Isolation and characterization of microsatellite markers in the gecko Gekko swinhonis and cross‐species amplification in other gekkonid species

Gekko swinhonis is a gekkonid lizard endemic to China, inhabiting Loess Plateau, Huabei Plain, Huanghuai Plain and areas north of the Yangtze River. We characterized 21 dinucleotide microsatellite loci from an AC/AG‐enriched genomic library of G. swinhonis. The number of alleles per locus ranged from eight to 24 and the observed and expected heterozygosities ranged from 0.160 to 0.834 and from 0.584 to 0.917, respectively. We also tested the utility of these loci in other Gekko and Hemidactylus species; many of these loci can be cross‐amplified.     

The incomplete history of mitochondrial lineages between two rockfishes, Sebastes longispinis and Sebastes hubbsi (Scorpaeniformes: Scorpaenidae)

The genetic divergence between two closely related rockfishes, Sebastes longispinis and Sebastes hubbsi, was inferred from both mitochondrial DNA (mtDNA) sequence variations and amplified fragment length polymorphism (AFLP) markers. The two species were placed into two distinct clades in a neighbour-joining tree based on the AFLP data, clearly indicating that they represented separate species. Although this evidence, together with a previous morphological study, revealed clear differences between the two species, no obvious clustering of haplotypes by species was detected in the minimum spanning network inferred from sequence variations in the mtDNA control region (c. 500 base pairs). In fact, the significant Φ(ST) estimates indicated only a restriction of gene flow between the two species. Uncorrected pairwise sequence differences in mtDNA between two species were small (1·8% at maximum, on the lower end of the range of control region divergence between previously studied sister species pairs), suggesting their speciation event as having been fairly recent. The incongruent results of AFLP and mtDNA phylogenies suggested incomplete lineage sorting and introgression of mtDNA in the course of the evolution of the two species. Differences in their main distributional ranges and the small level of sequence divergence in mtDNA suggests that speciation and dispersal may have been associated with glacio-eustatic sea level fluctuations between the Japanese Archipelago and the Korean Peninsula during the past 0·4 million years.     

Phylogeography of a salmonid fish,masu salmon Oncorhynchus masou subspecies-complex,with disjunct distributions across the temperate northern Pacific

1. Climate oscillations during the Pleistocene had profound effects on the evolutionary history of freshwater fishes now distributed across northern temperate regions. The extent of continental glaciation on the western side of the North Pacific, including areas of East Asia, was more limited as compared with regions of North America, Europe and high-latitude areas of the North Pacific. Therefore, the effects of climate oscillations might have influenced species in dissimilar ways depending on the species' distribution.
2. We used mitochondrial DNA (mtDNA) and microsatellite DNA (msDNA) markers to clarify the evolutionary history of masu salmon Oncorhynchus masou subspecies-complex (family Salmonidae) distributed in historically non-glaciated regions in the western North Pacific.
3. No marked regional or subspecies-specific mtDNA haplotype associations were recognised, except for O. masou subsp., a lacustrine form endemic to Lake Biwa, an ancient lake in central Honshu. The landlocked subspecies O. masou formosanus, with a disjunct distribution on Taiwan Island, exhibited no diagnostic population features differing from the other subspecies, in either mtDNA or msDNA markers. Mismatch distribution and Bayesian skyline plot analyses indicated relatively recent range expansion and rapid population growth for masu salmon during the last glacial period (c. 0.1–0.15 Ma).
4. Contrary to the mtDNA genealogy, Bayesian clustering using msDNA showed two main genetic clusters, mainly northern populations of the subspecies O. m. masou and populations of the subspecies O. m. ishikawae in southern areas of the Japanese Archipelago. Notably, O. m. formosanus on Taiwan Island was included in the O. m. masou group, and O. masou subsp. was included in the O. m. ishikawae group.
5. Our results suggest that the masu salmon subspecies-complex in historically non-glaciated regions of the Temperate Northern Pacific is characterised by weak population structuring and shallow genetic differentiation among the subspecies, except for O. masou subsp. owing to its long isolation in Lake Biwa. Incomplete lineage sorting and historical inter-subspecies hybridisation, possibly due to secondary contact, seem to be plausible explanations for discrepancies in the mitochondrial DNA genealogy and nuclear DNA genetic structure.

     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio

Three major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near-coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh- and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the paleohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid-Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern ('Cottus koshewnikowi') bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.     

Not an ancient relic: the endemic Livistona palms of arid central Australia could have been introduced by humans

Livistona mariae is an endemic palm localized in arid central Australia. This species is separated by about 1000 km from its congener L. rigida, which grows distantly in the Roper River and Nicholson-Gregory River catchments in northern Australia. Such an isolated distribution of L. mariae has been assumed to have resulted from contraction of ancestral populations as Australia aridified from the Mid-Miocene (ca 15 Ma). To test this hypothesis at the population level, we examined the genetic relationships among 14 populations of L. mariae and L. rigida using eight nuclear microsatellite loci. Our population tree and Bayesian clustering revealed that these populations comprised two genetically distinct groups that did not correspond to the current classification at species rank, and L. mariae showed closest affinity with L. rigida from Roper River. Furthermore, coalescent divergence-time estimations suggested that the disjunction between the northern populations (within L. rigida) could have originated by intermittent colonization along an ancient river that has been drowned repeatedly by marine transgression. During that time, L. mariae populations could have been established by opportunistic immigrants from Roper River about 15 000 years ago, concurrently with the settlement of indigenous Australians in central Australia, who are thus plausible vectors. Thus, our results rule out the ancient relic hypothesis for the origin of L. mariae.     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Intraspecific genetic diversity of the endemic freshwater crab Candidiopotamon rathbunae (Decapoda, Brachyura, Potamidae) reflects five million years of the geological history of Taiwan

Aim Candidiopotamon rathbunae (Crustacea: Brachyura: Potamidae) is a freshwater crab endemic to Taiwan, with a distribution covering almost the entire island. Crab populations from different river systems cannot be distinguished morphologically. In this study, we investigate the phylogeography of C. rathbunae from 18 of the main river systems of Taiwan, in order to reveal geographical differentiation and cryptic endemism. We used specimens of two congeners (C. okinawense and C. kumejimense) and the closely related Amamiku amamensis from the Ryukyu Islands as outgroups. Location Taiwan, with the Ryukyu Islands (Japan) as the outgroup locality. Methods Mitochondrial DNA sequences encoding 553 basepairs of the large subunit rRNA (16S rRNA) gene were obtained from 96 specimens throughout Taiwan and the Ryukyus. We compared these sequences by means of phylogenetic analyses (minimum evolution, maximum likelihood, maximum parsimony, and a genealogical parsimony network) and molecular‐clock time estimates. Results The estimated timing of the corresponding separations clearly correlates with geological events during the Penglai Orogeny of Taiwan (c. 5 Ma) following the collision of the Philippine Sea plate with the Eurasian continental plate. A deep split of 6.29% sequence divergence was found between the eastern clade (S, SE, and E groups) and the western clade (NW, W, and SW groups) of C. rathbunae. Separation of these groups reflects the isolating effect of the uplift of the Taiwan Central Range (c. 5 Ma). The separation of the SW group from the W group, and of the E group from the SE group can also be explained by geological events during the Taiwanese orogeny, the estimated geological timing being in close accordance with our molecular dating. Main conclusions According to the molecular results, the ancestral Candidiopotamon was among the earliest non‐marine colonizers of Taiwan, settling on this island no later than the early Pliocene. Our molecular data reveal that C. rathbunae can be subdivided into six groups in accordance with geography.     

Migration patterns of Gentiana crassicaulis,an alpine gentian endemic to the Himalaya–Hengduan Mountains

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.     

Multilocus analysis of nucleotide variation in Drosophila madeirensis, an endemic species of the Laurisilva forest in Madeira

Drosophila madeirensis is an endemic species of Madeira that inhabits the island Laurisilva forest. Nucleotide variation in D. madeirensis is analysed in six genomic regions and compared to that previously reported for the same regions in Drosophila subobscura, an abundant species in the Palearctic region that is closely related to D. madeirensis. The gene regions analysed are distributed along the O₃ inversion. The O₃ arrangement is monomorphic in D. madeirensis, and it was present in ancestral populations of D. subobscura but went extinct in this species after the origin of the derived O_ST and O₃₊₄ arrangements. Levels of nucleotide polymorphism in D. madeirensis are similar to those present in the O_ST and O₃₊₄ arrangements of D. subobscura, and the frequency spectrum is skewed towards rare variants. Purifying selection against deleterious nonsynonymous mutations is less effective in D. madeirensis. Although D. madeirensis and D. subobscura coexist at present in Madeira, no clear evidence of introgression was detected in the studied regions.     

A peninsula as an island: multiple forms of evidence for overwater colonization of Baja California by the gartersnake Thamnophis validus

The recent shift toward dispersal rather than vicariant explanations of disjunct distributions has been driven by the use of molecular data to estimate divergence dates between lineages. However, other kinds of evidence can also be critical in evaluating such biogeographic hypotheses. In the present study, we used a multifaceted approach employing diverse analyses of mitochondrial DNA sequences to assess explanations for the disjunct distribution of the gartersnake Thamnophis validus. The occurrence of this species in the Cape Region of the Baja California peninsula, isolated from mainland populations that occur along the west coast of Mexico, might be explained by: (1) separation of the peninsula from mainland Mexico through rifting 4–8 Mya (tectonic vicariance); (2) fragmentation of the range of this semi‐aquatic species because of post‐Pleistocene aridification (vicariance by aridification); (3) natural overwater dispersal across the Gulf of California; or (4) human introduction. Divergence dating indicates that peninsular and mainland T. validus separated from each other within the last 0.5 Myr, thus rejecting tectonic vicariance. In addition, the estimated closest mainland relatives of peninsular snakes are found farther north than expected under this hypothesis. Three findings argue against vicariance by aridification: (1) peninsular snakes and their closest mainland relatives are more genetically similar than predicted; (2) the location of closest mainland relatives is farther south than predicted; and (3) the species is absent from areas where one might expect to find relict populations. Taken together, refutation of the vicariance hypotheses and the fact that the estimated closest mainland relatives are found almost directly across the Gulf from the Cape Region supports some form of overwater colonization. Various additional arguments suggest that natural dispersal is more likely than human introduction. The present study emphasizes the need for multiple kinds of evidence, beyond divergence dates, to discriminate among hypotheses and to provide independent sources of corroboration or refutation in historical biogeography. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 409–424.     

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.     

Genetic structure, phylogeography and demography of two ground-beetle species endemic to the Tenerife laurel forest (Canary Islands)

The volcanic island of Tenerife (Canary archipelago) was formerly covered at 600-1200 m above sea level on most of its northern side by a cloud forest holding much of the endemic insect fauna. In the most significant surviving patches of this laurel forest at the eastern and western tips of the island occur two forest-specialist, closely related species of Eutrichopus (Coleoptera, Carabidae); here we present data on mitochondrial DNA variation among populations of these species. In total, 116 individuals from 16 localities were sampled and a 638 bp fragment of the cytochrome oxidase subunit II gene was sequenced, obtaining evidence for two distinct evolutionary lineages, in accordance with morphological and biogeographical data. Volcanic events at approximately 0.7 Ma might be responsible for vicariance and the fragmentation of the geographical range of an ancestral species, causing the establishment of two matrilineal lineages. Using nested clade and historical demography analyses we infer past cycles of demographic bottlenecks followed by population expansion, mostly in agreement with the geological time scale of volcanic events. Recent trends, however, refer to fragmentation of the cloud forest due to human intervention.     

The dynamics of natural selection and vicariance in the Dominican anole: patterns of within-island molecular and morphological divergence

The larger islands of the Lesser Antilles are ecologically and geologically complex and are inhabited by single, but morphologically variable, Anolis species. Although earlier work has indicated that a large part of the morphological variation in Anolis oculatus from Dominica can be attributed to selection, a history of recurrent volcanic activity over the last few million years suggests that vicariance may have also played a significant role. We report a study of variation in the cytochrome b gene of mitochondrial DNA across the island to address this issue. We uncovered a very high degree of polymorphism, with an overall gene diversity of 0.97 and a nucleotide diversity of 0.04. Sequences, on average, differ by 3.82% and the maximum pairwise divergence (corrected for multiple hits) is 9.29%. Most haplotypes are restricted to single localities (a pattern not changed by increasing the sample size). Phylogenetic analysis revealed the presence of two distinct lineages on the island with strong phylogeographic structure. One of these is geographically restricted to a relatively small part of the central Caribbean coast. Sublineages were also discernible within the other more widely distributed lineage, but resolution within and support for these sublineages was poor. The phylogeographic pattern is not congruent with generalized body shape and scalation, but is significantly correlated with color pattern. Even when correcting for this lineage effect with partial Matrix correspondence tests, the relationship between color pattern and vegetation is reaffirmed, suggesting that although both vicariance and selection have played a role in the morphological differentiation of this species, selection for current environmental conditions has been more important. We discuss the causes of the phylogeographic structure in light of the volcanic history of the island and highlight the exceptional instance of congruence between all morphological character systems and lineage boundaries, which occurs at the transition between the northern and southern Caribbean ecotypes.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Origin and diversification of Hibiscus glaber, species endemic to the oceanic Bonin Islands, revealed by chloroplast DNA polymorphism

Abstract Two woody Hibiscus species co-occur in the Bonin Islands of the northwestern Pacific Ocean: Hibiscus glaber Matsum. is endemic to the islands, and its putative ancestral species, Hibiscus tiliaceus L., is widely distributed in coastal areas of the tropics and subtropics. To infer isolating mechanisms that led to speciation of H. glaber and the processes that resulted in co-occurrence of the two closely related species on the Bonin Islands, we conducted molecular phylogenetic analyses on chloroplast DNA (cpDNA) sequences. Materials collected from a wide area of the Pacific and Indian Oceans were used, and two closely related species, Hibiscus hamabo Siebold Zucc. and Hibiscus macrophyllus Roxb., were also included in the analyses. The constructed tree suggested that H. glaber has been derived from H. tiliaceus, and that most of the modern Bonin populations of H. tiliaceus did not share most recent ancestry with H. glaber. Geographic isolation appears to be the most important mechanism in the speciation of H. glaber. The co-occurrence of the two species can be attributed to multiple migrations of different lineages into the islands. While a wide and overlapping geographical distribution of haplotypes was found in H. tiliaceus, localized geographical distribution of haplotypes was detected in H. glaber. It is hypothesized that a shift to inland habitats may have affected the mode of seed dispersal from ocean currents to gravity and hence resulted in geographical structuring of H. glaber haplotypes.     

The phylogeographical and management implications of genetic population structure in the imperiled snuffbox mussel, Epioblasma triquetra (Bivalvia: Unionidae)

Seven populations of the imperiled snuffbox mussel, Epioblasma triquetra , were sampled from across the central basin of North America. Samples were genotyped using 15 microsatellite DNA loci, and maternal history was inferred using mitochondrial DNA (mtDNA) cytochrome  c oxidase subunit-I (COI) sequences. Populations in the Clinch and St Francis rivers were quite distinct in their mtDNA. The population in the St Francis River had a unique, fixed haplotype. Among a suite of haplotypes, the population in the Clinch River had two unique haplotypes of common ancestry. The other populations were dominated by a common haplotype, which also occurred in the Clinch River population. Analysis of DNA microsatellites revealed much greater divergences and showed significant genetic structure between populations in the formerly glaciated regions. Divergence has occurred between the populations, as evidenced by moderate to high fixation indices ( F _ST and R _ST values) and nearly perfect assignment tests. These results indicate the occurrence of three glacial refugia for E. triquetra : the Tennessee River, rivers south of the Ozark Crest, and the lower Ohio River drainage near the confluence with the Mississippi. Populations in the lower Ohio River were likely to be responsible for the postglacial reinvasion into formerly glaciated regions, and into the upper Tennessee River drainage. The population of the St Francis River may constitute a distinct taxonomic entity. Conservation efforts, if necessary for this imperiled species, should not mix populations.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 371–384.     

The contemporary genetic pattern of European moose is shaped by postglacial recolonization,bottlenecks, and the geographical barrier of the Baltic Sea

To investigate genetic diversity and the population structure of the European moose (Alces alces), we analyzed 14 microsatellite loci for 694 samples collected across 16 localities. The highest genetic diversity was detected in Belarus and Russia and the lowest was found in Scandinavia. Two major genetic clusters existed, Scandinavian and continental, and some further spatial structure was detected. There was high concordance between the spatial distribution of microsatellite clusters analyzed in the present study and previously recognized mitochondrial DNA clades of moose. The split of genetic lineages calculated using approximate Bayesian computation (ABC) occurred at the beginning of the Last Glacial Maximum: approximately 29 000 and 28 000 years BP. A range‐wide bottleneck detected by ABC took place 1800–1200 years BP, although a more recent decline in moose numbers was also documented in the 18th to early 20th Century. Genetic differentiation in European moose increased with geographical distance, and the Baltic Sea appeared to be a barrier to gene flow. We conclude that isolation in different glacial refugia, postglacial colonization, and declines of range and numbers in Holocene shaped the present pattern of genetic diversity of European moose. Based on genetic divergence and a lack of apparent gene flow, the contemporary Scandinavian and continental subpopulations should be treated as separate management units.