Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila)

We studied the phylogenetic relationships among the three stone pine species, Pinus cembra, P. sibirica, and P. pumila, using chloroplast microsatellites and mitochondrial nad1 intron 2 sequences. The three chloroplast microsatellite loci combined into a total of 18 haplotypes. Fourteen haplotypes were detected in 15 populations of P. cembra and one population of P. sibirica, five of which were shared between the two species, and the two populations of P. pumila comprised four species-specific haplotypes. Mitochondrial intron sequences confirmed this grouping of species. Sequences of P. cembra and P. sibirica were identical, but P. pumila differed by several nucleotide substitutions and insertions/deletions. A repeat region found in the former two species showed no intraspecific variation. These results indicate a relatively recent evolutionary separation of P. cembra and P. sibirica, despite their currently disjunct distributions. The species-specific chloroplast and mitochondrial markers of P. sibirica and P. pumila should help to trace the hybridization in their overlapping distribution area and to identify fossil remains with respect to the still unresolved postglacial re-colonization history of these two species.     

Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography

The nuclear genetic variation within and among 21 populations of sessile oak was estimated at 31 RAPD loci in conjunction with previous estimates of variation at eight allozyme loci. The aim of the study was to assess the relative role of isolation-by-distance and postglacial history on patterns of nuclear variation. Because of its small effective population size and maternal transmission, the chloroplast genome is a good marker of population history. Both kinds of nuclear variation (RAPD and allozyme) were therefore compared, first, to the geographical distances among populations and, secondly, to chloroplast DNA restriction polymorphism in the same populations. Multiple Mantel tests were used for this purpose. Although RAPDs revealed less genetic diversity than allozymes, levels of genetic differentiation ( G _ST) were identical. The standard genetic distance calculated at all RAPD loci was correlated with geographical distances but not with the genetic distance calculated from chloroplast DNA data. Conversely, allozyme variation was correlated with chloroplast DNA variation, but not with geography. Possibly, divergent selection at two allozyme loci during the glacial period could explain this pattern. Because of its greater number of loci assayed, RAPDs probably provided a less biased picture of the relative role of geography and history.     

Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci

Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied by a recent population admixture following a recent population expansion.     

Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci

Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.     

Phylogeography of the pine processionary moth Thaumetopoea wilkinsoni in the Near East

Phylogeographic structure of the eastern pine processionary moth Thaumetopoea wilkinsoni was explored in this study by means of nested clade phylogeographic analyses of COI and COII sequences of mitochondrial DNA and Bayesian estimates of divergence times. Intraspecific relationships were inferred and hypotheses tested to understand historical spread patterns and spatial distribution of genetic variation. Analyses revealed that all T. wilkinsoni sequences were structured in three clades, which were associated with two major biogeographic events, the colonization of the island of Cyprus and the separation of southwestern and southeastern Anatolia during the Pleistocene. Genetic variation in populations of T. wilkinsoni was also investigated using amplified fragment length polymorphisms and four microsatellite loci. Contrasting nuclear with mitochondrial data revealed recurrent gene flow between Cyprus and the mainland, related to the long-distance male dispersal. In addition, a reduction in genetic variability was observed at both mitochondrial and nuclear markers at the expanding boundary of the range, consistent with a recent origin of these populations, founded by few individuals expanding from nearby localities. In contrast, several populations fixed for one single mitochondrial haplotype showed no reduction in nuclear variability, a pattern that can be explained by recurrent male gene flow or selective sweeps at the mitochondrial level. The use of both mitochondrial and nuclear markers was essential in understanding the spread patterns and the population genetic structure of T. wilkinsoni, and is recommended to study colonizing species characterized by sex-biased dispersal.     

Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes

Microsatellites and mitochondrial DNA (mtDNA) have traditionally been used in population genetics because of their variability and presumed neutrality, whereas genes of the major histocompatibility complex (MHC) are increasingly of interest because strong selective pressures shape their standing variation. Despite the potential for MHC genes, microsatellites, and mtDNA sequences to complement one another in deciphering population history and demography, the three are rarely used in tandem. Here we report on MHC, microsatellite, and mtDNA variability in a single large population of the eastern tiger salamander (Ambystoma tigrinum tigrinum). We use the mtDNA mismatch distribution and, on microsatellite data, the imbalance index and bottleneck tests to infer aspects of population history and demography. Haplotype and allelic variation was high at all loci surveyed, and heterozygosity was high at the nuclear loci. We find concordance among neutral molecular markers that suggests our study population originated from post-Pleistocene expansions of multiple, fragmented sources that shared few migrants. Differences in N(e) estimates derived from haploid and diploid genetic markers are potentially attributable to secondary contact among source populations that experienced rapid mtDNA divergence and comparatively low levels of nuclear DNA divergence. We find strong evidence of natural selection acting on MHC genes and estimate long-term effective population sizes (N(e)) that are very large, making small selection intensities significant evolutionary forces in this population.     

Genetically depauperate but widespread: the case of an emblematic Mediterranean pine

Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted.     

Genetic variation and seasonal migratory connectivity in Wilson's warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations

There is growing interest in understanding patterns of seasonal migratory connectivity between breeding and wintering sites, both because differences in migratory behaviour can be associated with population differentiation and because knowledge of migratory connectivity is essential for understanding the ecology, evolution and conservation of migratory species. We present the first broad survey of geographic variation in the nuclear genome of breeding and wintering Wilson's warblers (Wilsonia pusilla), which have previously served as a research system for the study of whether genetic markers and isotopes can reveal patterns of migratory connectivity. Using 153 samples surveyed at up to 257 variable amplified fragment length polymorphism markers, we show that Wilson's warblers consist of highly distinct western and eastern breeding groups, with all winter samples grouping with the western breeding group. Within the west, there is weak geographic differentiation, at a level insufficient for use in the assignment of wintering samples to specific areas. The distinctiveness of western and eastern genetic groups, with no known intermediates, strongly suggests that these two groups are cryptic species. Analysis of mitochondrial cytochrome b sequence variation shows that the estimated coalescence time between western and eastern clades is approximately 2.3 Ma, a surprisingly old time of divergence that is more typical of distinct species than of subspecies. Given their morphological similarity but strong genetic differences, western and eastern Wilson's warblers present a likely case of association between divergence in migratory behaviour and the process of speciation.     

Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea

Abstract We investigated the genetic structure of blacktip shark (Carcharhinus limbatus) continental nurseries in the northwestern Atlantic Ocean, Gulf of Mexico, and Caribbean Sea using mitochondrial DNA control region sequences and eight nuclear microsatellite loci scored in neonate and young-of-the-year sharks. Significant structure was detected with both markers among nine nurseries (mitochondrial PhiST = 0.350, P < 0.001; nuclear PhiST = 0.007, P < 0.001) and sharks from the northwestern Atlantic, eastern Gulf of Mexico, western Gulf of Mexico, northern Yucatan, and Belize possessed significantly different mitochondrial DNA haplotype frequencies. Microsatellite differentiation was limited to comparisons involving northern Yucatan and Belize sharks with nuclear genetic homogeneity throughout the eastern Gulf of Mexico, western Gulf of Mexico, and northwestern Atlantic. Differences in the magnitude of maternal vs. biparental genetic differentiation support female philopatry to northwestern Atlantic, Gulf of Mexico, and Caribbean Sea natal nursery regions with higher levels of male-mediated gene flow. Philopatry has produced multiple reproductive stocks of this commercially important shark species throughout the range of this study.     

Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe

We used chloroplast polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad-leaved wind-pollinated and wind-dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR-RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (GST= 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south-eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.     

五种落叶松遗传关系的等位酶分析

由于种间形态上的微弱区别,落叶松属的系统分类一直很混乱,落叶松属的系统发生也知之甚少。本文分析了西伯利亚落叶松(Larix sibirica Ledeb.),卡氏落叶松(L.cajanderi Mayr.),兴安落叶松(L.gmelinii Rupr.),苏氏落叶松(L.sukaczewii Dil.)和杂交种切氏落叶松L.czekanowskii(L.gmelinii×L.sibirica)天然种群的遗传结构。采用水平切片淀粉凝胶电泳技术,等位酶分析手段对5个酶系统(AAT,IDH,DIA,PGM,SKDH)的8个基因位点进行了遗传结构分析。结果表明各种间遗传距离(D)在0.067~0.260之间,明显大于各种群内居群间的遗传距离。等位酶的分析结果揭示了5种落叶松的遗传关系。结合以上每种落叶松的形态学、生物学和生态学特性,等位酶的证据了支持兴安落叶松、西伯利亚落叶松、卡氏落叶松、苏氏落叶松作为独立种的观点。     

Genetic variation within and among fragmented populations of lesser prairie-chickens (Tympanuchus pallidicinctus)

As a result of recurrent droughts and anthropogenic factors, the range of the lesser prairie-chicken (Tympanuchus pallidicinctus) has contracted by 92% and the population has been reduced by approximately 97% in the past century, resulting in the smallest population size and most restricted geographical distribution of any North American grouse. We examined genetic variation through DNA sequence analysis of 478 base pairs of the mitochondrial genome and by assaying allelic variation at five microsatellite loci from lesser prairie-chickens collected on 20 leks in western Oklahoma and east-central New Mexico. Traditional population genetic analyses indicate that lesser prairie-chickens maintain high levels of genetic variation at both nuclear and mitochondrial loci. Although some genetic structuring among lesser prairie-chicken leks was detected within Oklahoma and New Mexico for both nuclear and mitochondrial loci, high levels of differentiation were detected between Oklahoma and New Mexico populations. Nested-clade analysis of mitochondrial haplotypes revealed that both historic and contemporary processes have influenced patterns of haplotype distributions and that historic processes have most likely led to the level of differentiation found between the Oklahoma and New Mexico populations.     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)

African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal.     

Phylogenetic Relationships Among Fragmented Asian Black Bear (Ursus Thibetanus) Populations in Western Japan

The number of Asian black bears (Ursus thibetanus) in Japan has been reduced and their habitats fragmented and isolated because of human activities. Our previous study examining microsatellite DNA loci revealed significant genetic differentiation among four local populations in the western part of Honshu. Here, an approximate 700-bp nucleotide sequence of mitochondrial DNA (mtDNA) control region was analysed in 119 bears to infer the evolutionary history of these populations. Thirteen variable sites and variation in the number of Ts at a T-repeat site were observed among the analysed sequences, which defined 20 mtDNA haplotypes with the average sequence divergence of 0.0051 (SD = 0.00001). The observed haplotype frequencies differed significantly among the four populations. Phylogeographic analysis of the haplotypes suggested that black bears in this region have gone through two different colonisation histories, since the observed haplotypes belonged to two major monophyletic lineages and the lineages were distributed with an apparent border. The spatial genetic structure revealed by using mtDNA was different from that observed using microsatellite DNA markers, probably due to female philopatry and male-biased dispersal. Since nuclear genetic diversity will be lost in the three western populations because of the small population size and genetic isolation, their habitats need to be preserved, and these four populations should be linked to each other by corridors to promote gene flow from the easternmost population with higher nuclear genetic diversity.     

Genetic diversity and gene flow between the wild olive (oleaster, Olea europaea L.) and the olive: several Plio-Pleistocene refuge zones in the Mediterranean basin suggested by simple sequence repeats analysis

Aim The oleaster is believed to have originated in the eastern Mediterranean, implying that those in the western Mediterranean basin could be feral. Several studies with different molecular markers (isozymes, random amplified polymorphic DNA, amplified fragment length polymorphism) have shown a cline between the eastern and the western populations, which supports this hypothesis. To reconstruct the post‐glacial colonization history and establish a relationship between olive and oleaster populations in the Mediterranean basin, analyses were carried out on the genetic variation of chloroplast DNA (chlorotype) and at 12 unlinked simple sequence repeat (SSR) loci, sampling a total of 20 oleaster groves. Location This is the first known large‐scale molecular study of SSR loci based on samples of both oleasters and cultivars from the entire Mediterranean basin. Methods Samples were taken from 166 oleasters in 20 groves of modern populations, and 40 cultivars to represent molecular diversity in the cultivated olive. The Bayesian method and admixture analysis were used to construct the ancestral populations (RPOP; reconstructed panmictic oleaster populations) and to estimate the proportion of each RPOP in each tree. If one tree can be assigned to two or more RPOPs, it can be regarded as a product of hybridization between trees from different populations (i.e. admix origin). Results On this first examination of the SSR genetic diversity in the olive and oleaster, it was found to be structured in seven RPOPs in both eastern and western populations. Based on different population genetic methods, it was shown that: (1) oleasters are equally present in the eastern and the western Mediterranean, (2) are native, and (3) are not derived from cultivars. Chlorotypes (one and three in the eastern and western Mediterranean, respectively) revealed fruit displacement for the oleasters. Main conclusions Oleaster genetic diversity is divided into seven regions that could overlay glacial refuges. The gradient, or cline, of genetic diversity revealed by chloroplast and SSR molecular markers was explained by oleaster recolonization of the Mediterranean basin from refuges after the last glacial event, located in both eastern and western regions. It is likely that gene flow has occurred in oleasters mediated by cultivars spread by human migration or through trade. Animals may have helped spread oleasters locally, but humans have probably transported olives but not oleaster fruits over long distances. We found that cultivars may have originated in several RPOPs, and thus, some may have a more complex origin than expected initially.     

Molecular signatures of divergence and selection in closely related pine taxa

Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.     

Population genetic structure of savannah elephants in Kenya: conservation and management implications

We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (F(CT) = 0.264; P < 0.05) and a relatively lower differentiation among populations within regions (F(SC) = 0.218; P < 0.0001). Microsatellite variation significantly differentiated among populations within regions (F(SC) = 0.019; P < 0.0001) but not at the regional levels (F(CT) = 0.000; P > 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.     

Among population differentiation at nuclear genes in native Scots pine (Pinus sylvestris L.) in Scotland

In the Scottish Highlands, Scots pine is at the north-western extreme of its wide natural distribution. Here, the remaining native populations are patchily distributed in highly variable environments, from the more continental, drier eastern Highlands to the milder, wetter Atlantic Ocean coast. As these pinewoods are the remnants of a naturally established forest, they form a valuable system for analysis of genetic and adaptive variation in heterogeneous environments. Using samples from across the Scottish population, we analysed data from nuclear and mitochondrial genes to assess patterns of within and between population genetic variation. Within population diversity levels were high, and significant genetic differentiation among pairs of Scottish populations at relatively small spatial scales was present at several nuclear loci. At these loci, no differentiation had been found among continental populations, even those separated by large geographic distances. Overall, no clear clustering of Scottish samples was found in population structure analysis suggesting that geographically distant populations with high intra-population nucleotide diversity are not strongly isolated or diverged from each other. Scottish populations lacked a mitotype that is widespread in eastern and north-eastern Europe, indicating that pines from that area may not have participated in the most recent colonisation of the British Isles.     

Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus)

The Steller's sea lion Eumetopias jubatus is an endangered marine mammal that has experienced dramatic population declines over much of its range during the past five decades. Studies using mitochondrial DNA (mtDNA) have shown that an apparently continuous population includes a strong division, yielding two discrete stocks, western and eastern. Based on a weaker split within the western stock, a third Asian stock has also been defined. While these findings indicate strong female philopatry, a recent study using nuclear microsatellite markers found little evidence of any genetic structure, implying extensive paternal gene flow. However, this result was at odds with mark–recapture data, and both sample sizes and genetic resolution were limited. To address these concerns, we increased analytical power by genotyping over 700 individuals from across the species' range at 13 highly polymorphic microsatellite loci. We found a clear phylogenetic break between populations of the eastern stock and those of the western and Asian stocks. However, our data provide little support for the classification of a separate Asian stock. Our findings show that mtDNA structuring is not due simply to female philopatry, but instead reflects a genuine discontinuity within the range, with implications for both the phylogeography and conservation of this important marine mammal.