The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.     

The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.     

Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differences

Background

Ethnic minorities in Northern Thailand, often referred to as Hill Tribes, are considered an ideal model to study the different genetic impact of sex-specific migration rates expected in matrilocal (women remain in their natal villages after the marriage and men move to their wife's village) and patrilocal societies (the opposite is true). Previous studies identified such differences, but little is known about the possible interaction with another cultural factor that may potentially affect genetic diversity, i.e. linguistic differences. In addition, Hill Tribes started to migrate to Thailand in the last centuries from different Northern areas, but the history of these migrations, the level of genetic legacy with their places of origin, and the possible confounding effects related to this migration history in the patterns of genetic diversity, have not been analysed yet. Using both original and published data on the Hill Tribes and several other Asian populations, we focused on all these aspects.

Results

Genetic variation within population at mtDNA is lower in matrilocal, compared to patrilocal, tribes. The opposite is true for Y-chromosome microsatellites within the Sino-Tibetan linguistic family, but Hmong-Mien speaking patrilocal groups have a genetic diversity very similar to the matrilocal samples. Population divergence ranges between 5% and 14% at mtDNA sequences, and between 5% and 36% at Y- chromosomes STRs, and follows the sex-specific differences expected in patrilocal and matrilocal tribes. On the average, about 2 men and 14 women, and 4 men and 4 women, are exchanged in patrilocal and matrilocal tribes every generation, respectively. Most of the Hill Tribes in Thailand seem to preserve a genetic legacy with their likely geographic origin, with children adoption probably affecting this pattern in one tribe.

Conclusion

Overall, the sex specific genetic signature of different postmarital habits of residence in the Hill Tribes is robust. However, specific perturbations related to linguistic differences, population specific traits, and the complex migratory history of these groups, can be identified. Additional studies in different populations are needed, especially to obtain more precise estimates of the migration parameters.

     

Genealogy of the nuclear beta-fibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone

The study of nuclear genealogies in natural populations of nonmodel organisms is expected to provide novel insights into the evolutionary history of populations, especially when developed in the framework of well-established mtDNA phylogeographical scenarios. In the Iberian Peninsula, the endemic Schreiber's green lizard Lacerta schreiberi exhibits two highly divergent and allopatric mtDNA lineages that started to split during the late Pliocene. In this work, we performed a fine-scale analysis of the putative mtDNA contact zone together with a global analysis of the patterns of variation observed at the nuclear beta-fibrinogen intron 7 (beta-fibint7). Using a combination of DNA sequencing with single-strand conformational polymorphism (SSCP) analysis, we show that the observed genealogy at the beta-fibint7 locus reveals extensive admixture between two formerly isolated lizard populations while the two mtDNA lineages remain essentially allopatric. In addition, a private beta-fibint7 haplotype detected in the single population where both mtDNA lineages were found in sympatry is probably the result of intragenic recombination between the two more common and divergent beta-fibint7 haplotypes. Our results suggest that the progressive incorporation of nuclear genealogies in investigating the ancient demography and admixture dynamics of divergent genomes will be necessary to obtain a more comprehensive picture of the evolutionary history of organisms.     

DIFFERING LEVELS OF AMONG-POPULATION DIVERGENCE IN THE MITOCHONDRIAL DNA OF PERIODICAL CICADAS RELATED TO HISTORICAL BIOGEOGRAPHY

Mitochondrial DNA (mtDNA) haplotypes were determined for 118 individuals of 13-and 17-year periodical cicadas (genus Magicicada) collected from 16 localities throughout the Midwest and eastern United States. Two distinct mtDNA lineages, identified as A and B, differ by 2.5% based on analysis of fragment patterns and restriction maps. Observed levels of mtDNA diversity within each lineage are low compared to estimates for other taxa. The two lineages are regionally segregated, with the boundary line occurring at a latitude of approximately 33° North. The levels of mtDNA diversity and population genetic structure differ within the two lineages. There is a remarkably low level of mean mtDNA divergence and no genetic structure in lineage A, whereas lineage B exhibits an order of magnitude higher level of mtDNA diversity and significant genetic structure among sampled populations. The low level of mtDNA diversity in cicadas may be attributed to (1) a population bottleneck that most likely occurred during the Pleistocene, (2) recent colonization following the retreat of the glaciers and the expansion of deciduous forests, and/or (3) high among-family reproductive variance (as a consequence of large population size, high fecundity, aggregative behavior of adults, and clumping of eggs). The difference in mtDNA diversity and population genetic structure between the lineages suggests that they experienced different biogeographic histories; we relate this to Pleistocene changes.     

Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method

During the Late Pleistocene, glaciers sundered many species into multiple glacial refugia where populations diverged in allopatry. Although deeply divergent mitochondrial DNA (mtDNA) lineages often reflect the number of refugia occupied, it is unlikely that populations that split during the recent Wisconsin glaciations will have reached reciprocal monophyly. We examined mtDNA control region sequences from eastern and western populations of wood ducks (Aix sponsa) to determine whether their current, disjunct distribution is consistent with the occupancy of two glacial refugia. We used the 'isolation with migration' coalescent method (im) to simultaneously estimate effective population sizes, maternal gene flow, and time since divergence. We found 24 unique haplotypes, none of which were shared between the eastern and western populations, but we did not find diagnostic monophyletic lineages suggestive of long-term isolation in multiple glacial refugia. However, a high Phi ST (0.31) indicates that eastern and western populations are well differentiated in mtDNA, and results from im suggest that these populations have been diverging, without extensive gene flow, for 10,000 to 124,000 years. Results from im further suggest that these populations most likely split about 34,000 years ago, and this time of divergence is consistent with the occupancy of multiple glacial refugia during the Late Wisconsin glaciation. Eastern wood ducks are characterized by high genetic diversity, a large effective population size, and a recent population expansion, while western wood ducks have much less genetic diversity, a smaller population size, and have not undergone a recent population expansion.     

mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World.

mtDNA was successfully extracted from 108 individuals from the Norris Farms Oneota, a prehistoric Native American population, to compare the mtDNA diversity from a pre-Columbian population with contemporary Native American and Asian mtDNA lineages and to examine hypotheses about the peopling of the New World. Haplogroup and hypervariable region I sequence data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but that they were not the only lineages brought into the New World from Asia. The mtDNA evidence does not support the three-wave hypothesis of migration into the New World but rather suggests a single "wave" of people with considerable mtDNA diversity that exhibits a signature of expansion 23,000-37,000 years ago.     

Rapid genetic assimilation of native wall lizard populations (Podarcis muralis) through extensive hybridization with introduced lineages

The Common Wall Lizard (Podarcis muralis) has established more than 150 non-native populations in Central Europe, stemming from eight geographically distinct evolutionary lineages. While the majority of these introduced populations are found outside the native range, some of these populations also exist at the northern range margin in southwestern Germany. To (i) infer the level of hybridization in contact zones of alien and native lineages; and (ii) compare the genetic diversity among purebred introduced, native and hybrid populations, we used a combination of maternally inherited markers (mtDNA: cytb) and Mendelian markers (microsatellites). Our results suggest a rapid genetic assimilation of native populations by strong introgression from introduced lineages. Discordant patterns of mtDNA and nDNA variation within hybrid populations may be explained by directed mate choice of females towards males of alien lineages. In contrast to previous studies, we found a nonlinear relationship between genetic diversity and admixture level. The genetic diversity of hybrid populations was substantially higher than in introduced and native populations belonging to a single lineage, but rapidly reaching a plateau of high genetic diversity at an admixture level of two. However, even introduced populations with low founder sizes and from one source population retained moderate levels of genetic diversity and no evidence for a genetic bottleneck was found. The extent of introgression and the dominance of alien haplotypes in mixed populations indicate that introductions of non-native lineages represent a serious threat to the genetic integrity of native populations due to the rapid creation of hybrid swarms.     

Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality

The endemic New Zealand Hector's dolphin is considered the rarest species of marine dolphin with a total abundance of less than 4000. The species is listed as vulnerable because of fisheries-related mortality due to entanglement in set nets. The vulnerability of this species is further increased by its fidelity to local natal ranges and the genetic isolation of regional populations. Here we present evidence, based on 108 contemporary samples and 55 historical samples dating back to 1870, of a significant loss of mitochondrial DNA (mtDNA) diversity in two regional populations of Hector's dolphin. The haplotype diversity (h) was calculated from sequences of a 206 bp fragment in the mtDNA control region, designed to identify 13 out of the 14 known maternal lineages. Over the last 20 years, the North Island population has been reduced from at least three lineages (h = 0.41) to a single lineage (h = 0; p < 0.05). Given its small size, reproductive isolation and reduced genetic diversity, this population is likely to become extinct. The diversity of the East Coast South Island population has declined significantly from h = 0.65 to h = 0.35 (p < 0.05). Based on trend analysis of the mtDNA diversity, we predict that the East Coast population will lose all mtDNA diversity within the next 20 years. This time-series of reduction in genetic variation provides independent evidence of the severity of population decline and habitat contraction resulting from fisheries and perhaps other human activities.     

Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.     

The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.     

Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan

To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3–13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.     

Patrilineal perspective on the Austronesian diffusion in Mainland Southeast Asia

The Cham people are the major Austronesian speakers of Mainland Southeast Asia (MSEA) and the reconstruction of the Cham population history can provide insights into their diffusion. In this study, we analyzed non-recombining region of the Y chromosome markers of 177 unrelated males from four populations in MSEA, including 59 Cham, 76 Kinh, 25 Lao, and 17 Thai individuals. Incorporating published data from mitochondrial DNA (mtDNA), our results indicated that, in general, the Chams are an indigenous Southeast Asian population. The origin of the Cham people involves the genetic admixture of the Austronesian immigrants from Island Southeast Asia (ISEA) with the local populations in MSEA. Discordance between the overall patterns of Y chromosome and mtDNA in the Chams is evidenced by the presence of some Y chromosome lineages that prevail in South Asians. Our results suggest that male-mediated dispersals via the spread of religions and business trade might play an important role in shaping the patrilineal gene pool of the Cham people.     

Indo-Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine-dispersed species, Birgus latro . Crabs were collected from eight locations throughout the species' Indo-Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different ( G _ST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro . Long-term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.     

African DNA Lineages in the Mitochondrial Gene Pool of Europeans

Mitochondrial DNA (mtDNA) nucleotide sequences of African origin are found in various European populations at a low frequency (on average, less than 1%). Data on mtDNA variation in Eurasian and African populations have been analyzed, and African mtDNA lineages have been found in Europeans. It has been demonstrated that, despite the high diversity of mtDNA haplotypes of African origin in Europeans, few monophyletic clusters of African lineages are characterized by long-term diversity formed in Europe. Only two such mtDNA clusters (from haplogroups L1b and L3b) have been found, their evolutionary age not exceeding 6500 years. European and African populations have been compared with respect to the frequency distributions of the alleles of autosomal microsatellite loci found in Russian carriers of African mtDNA haplotypes. It has been demonstrated that alleles typical of Europeans are characteristic of the autosomal genotypes of these Russian individuals.     

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the “slow boat” and “entangled bank” models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 ± 3.8 thousand years (or 9.3 ± 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal.     

Allozymic differentiation in the land snail Arianta arbustorum (Stylommatophora, Helicidae): historical inferences

The intraspecific genetic differentiation depends to a large part on historical factors. The mode of dispersal is an important determinant of the genetic diversity especially of newly founded populations. Fast long-distance colonization of formerly unsuitable habitats results in reduced genetic diversity and lineages originating from different glacial refugia form well-defined hybrid zones, where they meet. Slow dispersers, on the other hand, preserve their refugial genetic diversity. Paleontological findings and a previous analysis of mtDNA suggest that the land snail Arianta arbustorum, which today is widely spread across Europe, has survived the Pleistocene glaciations within the boundaries of permafrost. In the present paper, we asked, whether the differentiation of nuclear markers, i.e. allozymes, supports these results. We investigated the allozymic differentiation at 15 polymorphic loci in 14 Alpine and one English populations of the land snail A. arbustorum. Various tests of genetic population differentiation yielded ambiguous results. Allele frequencies differed significantly across populations and all but five pairwise F_ST values were significant. Genetic distances between populations were comparatively high. On the other hand, an exact test of population differentiation found no differences and the assignment of individuals to their populations of origin was poor. This indicates that allozymic differentiation is constrained. Whether these constraints are of natural or methodological nature remains open. Matrices of genetic and geographical distances were correlated only after removal of the English population from the analysis. Similarly, with one exception F_ST values increased as the number of regions included in the calculations increased. Thus, on a regional scale, we largely observed a pattern of isolation by distance, which does no longer hold on a larger scale. This is well in accordance with the previous findings based on mtDNA. Mitochondrial lineages were widely distributed across Europe and overlapped extensively. Considering the low potential for dispersal of a land snail, the patchy distribution of lineages, and the high genetic diversity also found in the present study suggests that A. arbustorum has survived the Pleistocene within the boundaries of permafrost.     

MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.     

Autosomal, mitochondrial, and Y chromosome DNA variation in Finland: evidence for a male-specific bottleneck

The high prevalence of rare genetic diseases in Finland has been attributed to a founder effect some 2,000 years ago. However, this hypothesis has not been supported from mtDNA sequence and autosomal microsatellite data which indicate high levels of gene diversity. Here we have identified genetic evidence for a population bottleneck by examining variable microsatellite loci on the nonrecombining portion of Y chromosomes from Finland and four populations from Europe and the Americas. Sequence data from segment I of the control region (HVS-1) of mtDNA (360 bases) and 20 autosomal dinucleotide repeat markers were also analyzed. Partitions of genetic variance within and between populations revealed significant levels of Y-chromosome differentiation between populations. Phylogenetic and diversity analyses revealed divergent Finnish Y-haplotype clades and significantly lower Y-haplotype diversity among Finns as compared to other populations. Surprisingly, Finnish Y-haplotype diversity was even lower than the Native American populations. These results provide support for the Finnish bottleneck hypothesis. Evidence for two separate founding Finnish Y-chromosome lineages was also observed from the Y-chromosome phylogeny. A limited number of closely related founding males may have contributed to the low number of paternal lineages in the Finnish population. In contrast, high levels of genetic diversity for mtDNA and autosomal STRs may be the result of sex-biased gene flow and recent immigration to urban areas from established internal isolates within Finland.     

Origins of clonal diversity in the hypervariable asexual ostracode Cypridopsis vidua

Prior allozyme studies have indicated that populations of the asexual ostracode, Cypridopsis vidua (Müller), show extraordinary clonal diversity. Based on a joint examination of allozyme variation and sequence divergence at the mitochondrial cytochrome c oxidase I (COI) gene, the present analysis provides new insights concerning the origins of this variation. The results establish that populations of C. vidua in one recently deglaciated region of North America are not only allozymically diverse, but also include several divergent mitochondrial DNA (mtDNA) lineages. The extent of sequence divergence among these lineages is so large as to suggest their diversification over the past 7–8 million years. The patterning of genetic divergence among co-occurring clones makes it apparent that much of the mtDNA and allozyme diversity in local populations owes its origins to recurrent colonization events. However, in situ mutational diversification also appears to explain some variation. The mechanisms enabling the sustained coexistence of such a large array of closely allied genotypes remain unclear, but there is an apparent difference in equilibrium diversity between benthic and planktonic asexual organisms.