorphism

The present study, which is one of the longest temporal (two decades) and largest spatial (different parts of India covered) investigations on inversion polymorphism in natural populations of D. ananassae, was undertaken to understand the dynamics of inversion polymorphism in a broad and comprehensive manner. Forty-five natural populations from different ecogeographic regions of the country (covering the regions from Kashmir to Kanniyakumari and Gujarat to Nagaland) were analysed for chromosomal inversions. All the populations show the presence of the three cosmopolitan inversions, frequencies of which vary among the populations analysed. Simple correlations between frequencies of different inversions and regression analysis of inversion frequencies with latitude, longitude and altitude were insignificant. This reinforces the concept of rigid polymorphism in D. ananassae. Genetic divergence (spatial and temporal) at the level of chromosomal polymorphism among natural populations was calculated. Results show spatial divergence but no temporal divergence. Rigid polymorphic systems of D. ananassae did not show long-term directional trends. On the basis of the present study, and after including comparisons with the studies conducted more than two decades ago, the most important conclusion to be drawn is that the three cosmopolitan inversions in D. ananassae segregate within populations at fairly similar frequencies, and the general geographic pattern has remained constant.     

Behavioral genetics of Drosophila ananassae

Drosophila ananassae has a unique status among Drosophila species because of certain peculiarities in its genetic behavior. The most unusual feature of this species is its relatively high frequency of spontaneous male recombination. The results of studies on non-sexual behavior, such as phototactic responses, eclosion rhythm, and preferences for oviposition and pupation sites, lead us to suggest that this behavior is under polygenic control, with a substantial amount of additive genetic variation. Sexual isolation has been reported in D. ananassae with the degree of such isolation being stronger in isofemale lines than in natural populations. The significant variations seen in the mating propensity of several isofemale strains, inversion karyotypes and wild type strains, the diminishing effects of certain mutations on the sexual activity of males, and the positive responses to selection for high and low mating propensity point to a genetic control of sexual behavior in D. ananassae. Males contribute more to variation and thus are more subject to intrasexual selection than females. There is a positive correlation between sternopleural bristle number, mating propensity and fertility in D. ananassae. This correlation between morphometric traits and mating success suggests that larger flies are more successful in mating than smaller ones. There is also evidence for adaptive plasticity and a trade-off between longevity and productivity in D. ananassae. Rare, specific courtship song parameters that provide males with a mating advantage have also been reported in different geographic strains of D. ananassae. The remating behavior of males and females, sperm displacement, and the bi-directional selection for female remating speed indicate that post-mating behavior in this species may also be under genetic control. The occurrence of size assortative mating further indicates that there is size-dependent sexual selection in D. ananassae.     

Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data

Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.     

Reduced Levels of DNA Polymorphism and Fixed between-Population Differences in the Centromeric Region of Drosophila Ananassae

We have estimated DNA sequence variation within and between two populations of Drosophila ananassae, using six-cutter restriction site variation at vermilion (v) and furrowed (fw). These two gene regions are located close to the centromere on the left and right X chromosome arms, respectively. In the fw region, no DNA polymorphism was detected within each population. In the v region, average heterozygosity per nucleotide was very low in both populations (pi = 0.0005 in the Burma population, and 0.0009 in the India population). These estimates are significantly lower than those from loci in more distal gene regions. The distribution of DNA polymorphisms between both populations was also striking. At fw, three fixed differences between the Burma and India populations were detected (two restriction site differences and one insertion/deletion of approximately 2 kb). At v, each DNA polymorphism in high frequency in the total sample was nearly fixed in one or the other population, although none of them reached complete fixation. The observed pattern of reduced variation within populations and fixed differences between populations appears to correlate with recombination rate. We conclude that recent hitchhiking associated with directional selection is the best explanation for this pattern. The data indicate that different selective sweeps have occurred in the two populations. The possible role of genetic hitchhiking in rapid population differentiation in gene regions of restricted recombination is discussed.     

Genetic differentiation among migrant and resident populations of the threatened Asian houbara bustard

The Asian houbara bustard Chlamydotis macqueenii is a partial migrant of conservation concern found in deserts of central Asia and the Middle East. In the southern part of the species range, resident populations have been greatly fragmented and reduced by sustained human pressure. In the north, birds migrate from breeding grounds between West Kazakhstan and Mongolia to wintering areas in the Middle East and south central Asia. Extensive satellite tracking has shown substantial partitioning in migration routes and wintering grounds, suggesting a longitudinal barrier to present-day gene flow among migrants. In this context, we explored genetic population structure using 17 microsatellite loci and sampling 108 individuals across the range. We identified limited but significant overall differentiation (F(CT) = 0.045), which was overwhelmingly due to the differentiation of resident Arabian populations, particularly the one from Yemen, relative to the central Asian populations. Population structure within the central Asian group was not detectable with the exception of subtle differentiation of West Kazakh birds on the western flyway, relative to eastern populations. We interpret these patterns as evidence of recent common ancestry in Asia, coupled with a longitudinal barrier to present-day gene flow along the migratory divide, which has yet to translate into genetic divergence. These results provide key parameters for a coherent conservation strategy aimed at preserving genetic diversity and migration routes.     

Phylogeography of the white-tailed eagle, a generalist with large dispersal capacity

Aim Late Pleistocene glacial changes had a major impact on many boreal and temperate taxa, and this impact can still be detected in the present‐day phylogeographic structure of these taxa. However, only minor effects are expected in species with generalist habitat requirements and high dispersal capability. One such species is the white‐tailed eagle, Haliaeetus albicilla, and we therefore tested for the expected weak population structure at a continental level in this species. This also allowed us to describe phylogeographic patterns, and to deduce Ice Age refugia and patterns of postglacial recolonization of Eurasia. Location Breeding populations from the easternmost Nearctic (Greenland) and across the Palaearctic (Iceland, continental Europe, central and eastern Asia, and Japan). Methods Sequencing of a 500 base‐pair fragment of the mitochondrial DNA control region in 237 samples from throughout the distribution range. Results Our analysis revealed pronounced phylogeographic structure. Overall, low genetic variability was observed across the entire range. Haplotypes clustered in two distinct haplogroups with a predominantly eastern or western distribution, and extensive overlap in Europe. These two major lineages diverged during the late Pleistocene. The eastern haplogroup showed a pattern of rapid population expansion and colonization of Eurasia around the end of the Pleistocene. The western haplogroup had lower diversity and was absent from the populations in eastern Asia. These results suggest survival during the last glaciation in two refugia, probably located in central and western Eurasia, followed by postglacial population expansion and admixture. Relatively high genetic diversity was observed in northern regions that were ice‐covered during the last glacial maximum. This, and phylogenetic relationships between haplotypes encountered in the north, indicates substantial population expansion at high latitudes. Areas of glacial meltwater runoff and proglacial lakes could have provided suitable habitats for such population growth. Main conclusions This study shows that glacial climate fluctuations had a substantial impact on white‐tailed eagles, both in terms of distribution and demography. These results suggest that even species with large dispersal capabilities and relatively broad habitat requirements were strongly affected by the Pleistocene climatic shifts.     

Molecular Evolution of the Metallothionein Gene Mtn in the Melanogaster Species Group: Results from Drosophila Ananassae

Three distinctly different alleles of the metallothionein gene Mtn have been identified in natural Drosophila melanogaster populations: Mtn(.3), Mtn(1), and Dp(Mtn(1)), where the latter designates a tandem duplication of Mtn(1). In Drosophila simulans, only Mtn(.3)-type alleles have been found. It has been suggested that Mtn(.3) is the ancestral allele and demonstrated that a presumed two-step transition from Mtn(.3) to Mtn(1) to Dp(Mtn(1)) is accompanied by an approximate 5-fold increase in RNA levels. We analyzed the evolutionary genetics of the Mtn locus of Drosophila ananassae, a distant relative of D. melanogaster and D. simulans within the melanogaster species group. The Mtn gene of D. ananassae is most similar to Mtn(.3). (i) it is identical with Mtn(.3) at the amino acid level, but differs from Mtn(1) in its terminal codon; (ii) its 3'' UTR contains a characteristic extra DNA segment of about 50 bp which is present in Mtn(.3), but lacking in Mtn(1); (iii) duplications of Mtn were not found in a worldwide sample of 110 wild D. ananassae chromosomes. However, the intron of the Mtn gene in D. ananassae is only 69 bp long, whereas the length of the Mtn(.3) and Mtn(1) introns is 265 bp; and it lacks a polypyrimidine stretch upstream of the 3'' splice site in contrast to the much greater pyrimidine-richness found in the Mtn(.3) and Mtn(1) introns. A short intron (67 bp) was also identified in a D. pseudoobscura Mtn allele, suggesting that the short intron is the ancestral form and that the transition from the short to the long intron occurred within the melanogaster species group. We discuss the significance of this observation with regard to the recently proposed classification of D. melanogaster introns into two groups: short introns (<90 bp) which tend to lack polypyrimidine stretches, and longer ones which have strong 3'' splice signals similar to mammalian introns. A database search revealed that this length dimorphism is an evolutionarily conserved feature of Drosophila introns; transitions from one size class to the other appear to be rare between closely related species (e.g., within the melanogaster subgroup).     

Archaic African and Asian lineages in the genetic ancestry of modern humans.

A 3-kb region encompassing the beta-globin gene has been analyzed for allelic sequence polymorphism in nine populations from Africa, Asia, and Europe. A unique gene tree was constructed from 326 sequences of 349 in the total sample. New maximum-likelihood methods for analyzing gene trees on the basis of coalescence theory have been used. The most recent common ancestor of the beta-globin gene tree is a sequence found only in Africa and estimated to have arisen approximately 800,000 years ago. There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained. Modest differences in levels of beta-globin diversity between Africa and Asia are better explained by greater African effective population size than by greater time depth. There may have been a reduction of Asian effective population size in recent evolutionary history. Characteristically Asian ancestry is estimated to be older than 200,000 years, suggesting that the ancestral hominid population at this time was widely dispersed across Africa and Asia. Patterns of beta-globin diversity suggest extensive worldwide late Pleistocene gene flow and are not easily reconciled with a unidirectional migration out of Africa 100,000 years ago and total replacement of archaic populations in Asia.     

Population Structure of Wild Musk Shrews (Suncus murinus) in Asia Based on Mitochondrial DNA Variation, with Research in Cambodia and Bhutan

The musk shrew (Suncus murinus) is a small mammalian species belonging to Insectivora. It is widely distributed in Asia. To identify the genetic relationship among wild musk shrew populations and examine its migration route, we investigated the populations of Cambodia and Bhutan by using mitochondrial DNA restriction fragment length polymorphism analysis and compared them with other Asian populations previously described. Four haplotypes were detected in Cambodia and eight in Bhutan. A total of 53 haplotypes were detected in Asia and were classified largely into two groups, the Continental and Island types, based on a minimum spanning network. From the distribution of mtDNA types in wild musk shrews, three major population groups are identified in Asia: South Asia, Southeast Asia, and Malay. It is suggested that the Malay population group was a mix of South and Southeast Asian population groups and that this was a contact area of the two groups. In addition, other contact areas between the South and Southeast Asian groups exist in Myanmar, but unlike the Malay, the Myanmar area was the border of these groups.     

Low genetic diversity in the vulnerable Goitred Gazelle,Gazella subgutturosa (Cetartiodactyla: Bovidae), in Iran: potential genetic consequence of recent population declines

The Goitered Gazelle, Gazella subgutturosa, is the most widespread gazelle species in the Middle East and central Asia inhabiting desert and semi-desert habitats. Today it is threatened and its geographic range and population size have experienced significant decline in the last decades. In Iran, the remnant populations are confined to fragmented habitats. We aimed to characterise genetic diversity and phylogenetic status of the populations of Goitered Gazelle in Central Iran and to evaluate the potential effect of a historic population bottleneck on the genetic variation of today’s population. We used noninvasive sampling to uncover structure and level of genetic variation in a fragment of the cytochrome-b gene from 170 samples. Genealogical analyses were performed using HKY+I model and phylogenetic trees reconstructed using Bayesian inference and maximum likelihood. We found extremely low levels of genetic variation, with altogether only five haplotypes in samples from different populations. Overall haplotype diversity was 0.081 and nucleotide diversity 0.0003. The mean observed mismatch between any two sequences was 0.093 with the largest peak for small numbers. The mismatch distribution fit the model of population expansion and suggested that gazelles had experienced a sudden expansion. An unrooted median-joining network analysis of mtDNA haplotypes showed a star-like structure which few mutations steps separating the haplotypes from other regions. Our findings strengthen the urgency of preserving the species’ genetic diversity to prevent local extinction.     

Genetic analyses of several Drosophila ananassae-complex species show a low-frequency major gene for parthenogenesis that maps to chromosome 2

Parthenogenetic strains of several species have been found in the genus Drosophila. The mode of diploidization in the eggs of females has been found to be post-meiotic nuclear fusion. The genetic basis for this parthenogenesis is not understood but is believed to be under the control of a complex polygenic system. We found parthenogenetic females in an isofemale strain (LAE345) of D. pallidosa-like collected in 1981 at Lae, Papua New Guinea, and established a parthenogenetically reproducing strain. Parthenogenetic strains of D. ananassae and D. pallidosa collected at Taputimu, American Samoa had also been established by Futch (1972). D. ananassae, D. pallidosa and D. pallidosa-like are very closely related species belonging to the ananassae complex of the ananassae species subgroup of the melanogaster species group. Using these three species, we found that more than 80% of females from parthenogenetic strains produced progeny parthenogenetically and that inter-specific hybrid females also produced impaternate progeny. In the present report, we demonstrate that the mode of parthenogenesis of D. ananassae appears to be the post-meiotic nuclear doubling of a single meiotic product, and that a major gene responsible for the parthenogenesis maps to the left arm of the second chromosome of D. ananassae. We also suggest that the genetic basis for parthenogenesis capacity may be identical among the three closely related species. We discuss the function of the gene required for parthenogenesis and its significance for the evolutionary process.     

Extremely low genetic diversity and extensive genetic admixture at the northern range margins of Bombax ceiba

Understanding the evolutionary processes in species at the margins of their range is of great significance, because marginal populations may harbor local adaptations and will initiate further expansion in response to changes in the environment. Here we examined genetic variation in two nuclear genes and one chloroplast intergenic spacer in 13 northern marginal populations and one geographically central population of Bombax ceiba, a tree distributed mainly in tropical regions. Our results revealed an extremely low level of genetic diversity in each population at the northern margin of its range and strong genetic differentiation between southern China and South Asia. Cultivated and natural populations showed no significant differences in genetic variability. Genetic admixture in a nuclear gene was detected in 10 of the 13 populations at the northern margin of their range. The founder effect, in which a small number of individuals colonize the northern margins of its range, may explain the extremely low genetic diversity. During the establishment of new populations, different source populations may mix and undergo further genetic drift and differentiation. This study indicates that patterns of genetic diversity in tropical species at the margin of their range may also be severely influenced by founder effects.     

Genetic diversity of wild Cymbidium goeringii (Orchidaceae) populations from Hubei based on Inter-simple sequence repeats analysis

Cymbidium goeringii is a diploid and nonrewarding,bumblebee-pollinated species,which is distributed in China,Japan and Korea Peninsula.This species is now highly endangered due to the mass collection and forest clearance in China.In the present study,we investigated the distribution of genetic variation within and between eleven populations of Cymbidium goeringii in central China by using Inter-simple sequence repeats (ISSR) markers.Eleven primers produced a total of 127 clear and reproducible bands of which 112 were polymorphic.High genetic diversity was detected in Cymbidium goeringii for both population level (P = 63.1%;He = 0.194 5) and species level (P = 88.2%;He = 0.262 8).A higher level of genetic differentiation was detected among populations (GST = 0.244 0,FST = 0.220 7)with Nei's Gsr analysis and analysis of molecular variance (AMOVA),and no correlation was found between geographical and genetic distance.Genetic drift rather than gene flow played an important role in forming the present population structure of Cymbidium goeringii.Limited gene flow among populations and gene drift increase the extinction risk of local populations.Some conservation concerns are therefore discussed together with possible strategies for implementing in situ and ex situ conservation.     

Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122

The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred approximately 25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.     

The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago

Aim To test hypotheses that: (1) late Pleistocene low sea‐level shorelines (rather than current shorelines) define patterns of genetic variation among mammals on oceanic Philippine islands; (2) species‐specific ecological attributes, especially forest fidelity and vagility, determine the extent to which common genetic patterns are exhibited among a set of species; (3) populations show reduced within‐population variation on small, isolated oceanic islands; (4) populations tend to be most highly differentiated on small, isolated islands; and (5) to assess the extent to which patterns of genetic differentiation among multiple species are determined by interactions of ecological traits and geological/geographic conditions. Location The Philippine Islands, a large group of oceanic islands in Southeast (SE) Asia with unusually high levels of endemism among mammals. Methods Starch‐gel electrophoresis of protein allozymes of six species of small fruit bats (Chiroptera, Pteropodidae) and one rodent (Rodentia, Muridae). Results Genetic distances between populations within all species are not correlated with distances between present‐day shorelines, but are positively correlated with distances between shorelines during the last Pleistocene period of low sea level; relatively little intraspecific variation was found within these ‘Pleistocene islands’. Island area and isolation of oceanic populations have only slight effects on standing genetic variation within populations, but populations on some isolated islands have heightened levels of genetic differentiation, and reduced levels of gene flow, relative to other islands. Species associated with disturbed habitat (all of which fly readily across open habitats) show more genetic variation within populations than species associated with primary rain forest (all of which avoid flying out from beneath forest canopy). Species associated with disturbed habitats, which tend to be widely distributed in SE Asia, also show higher rates of gene flow and less differentiation between populations than species associated with rain forest, which tend to be Philippine endemic species. One rain forest bat has levels of gene flow and heterozygosity similar to the forest‐living rodent in our study. Main conclusions The maximum limits of Philippine islands that were reached during Pleistocene periods of low sea level define areas of relative genetic homogeneity, whereas even narrow sea channels between adjacent but permanently isolated oceanic islands are associated with most genetic variation within the species. Moreover, the distance between ‘Pleistocene islands’ is correlated with the extent of genetic distances within species. The structure of genetic variation is strongly influenced by the ecology of the species, predominantly as a result of their varying levels of vagility and ability to tolerate open (non‐forested) habitat. Readily available information on ecology (habitat association and vagility) and geological circumstances (presence or absence of Pleistocene land‐bridges between islands, and distance between oceanic islands during periods of low sea level) are combined to produce a simple predictive model of likely patterns of genetic differentiation (and hence speciation) among these mammals, and probably among other organisms, in oceanic archipelagos.