Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.     

Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal

Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before.     

Mitochondrial DNA variation in the malaria vector Anopheles minimus across China,Thailand and Vietnam: evolutionary hypothesis,population structure and population history

The effects of Pleistocene environmental fluctuations on the distribution and diversity of organisms in Southeast Asia are much less well known than in Europe and North America. In these regions, the combination of palaeoenvironmental reconstruction and inferences about population history from genetic data has been very powerful. In Southeast Asia, mosquitoes are good candidates for the genetic approach, with the added benefit that understanding the relative contributions of historical and current processes to population structure can inform management of vector species. Genetic variation among populations of Anopheles minimus was examined using 144 mtDNA COII sequences from 23 sites in China, Thailand and Vietnam. Haplotype diversity was high, with two distinct lineages that have a sequence divergence of over 2% and exhibit different geographical distributions. We compare alternative hypotheses concerning the origin of this pattern. The observed data deviate from the expectations based on a single-panmictic population with or without growth, or a stable but spatially structured population. However, they can be readily accommodated by a model of past fragmentation into eastern and western refugia, followed by growth and range expansion. This is consistent with the palaeoenvironmental reconstructions currently available for the region.     

Independent maternal origin of Chinese swamp buffalo (Bubalus bubalis)

To obtain more knowledge on the origin and genetic diversity of the swamp buffalo (Bubalus bubalis) in China, the complete mitochondrial D-loop sequences of 119 samples representing seven native types were compared. Two mitochondrial DNA (mtDNA) lineages (lineages A and B) were determined for the Chinese swamp buffalo. Examination of the diversity patterns suggest that lineage A has undergone a population expansion event. Divergence of lineages A and B was estimated at 18,000 years ago. Combined analyses of mtDNA sequences from Chinese, Indian, Brazilian/Italian and Southeast Asian/Australian buffalo samples showed independent domestication events in the swamp buffalo from China and the river buffalo from the India subcontinent. The spread of swamp and river buffalo from China and India respectively to mainland Southeast Asia suggests that Southeast Asia is a hybrid zone for buffalo. Our data support the hypothesis of the evolution of domesticated swamp and river buffalo from ancestral swamp-like animals. These ancestral animals were extensively distributed across mainland Asia and most likely are represented today by the wild Asian buffalo (Bubalus arnee).     

Population structure and population history of Anopheles dirus mosquitoes in Southeast Asia

Separating the confounding effects of long-term population history from gene flow can be difficult. Here, we address the question of what inferences about gene flow can be made from mitochondrial sequence data in three closely related species of mosquitoes, Anopheles dirus species A, C, and D, from southeast Asia. A total of 84 sequences of 923 bp of the mitochondrial cytochrome oxidase I gene were obtained from 14 populations in Thailand, Myanmar, and Bangladesh. The genealogy of sequences obtained from two populations of AN: dirus C indicates no contemporary gene flow between them. The F(ST) value of 0.421 therefore probably represents a recent common history, perhaps involving colonization events. Anopheles dirus A and D are parapatric, yet no differentiation was seen either within or between species. The starlike genealogy of their haplotypes, smooth unimodal mismatch distributions, and excess of low frequency mutations indicate population expansion in An. dirus A and D. This, rather than widespread gene flow, explains their low within-species F(ST) values (0.018 and 0.022). The greater genetic diversity of An. dirus D suggests that expansion occurred first in species D and subsequently in species A. The current geographical separation and low hybrid fitness of these species also argue against ongoing interspecific gene flow. They suggest instead either historical introgression of mtDNA from An. dirus D into species A followed by independent range expansions, or a selective sweep of mtDNA that originated in An. dirus D. While not excluding contemporary gene flow, historical population processes are sufficient to explain the data in An. dirus A and D. The genealogical relationships between haplotypes could not be used to make inferences of gene flow because of extensive homoplasy due to hypervariable sites and possibly also recombination. However, it is concluded that this approach, rather than the use of fixation indices, is required in the future to understand contemporary gene flow in these mosquitoes. The implications of these results for understanding gene flow in another important and comparable group of malaria vector mosquitoes in Africa, the An. gambiae complex, are also discussed.     

Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs

In the late stages of the global dispersal of dogs, dingoes appear in the Australian archaeological record 3500 years BP, and dogs were one of three domesticates brought with the colonization of Polynesia, but the introduction routes to this region remain unknown. This also relates to questions about human history, such as to what extent the Polynesian culture was introduced with the Austronesian expansion from Taiwan or adopted en route, and whether pre-Neolithic Australia was culturally influenced by the surrounding Neolithic world. We investigate these questions by mapping the distribution of the mtDNA founder haplotypes for dingoes (A29) and ancient Polynesian dogs (Arc1 and Arc2) in samples across Southern East Asia (n = 424) and Island Southeast Asia (n = 219). All three haplotypes were found in South China, Mainland Southeast Asia and Indonesia but absent in Taiwan and the Philippines, and the mtDNA diversity among dingoes indicates an introduction to Australia 4600-18 300 years BP. These results suggest that Australian dingoes and Polynesian dogs originate from dogs introduced to Indonesia via Mainland Southeast Asia before the Neolithic, and not from Taiwan together with the Austronesian expansion. This underscores the complex origins of Polynesian culture and the isolation from Neolithic influence of the pre-Neolithic Australian culture.     

Global invasive potential of the house crow Corvus splendens based on ecological niche modelling

Summaries of recent rapid range expansions shown by the house crow Corvus splendens have provided insights into the global nature of this invasion process, but its long-term potential has not yet been evaluated. To explore the potential dimensions of this geographic expansion, we used ecological niche modeling based on known occurrences of the species on its native distributional area, in the context of GIS data sets describing climatic variables, topographic information, and human presence. Our models provided predictions of areas already invaded that were statistically significantly more coincident than expected under random (null) models. The predicted potential range of the species includes areas already affected, as well as potentially suitable areas in Central America, the Caribbean, equatorial and West Africa, and mainland and insular Southeast Asia, not yet colonized.     

Colonization of the Philippines from Taiwan: a multi‐locus test of the biogeographic and phylogenetic relationships of isolated populations of shrews

Aim Colonization of the Philippines from Taiwan or neighbouring areas of the Asian mainland has been proposed as an important source of diversity for some plant and animal groups in the northern Philippines. Previous inferences, however, were based on taxonomic groupings, which sometimes fail to reflect phylogenetic history. Here, we test for colonization of the Philippines from the north in a group of shrews (Soricomorpha: Crocidura) using explicit inferences of evolutionary history. Location Southeast Asia. Methods We estimate the phylogenetic relationships of populations of shrews from Batan and Sabtang islands in the northern Philippines using DNA sequences from two mitochondrial genes and three nuclear loci. We employ topology tests to evaluate the possible relationships of these shrews to species from throughout Southeast Asia. Results We find conclusive evidence that shrews from Batan and Sabtang are closely related to Crocidura tanakae from Taiwan and additional specimens from the Asian mainland. Bayesian and frequentist topology tests using alignments of individual loci strongly reject any notion that shrews from Batan and Sabtang are part of the main Philippine radiation of Crocidura, indicating that the northernmost Philippine islands were almost certainly colonized by shrews from Taiwan or mainland Asia. Main conclusions Our results provide the first compelling evidence for colonization of the Philippine archipelago by a terrestrial vertebrate via a northern route. Invasion of the northern Philippines by shrews, however, did not lead to further range expansion to more southerly parts of the Philippines. This study, combined with previous results, documents that Crocidura colonized the Philippines at least three times. However, only one of these invasions led to in situ speciation and ubiquity across the archipelago. Our findings are part of a growing body of literature suggesting that oceanic archipelagos are often colonized multiple times by groups of closely related species, and occasionally from multiple sources.     

A morphometric analysis of the Late Pleistocene Human Skeleton from the Moh Khiew Cave in Thailand.

Few Late Pleistocene human remains have been found in Southeast Asia and the morphological features of the people of that age are still largely unknown due to the virtual lack of human remains in the area. Recent excavations at the Moh Khiew Cave in Thailand resulted in the discovery of a Late Pleistocene human skeleton in a relatively good state of preservation. An AMS radiocarbon date on the charcoal sample gathered from the burial gave a result of 25,800 +/- 600 BP, implying that the inhabitants of Moh Khiew Cave resided in a part of Sundaland during the last glacial age. In debates on the population history of Southeast Asia, it has been repeatedly advocated that Southeast Asia was occupied by indigenous people akin to present-day Australo-Melanesians prior to an expansion of migrants from Northeast Asia into this area. Morphometric analyses were undertaken to test the validity of this hypothesis. In the present study, cranial and dental measurements recorded from the Moh Khiew remains are compared with those of early and modern samples from Southeast Asia and Australia. These comparisons demonstrate that the Moh Khiew specimen resembles the Late Pleistocene series from Coobool Creek, Australia in both cranial and dental measurements. These results suggest that the Moh Khiew skeleton, as well as other fossil remains from the Tabon, Niah and Gua Gunung sites, represents a member of the Sundaland population during the Late Pleistocene, who may share common ancestry with the present-day Australian Aborigines and Melanesians.     

Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast (SE) Asia. The history of dispersal across islands of SE Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice to Taiwan and the northern Philippines using whole-genome resequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3,500 years before present (BP). In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland SE Asia, respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2,600 BP, whereas gene flow from the northern Philippines had begun before ∼1,300  BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.     

Comparative population structure of Cynopterus fruit bats in peninsular Malaysia and southern Thailand

The extent to which response to environmental change is mediated by species-specific ecology is an important aspect of the population histories of tropical taxa. During the Pleistocene glacial cycles and associated sea level fluctuations, the Sunda region in Southeast Asia experienced concurrent changes in landmass area and the ratio of forest to open habitat, providing an ideal setting to test the expectation that habitat associations played an important role in determining species' response to the opportunity for geographic expansion. We used mitochondrial control region sequences and six microsatellite loci to compare the phylogeographic structure and demographic histories of four broadly sympatric species of Old World fruit bats in the genus, Cynopterus. Two forest-associated species and two open-habitat generalists were sampled along a latitudinal transect in Singapore, peninsular Malaysia, and southern Thailand. Contrary to expectations based on habitat associations, the geographic scale of population structure was not concordant across ecologically similar species. We found evidence for long and relatively stable demographic history in one forest and one open-habitat species, and inferred non-coincident demographic expansions in the second forest and open-habitat species. Thus, while these results indicate that Pleistocene climate change did not have a single effect on population structure across species, a correlation between habitat association and response to environmental change was supported in only two of four species. We conclude that interactions between multiple factors, including historical and contemporary environmental change, species-specific ecology and interspecific interactions, have shaped the recent evolutionary histories of Cynopterus fruit bats in Southeast Asia.     

Phylogeny and biogeography of exacum (gentianaceae): a disjunctive distribution in the Indian ocean basin resulted from long distance dispersal and extensive radiation

Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacum is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacum, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India-Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance dispersals followed by extensive range expansion and subsequent fragmentation. The extant African species E. oldenlandioides is confirmed to be recently dispersed from Madagascar.     

SCAR markers and multiplex PCR-based identification of isomorphic species in the Anopheles dirus complex in Southeast Asia

The Anopheles dirus Peyton & Harrison complex of mosquitoes (Diptera: Culicidae) comprises seven known species, including important malaria vectors in Southeast Asia. Specific identification of each species of the complex, which cannot be distinguished using morphological characters, is crucial for understanding vector ecology and implementing effective control measures. Derived from individual random amplified polymorphic DNA (RAPD) markers, sequence characterized amplified regions (SCAR) were analysed for the design of specific paired-primers. Combination of six SCAR primers resulted in the development of a simple, robust, single multiplex PCR able to identify three important malaria vectors among the four most common species (A, B, C, D) of the complex: species A from several Southeast Asian countries, species B from Perlis, Malaysia, and species C and D from Thailand.     

Mitochondrial DNA variation in Nicobarese Islanders.

The aboriginal populations living in the Nicobar Islands are hypothesized to be descendants of people who were part of early human dispersals into Southeast Asia. However, analyses of ethnographic histories, languages, morphometric data, and protein polymorphisms have not yet resolved which worldwide populations are most closely related to the Nicobarese. Thus, to explore the origins and affinities of the Nicobar Islanders, we analyzed mitochondrial DNA (mtDNA) hypervariable region 1 sequence data from 33 Nicobarese Islanders and compared their mtDNA haplotypes to those of neighboring East Asians, mainland and island Southeast Asians, Indians, Australian aborigines, Pacific Islanders, and Africans. Unique Nicobarese mtDNA haplotypes, including five Nicobarese mtDNA haplotypes linked to the COII/tRNA(Lys) 9-bp deletion, are most closely related to mtDNA haplotypes from mainland Southeast Asian Mon-Kmer-speaking populations (e.g., Cambodians). Thus, the dispersal of southern Chinese into mainland Southeast Asia may have included a westward expansion and colonization of the islands of the Andaman Sea.     

Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus

Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.     

Asian water buffalo: domestication,history and genetics

The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000–7000 years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.     

Phylogeography of Simulium siamense Takaoka and Suzuki complex (Diptera: Simuliidae) in Thailand

The phylogeography of Simulium siamense complex was inferred from mitochondrial DNA sequences. A 586‐bp fragment of the cytochrome oxidase I was sequenced for 92 individuals from 13 populations throughout Thailand, representing five cytoforms (A, B, C, F and G). The cytoforms are not genetically different at the molecular level except for cytoform B, which is genetically distinct from the others. This might indicate that cytoform B is a distinct species. Further morphological and molecular work using other genes is needed to clarify this. Our results also argue for the need of integrated approach, both cytological and molecular studies to understanding biodiversity of black flies. The star‐like shape of the mtDNA genealogy is consistent with the sudden population expansion of the mismatch distribution analysis and large negative values of Fu's F_s and Tajima's D‐tests, indicating a population demographic expansion. The expansion time is estimated to be in the late Pleistocene (about 120 000 years ago). Therefore, the overall low level of genetic structure could be due to sharing a recent history. The ancestral haplotype was found in the mountainous area in northeastern Thailand, suggesting that this area could have been the refugium of the species complex during the Pleistocene glaciations. Our results are consistent with previous findings about population expansion in response to the Pleistocene climatic change, thus revealing the importance of this historical event in shaping the genetic structure and diversity of Southeast Asian mainland species.     

Numerous mitochondrial DNA haplotypes reveal multiple independent polyploidy origins of hexaploids in Carassius species complex

Evolutionary trajectory and occurrence history of polyploidy have been extensively studied in plants, but they remain quite elusive in vertebrates. Here, we sampled and gathered 4,159 specimens of polyploid Carassius species complex including 1,336 tetraploids and 2,823 hexaploids from a large geographic scale (49 localities) across East Asia, and identified a huge number of 427 diverse haplotypes of mitochondrial control region, in which 74 haplotypes with total occurrence frequency up to 75.498% were shared by hexaploids and tetraploids. Significantly, these diverse haplotypes were clustered into four major lineages, and many haplotypes of hexaploids and tetraploids were intermixed in every lineage. Moreover, the evolutionary trajectory and occurrence history of four different lineages were revealed by a simplified time‐calibrated phylogenetic tree, and their geographic distribution frequencies and haplotype diversity were also analyzed. Furthermore, lineage C and D were revealed to undergo population expansion throughout mainland China. Therefore, our current data indicate that hexaploids should undergo multiple independent polyploidy origins from sympatric tetraploids in the polyploid Carassius species complex across East Asia.     

Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.     

Post-glacial partitioning of mitochondrial genetic variation in the field vole

Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12,000 years BP) rather than the Last Glacial Maximum (LGM, ca 24,000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 × 10(-7) substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.