Intraspecific comparison of population structure, genetic diversity, and dispersal among three subspecies of Townsend’s big-eared bats, Corynorhinus townsendii townsendii, C. t. pallescens, and the endangered C. t. virginianus

Townsend’s big-eared bat, Corynorhinus townsendii, is distributed broadly across western North America and in two isolated, endangered populations in central and eastern United States. There are five subspecies of C. townsendii; C. t. pallescens, C. t. australis, C. t. townsendii, C. t. ingens, and C. t. virginianus with varying degrees of concern over the conservation status of each. The aim of this study was to use mitochondrial and microsatellite DNA data to examine genetic diversity, population differentiation, and dispersal of three C. townsendii subspecies. C. t. virginianus is found in isolated populations in the eastern United States and was listed as endangered under the Endangered Species Act in 1979. Concern also exists about declining populations of two western subspecies, C. t. pallescens and C. t. townsendii. Using a comparative approach, estimates of the genetic diversity within populations of the endangered subspecies, C. t. virginianus, were found to be significantly lower than within populations of the two western subspecies. Further, both classes of molecular markers revealed significant differentiation among regional populations of C. t. virginianus with most genetic diversity distributed among populations. Genetic diversity was not significantly different between C. t. townsendii and C. t. pallescens. Some populations of C. t. townsendii are not genetically differentiated from populations of C. t. pallescens in areas of sympatry. For the western subspecies gene flow appears to occur primarily through male dispersal. Finally, geographic regions representing significantly differentiated and genetically unique populations of C. townsendii virginianus are recognized as distinct evolutionary significant units.     

Intraspecific structure within three caviar-producing sturgeons (Acipenser gueldenstaedtii, A. stellatus, and Huso huso) based on mitochondrial DNA analysis

A survey of three mitochondrial DNA regions (control region, NADH5, cytochrome b) and comprehensive sequencing of the control region (631–646 bps) was conducted to examine whether subspecies and geographic populations within three species of Eurasian sturgeons, Acipenser gueldenstaedtii, A. stellatus, and Huso huso, are genetically distinct. Neither subspecies nor populations exhibited diagnostic distinction or reciprocal monophyly in any gene region examined. For the control region, molecular variance analyses (amova ) indicate that most of the variance is because of differences among haplotypes within subspecies (H. huso: 99.6%; A. stellatus: 95.0%; A. gueldenstaedtii: 81.0%) and populations (A. gueldenstaedtii: 76.1%). Significant pairwise F‐values were found for all pairwise comparisons except for Sea of Azov and Caspian Sea A. gueldenstaedtii and Caspian Sea and Black Sea A. stellatus and H. huso. Only weak genetic differentiation is apparent between select subspecies and populations, reflective of biogeographic and management history. High genetic diversity within A. gueldenstaedtii suggests the possibility of additional population structure. Future research and management projects should consider these results.     

Genetic diversity among African great apes based on mitochondrial DNA sequences

The mitochondrial DNA D-Loop region was sequenced, analyzed and used as a molecular marker for populations of chimpanzee (Pan troglodytes), bonobo (P. paniscus) and gorilla (Gorilla gorilla and G. beringei), and also compared with data previously reported for these taxa. In Gorilla, a main disjunction between western (G. gorilla) and eastern (G. beringei, including G. b. graueri) species was observed, as well as high mitochondrial diversity within the western species. The genetic distance values within G. gorilla (0.14) were higher than those between subspecies (eastern lowland and mountain 0.12). Likewise, values of genetic diversity within this species (0.05) were higher than those between species (western and eastern lowland gorilla 0.04). Similarly, in genus Pan a main differentiation between western (P. t. verus) and central forms (P. t. troglodytes and P. t. schweinfurthii) was observed. The obtained values of genetic distance and genetic diversity revealed that the central subspecies are closer to each other than either of them is to the western one, while bonobos composed a distinct clade that expresses a well-defined specific identity. The current distribution, phylogeny and levels of genetic diversity in African great ape populations are consistent with the hypothesis that Pleistocene climatic events led to cyclical periods of isolation in forest refugia followed by expansion and dispersal. The implications of this high level of genetic diversity for taxonomic classification, wildlife management and conservation are discussed.     

Origin and Evolution of Tandem Repeats in the Mitochondrial DNA Control Region of Shrikes (<Emphasis Type="BoldItalic">Lanius</Emphasis> spp.)

The origin and evolution of a 128-bp tandem repeat in the mtDNA control region of shrikes (Lanius: Aves) were investigated. The tandem repeat is present in only two species, L. excubitor and L. ludovicianus. In contrast to the variation in repeat number in L. ludovicianus, all individuals of three subspecies of L. excubitor had three repeats. Comparative analysis suggests that a short direct repeat, and a secondary structure including the tandem repeat and a downstream inverted repeat, may be important in the origin of the tandem repeat by slipped-strand mispairing and its subsequent turnover. Homogenization of repeat sequences is most simply explained by expansion and contraction of the repeat array. Surprisingly, mtDNA sequences from L. excubitor were found to be paraphyletic with respect to L. ludovicianus. These results show the utility of a comparative analysis for insights into the evolutionary dynamics of mtDNA tandem repeats.[Reviewing Editor: Martin Kreitman]     

Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages

Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l. elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l. elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted.     

High genetic diversity in the blue-listed British Columbia population of the purple martin maintained by multiple sources of immigrants

To assess genetic diversity in the blue-listed purple martin (Progne subis) population in British Columbia, we analysed mitochondrial control region sequences of 93 individuals from British Columbia and 121 individuals collected from seven localities of the western and eastern North American subspecies P. s. arboricola and P. s. subis, respectively. Of the 47 haplotypes we detected, 34 were found exclusively in western populations, and 12 were found only in eastern populations. The most common eastern haplotype (25) was also found in three nestlings in British Columbia and one in Washington. Another British Columbia nestling had a haplotype (35) that differed by a C to T transition from haplotype 25. Coalescent analysis indicated that these five nestlings are probably descendents of recent immigrants dispersing from east to the west, because populations were estimated to have diverged about 200,000–400,000 ybp, making ancestral polymorphism a less likely explanation. Maximum likelihood estimates of gene flow among all populations detected asymmetrical gene flow into British Columbia not only of rare migrants from the eastern subspecies in Alberta but also a substantial number of migrants from the adjacent Washington population, and progressively lower numbers from Oregon in an isolation-by distance pattern. The influx of migrants from different populations is consistent with the migrant-pool model of recolonization which has maintained high genetic diversity in the small recovering population in British Columbia. Thus, the risk to this population is not from genetic erosion or inbreeding following a severe population crash, but from demographic stochasticity and extinction in small populations.     

Taxonomy of the bean goose-pink-footed goose

The bean goose Anser fabalis and the pink-footed goose A. brachyrhynchus breed in the tundra and taiga zones of Eurasia and eastern Greenland, and the taxonomy of the group based on morphology has been controversial. We investigated the phylogenetic relationships within the bean goose–the pink-footed goose complex using mitochondrial control region sequences of 199 individuals collected from the breeding areas in the Palaearctic and Eastern Nearctic. We found three mitochondrial clades geographically distributed to (1) Greenland, Iceland and Svalbard (A. brachyrhynchus), (2) the eastern taiga zone (former subspecies A. fabalis middendorffii), and (3) the western taiga and the tundra zone (subspecies A. fabalis rossicus, serrirostris and fabalis). MtDNA phylogeny suggests that morphological affinities between the taxa, e.g. in the bill structure, result from convergent evolution due to adaptation to similar habitats. Although a latitudinal cline in morphology was observed, clear phylogenetic discontinuities exist in the taiga and tundra zones supporting a species status for brachyrhynchus and middendorffii.     

Synchronic east–west divergence in azure‐winged magpies (Cyanopica cyanus) and magpies (Pica pica)*

Morphometric and genetic analyses were performed to investigate the relationships between populations of the azure‐winged magpie (Cyanopica cyanus). In the morphometric analysis 193 specimens were included representing seven of the nine currently accepted subspecies. Among eight characters analysed, four showed significant differences between samples from Spain and Asia. In contrast, the Asian populations/subspecies are not differentiated morphologically except Cyanopica cyanus japonica. The genetic analysis was based on two mitochondrial sequences (control region, cytochromeb gene). The results are in accordance with the morphometric analysis, showing a clear distinction between birds from the western and eastern distribution ranges. The differentiation of C. c. japonica is not found at the sequence level. Both genetic and morphological data support species status of C. cyanus and Cyanopica cooki. The magpie (Pica pica) was included in the phylogenetic study for comparing intraspecific variation. As in C. cyanus, two clearly separated groups are found, one of them containing the far‐eastern populations (Pica pica jankowskii and Pica pica sericea) and the other the remaining subspecies studied. For both the azure‐winged magpie and the magpie the sequence data imply an east–west differentiation, probably caused by long lasting isolation that may have even started in the Pliocene or repeated expansions/restrictions of distribution ranges during the Pleistocene.     

Phylogeography of the Black-tailed Godwit Limosa limosa: substructuring revealed by mtDNA control region sequences

Black-tailed (Limosa limosa) and Hudsonian Godwits (L. haemastica) are sometimes described as a superspecies. The Black-tailed Godwit is further split into three subspecies on the basis of morphological differences (L. l. limosa, L. l. islandica and L. l. melanuroides). We studied variation in partial mtDNA control region sequences among Black-tailed and Hudsonian Godwits which showed 5% divergence. Black-tailed and Hudsonian Godwits were thus clearly differentiated and the separate species status for the two taxa is validated. All three subspecies described for the Black-tailed Godwit had unique haplotypes but the genetic distances were small (0.3–0.6%). Despite small genetic differences we could not detect any substantial gene flow between any of the subspecies as haplotypes were private to each subspecies. Thus, genetic variation within Black-tailed Godwits showed a clear geographic structure. We found a high proportion of rare private haplotypes in three fringe populations of the nominate subspecies of the Black-tailed Godwit (L. l. limosa) where godwits breed in low numbers, but no genetic variation at all in a sample from the Netherlands where godwits are abundant. This suggests that Dutch Godwits may have been affected by a founder effect.     

Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817)

The koala, Phascolarctos cinereus, is a geographically widespread species endemic to Australia, with three currently recognized subspecies: P.c. adustus, P.c. cinereus, and P.c. victor. Intraspecific variation in the mitochondrial DNA (mtDNA) control region was examined in over 200 animals from 16 representative populations throughout the species’ range. Eighteen different haplotypes were defined in the ≈ 860 bp mtDNA control region, as determined by heteroduplex analysis/temperature gradient gel electrophoresis (HDA/TGGE). Any single population typically possessed only one or two haplotypes yielding an average within-population haplotypic diversity of 0.180 ± 0.003, and nucleotide diversity of 0.16%. Overall, mtDNA control region sequence diversity between populations averaged 0.67%, and ranged from 0% to 1.56%. Nucleotide divergence between populations averaged 0.51%, and ranged from 0% to 1.53%. Neighbour-joining methods revealed limited phylogenetic distinction between geographically distant populations of koalas, and tentative support for a single evolutionarily significant unit (ESU). This is consistent with previous suggestions that the morphological differences formalized by subspecific taxonomy may be interpreted as clinal variation. Significant differentiation in mtDNA-haplotype frequencies between localities suggested that little gene flow currently exists among populations. When combined with microsatellite analysis, which has revealed substantial differentiation among koala populations, we conclude that the appropriate short-term management unit (MU) for koalas is the local population.     

Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F_ST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.     

Low Levels of Nucleotide Diversity in Crocodylus moreletii and Evidence of Hybridization with C. acutus

Examinations of both population genetic structure and the processes that lead to such structure in crocodilians have been initiated in several species in response to a call by the IUCN Crocodile Specialist Group. A recent study used microsatellite markers to characterize Morelet's crocodile (Crocodylus moreletii) populations in north-central Belize and presented evidence for isolation by distance. To further investigate this hypothesis, we sequenced a portion of the mitochondrial control region for representative animals after including samples from additional locales in Belize, Guatemala and Mexico. While there is limited evidence of subdivision involving other locales, we found that most of the differentiation among populations of C. moreletiican be attributed to animals collected from a single locale in Belize, Banana Bank Lagoon. Furthermore, mitochondrial DNA sequence analysis showed that animals from this and certain other locales display a haplotype characteristic of the American crocodile, C. acutus, rather than C. moreletii. We interpret this as evidence of hybridization between the two species and comment on how these new data have influenced our interpretation of previous findings. We also find very low levels of nucleotide diversity in C. moreletiihaplotypes and provide evidence for a low rate of substitution in the crocodilian mitochondrial control region. Finally, the conservation implications of these findings are discussed.     

A TEST OF THE GLACIAL REFUGIUM HYPOTHESIS USING PATTERNS OF MITOCHONDRIAL AND NUCLEAR DNA SEQUENCE VARIATION IN ROCK PTARMIGAN (LAGOPUS MUTUS)

The glacial refugium hypothesis (GRH) proposes that glaciers promoted differentiation and generation of intraspecific diversity by isolating populations in ice-free refugia. We tested three predictions of this hypothesis for the evolutionary divergence of rock ptarmigan (Lagopus mutus) during the Wisconsin glaciation of the late Pleistocene. To do this, we examined subspecies distributions, population genetic structure, and phylogenetic relationships in 26 populations across North America and the Bering Sea region. First, we analyzed sequence variation in the mitochondrial control region, in a nuclear intron (Gapdh), and in an internal transcribed spacer (ITS1). Control region sequences of 154 rock ptarmigan revealed strong population and phylogeographic structure. Variation in intron sequences of 114 rock ptarmigan also revealed significant population structure compatible with results for the control region. Rock ptarmigan were invariant for ITS1. Second, we show that five known Nearctic refugia and an Icelandic refugium are concordant with the current distribution of morphologically distinct subspecies; five of these six refugia are geographically concordant with the distribution of closely related control region haplotypes. Third, our estimates of the time since phylogenetic lineages diverged predated the last glacial maximum for all but two lineages. In addition, all lines of evidence suggest that two unknown refugia in the Bering Sea region supported rock ptarmigan during the Wisconsin glaciation. Overall, our results are most consistent with the hypothesis that isolated populations of rock ptarmigan diverged in multiple refugia during the Wisconsin and that geographic variation reflects patterns of recolonization of the Nearctic after the ice receded. The GRH may therefore offer the most plausible explanation for similar biogeographic patterns in a variety of Nearctic vertebrates.     

Comparison of genetic population structure between two cyprinids, <Emphasis Type="Italic">Hemigrammocypris rasborella</Emphasis> and <Emphasis Type="Italic">Pseudorasbora pumila</Emphasis> subsp., in the Ise Bay basin,central Honshu,Japan

Two small cyprinid fishes, Hemigrammocypris rasborella and Pseudorasbora pumila subsp. (sensu Nakamura 1963), inhabit similar habitats and often occur sympatrically in the Ise Bay basin, central Honshu Island, Japan. Their genetic population structures were revealed, using sequence data from the mitochondrial cytochrome b gene, and then compared. Hemigrammocypris rasborella populations in the Ise Bay area formed a monophyletic group that has been isolated from eastern (Tenryu River) and western (Lake Biwa–Yodo River) populations at least for several hundred thousand years. Pseudorasbora pumila subsp., endemic to the Ise Bay area, was estimated to have become isolated from its sister subspecies, P. p. pumila, about 5 million years ago. Both H. rasborella and P. pumila subsp. had centers of genetic diversity around the Okazaki Plain in the eastern part of the basin and showed trans-bay distribution of haplotypes or haplotype groups. Their common population structure was explained by geological features in the Ise Bay area, in which a large paleo-river system developed in regression periods, suggesting gene flow among populations of each species in the mid to lower reaches of the paleo-river. Based on the estimated expansion or divergence time, however, not all populations experienced gene flow during the Last Glacial. In contrast to the maintenance of high genetic diversity in H. rasborella, almost all populations of P. pumila subsp. have lost mitochondrial DNA genetic diversity. This implies that effective population size of P. pumila subsp. tended to be smaller, probably because of differences in reproductive ecology, even though the two species have been exposed to similar environmental changes. For conservation of the two species, genetic and adaptive differentiation among local populations should be considered, and attention should be paid to inbreeding depression, especially in P. pumila subsp. An erratum to this article can be found at     

Conservation genetics of the threatened horned grebe (<Emphasis Type="Italic">Podiceps auritus</Emphasis> L.) population of the Magdalen Islands,Québec

The horned grebe (Podiceps auritus) population of the Magdalen Islands in the St. Lawrence Gulf (Québec, Canada) has declined sharply over the last decades. It is the only breeding population of this species in eastern North America with nearest breeding populations being >2500 km apart in western North America and Europe, We used three types of genetic markers: mitochondrial (mt) DNA ND2 sequence, α-enolase intron sequence, and 25 amplified fragment length polymorphism loci (AFLPs) to quantify the genetic diversity within the Magdalen Island population and to assess its genetic distinctiveness relative to populations from western Canada (five sites) and Iceland (one site). The Magdalen Island population retained a comparable amount of genetic diversity to the average diversity observed across all populations in all three markers. Horned grebe mtDNA sequences formed a monophyletic group and nearly all haplotypes present in Québec were found elsewhere. In the ND2 fragment, populations partitioned into two groups corresponding to subspecies (Iceland versus North American sites) and more strongly in three groups according to geographic disjunctions (Iceland versus Québec versus western Canada). In contrast, there was no evidence of structure between sites in the α-enolase intron. In the AFLPs, Iceland showed the greatest level of differentiation, followed by the Québec and British Columbia populations. For conservation purposes, we suggest that the Magdalen Islands population should be recognized as a separate unit.     

Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae)

The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the Structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.     

Haplotype and ribotype diversity of Saxifraga cuneifolia s. l. (Saxifragaceae)

Saxifraga cuneifolia L. (sect. Gymnopera, Saxifragaceae) is a plant distributed in the main mountain ranges of southern Europe, from the eastern Pyrenees to the eastern Carpathian. Currently, two subspecies are recognized based on morphological characteristics: S. cuneifolia subsp. cuneifolia grows in the Maritime Alps and North Apennines and S. cuneifolia subsp. robusta is located in the remaining area of distribution. A more delicate form and a smaller number of flowers in S. cuneifolia subsp. cuneifolia are the morphological characteristics that differentiate this subspecies from the widespread S. cuneifolia subsp. robusta. To explore the genetic diversity and the subspecific geographic patterns of S. cuneifolia s. l. we conducted a molecular study of nuclear and plastid sequences. Samples of S. cuneifolia s. l. have been analysed throughout the distribution area of this species. Our results, based on nuclear (ITS) and plastid (rbcL, trnL–F, and psbA–trnH) markers, showed a genetic characterization of both subspecies presenting discriminant haplotypes and ribotypes that confirm the current subspecific systematics.     

Intraspecific Phylogeography of Red Squirrels (Tamiasciurus hudsonicus) in the Central Rocky Mountain Region of North America

We used variation in a portion of the mitochondrial DNA control region to examine phylogeography of Tamiasciurus hudsonicus, a boreal-adapted small mammal in the central Rocky Mountain region. AMOVA revealed that 65.66% of genetic diversity was attributable to variation within populations, 16.93% to variation among populations on different mountain ranges, and 17.41% to variation among populations within mountain ranges. Nested clade analysis revealed two major clades that likely diverged in allopatry during the Pleistocene: a southern clade from southern Colorado and a northern clade comprising northern Colorado, Wyoming, eastern Utah, and eastern Idaho. Historically restricted gene flow as a result of geographic barriers was indicated between populations on opposite sides of the Green River and Wyoming Basin and among populations in eastern Wyoming. In some instances genetic structure indicated isolation by distance.     

Experimental studies of adaptation in Clarkia xantiana. III. Phenotypic selection across a subspecies border

Sister taxa with distinct phenotypes often occupy contrasting environments in parapatric ranges, yet we generally do not know whether trait divergence reflects spatially varying selection. We conducted a reciprocal transplant experiment to test whether selection favors “native phenotypes” in two subspecies of Clarkia xantiana (Onagraceae), an annual plant in California. For four quantitative traits that differ between subspecies, we estimated phenotypic selection in subspecies’ exclusive ranges and their contact zone in two consecutive years. We predicted that in the arid, pollinator‐scarce eastern region, selection favors phenotypes of the native subspecies parviflora: small leaves, slow leaf growth, early flowering, and diminutive flowers. In the wetter, pollinator‐rich, western range of subspecies xantiana, we expected selection for opposite phenotypes. We investigated pollinator contributions to selection by comparing naturally pollinated and pollen‐supplemented individuals. For reproductive traits and for subspecies xantiana, selection generally matched expectations. The contact zone sometimes showed distinctive selection, and in ssp. parviflora selection sometimes favored nonnative phenotypes. Pollinators influenced selection on flowering time but not on flower size. Little temporal variation in selection occurred, possibly because of plastic trait responses across years. Though there were exceptions and some causes of selection remain obscure, phenotypic differentiation between subspecies appears to reflect spatially variable selection.     

Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe

After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human‐induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present‐day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting‐associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.