Mitochondrial DNA data imply a stepping‐stone colonization of Beringia by arctic warbler Phylloscopus borealis

Arctic warbler Phylloscopus borealis is one of several high‐latitude Passerines which are widely distributed across one northern continent but restricted to the Beringian part of the other. Most species with such asymmetric intercontinental ranges are monomorphic across Beringia, suggesting either recent colonization of the second continent or considerable gene flow across the Bering Strait. Arctic warbler is the only migratory species in this group that has three different subspecies in Beringia: Ph. b. borealis (Scandinavia to western Beringia, south to Mongolia), Ph. b. xanthodryas (Japan, Sakhalin, Kamchatka, western Beringia), and Ph. b. kennicotti (Alaska). This polymorphism may indicate that Arctic warbler has a unique and complex phylogeographic history that differs significantly from other species with similar ranges. Our analyses of complete mtDNA ND2 sequences of 88 Arctic warblers collected across the species range showed that the clade comprised of birds breeding on Sakhalin Island and Kamchatka Peninsula diverged from the Palearctic/Beringian clade by 3.8% in ND2 sequence. Beringian birds formed a recently derived clade embedded within the Palearctic clade. Nucleotide diversity declined sharply eastward from Palearctic to western Beringia and then to eastern Beringia. Our data provided no support for currently recognized subspecies. They suggested that the barrier at the western edge of Beringia was crossed by Arctic warbler earlier than the Bering Strait resulting in a stepping‐stone colonization of Beringia by this species. Gene flow appears to be restricted across the western border of Beringia but not the Bering Strait.     

The extreme Beringian/Atlantic disjunction in Saxifraga rivularis (Saxifragaceae) has formed at least twice

Aim The oceanic Saxifraga rivularis L. presents one of the most extreme disjunctions known in the arctic flora: it has a small amphi‐Beringian range and a larger amphi‐Atlantic one. It was recently suggested to have had a single allopolyploid origin in Beringia at least one glacial cycle ago, followed by gradual expansion in a more humid period and differentiation into two allopatric subspecies (the Atlantic ssp. rivularis and the Beringian ssp. arctolitoralis). Here we explore the history of its extreme disjunction. Location The amphi‐Beringian and northern amphi‐Atlantic regions. Methods We obtained amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences from 36 populations (287 individuals) and 13 populations (15 individuals), respectively. The data were analysed using principal coordinates analyses, Bayesian clustering methods, and analyses of molecular variance. Results Two distinctly divergent AFLP groups were observed, corresponding to the two described subspecies, but, surprisingly, four of the West Atlantic populations belonged to the supposedly Beringian endemic ssp. arctolitoralis. This was confirmed by re‐examination of their morphological characteristics. The overall AFLP diversity in the species was low (26.4% polymorphic markers), and there was no variation in the five investigated chloroplast DNA (cpDNA) regions. There was little geographic structuring of the AFLP diversity within each subspecies, even across the extreme disjunction in ssp. arctolitoralis, across the Bering Sea, and across the Atlantic Ocean, except that most plants from the arctic Svalbard archipelago formed a separate genetic group with relatively high diversity. Main conclusions The extreme disjunction in S. rivularis has evidently formed at least twice. The first expansion from Beringia was followed by allopatric differentiation into one Beringian and one Atlantic subspecies, which are distinctly divergent at AFLP loci but still harbour identical cpDNA haplotypes, suggesting that the expansion was quite recent but before the last glaciation. The next expansion from Beringia probably occurred by means of several long‐distance dispersals in the current interglacial, resulting in the colonization of the western Atlantic region by ssp. arctolitoralis. The poor geographic structuring within each subspecies suggests frequent long‐distance dispersals from two main Weichselian refugia, one Beringian and one western‐central European, but it is possible that the genetic group in Svalbard originates from an additional refugium.     

Divergence,gene flow,and speciation in eight lineages of trans‐Beringian birds

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (F_ST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.     

Flyway structure in the circumpolar greater white‐fronted goose

Dispersal and migratory behavior are influential factors in determining how genetic diversity is distributed across the landscape. In migratory species, genetic structure can be promoted via several mechanisms including fidelity to distinct migratory routes. Particularly within North America, waterfowl management units have been delineated according to distinct longitudinal migratory flyways supported by banding data and other direct evidence. The greater white‐fronted goose (Anser albifrons) is a migratory waterfowl species with a largely circumpolar distribution consisting of up to six subspecies roughly corresponding to phenotypic variation. We examined the rangewide population genetic structure of greater white‐fronted geese using mtDNA control region sequence data and microsatellite loci from 23 locales across North America and Eurasia. We found significant differentiation in mtDNA between sampling locales with flyway delineation explaining a significant portion of the observed genetic variation (~12%). This is concordant with band recovery data which shows little interflyway or intercontinental movements. However, microsatellite loci revealed little genetic structure suggesting a panmictic population across most of the Arctic. As with many high‐latitude species, Beringia appears to have played a role in the diversification of this species. A common Beringian origin of North America and Asian populations and a recent divergence could at least partly explain the general lack of structure at nuclear markers. Further, our results do not provide strong support for the various taxonomic proposals for this species except for supporting the distinctness of two isolated breeding populations within Cook Inlet, Alaska (A. a. elgasi) and Greenland (A. a. flavirostris), consistent with their subspecies status.     

Molecular genetic evidence for the post-Pleistocene divergence of populations of the arctic-alpine ground beetle Amara alpina (Paykull) (Coleoptera: Carabidae)

Aim This study examines the hypothesis that the biogeographic history of a species is reflected in the distribution of molecular genetic diversity and the phylogenies of extant populations. Location Populations of arctic-alpine ground beetle Amara alpina were analysed from Beringia (Alaska and northernmost British Columbia), the Hudson Bay region, the northern Appalachian Mountains, and the central Rocky Mountains of North America. Methods Mitochondrial restriction site variation of specimens from twenty-two populations were assayed by using radioactively labelled mtDNA to probe Southern membranes containing restriction enzyme digested total DNA. Restriction sites were mapped and genetic distances were calculated by pairwise comparison of presence and absence of restriction sites. Genetic distances were used in a molecular analysis of variance and to construct a minimal spanning tree. Parsimony methods were used to investigate the phylogenetic relationships between the haplotypes. These results were compared to an existing model for postglacial dispersal based on fossil and modern occurrences of arctic-alpine beetles. Results Among the twenty-two populations, fifteen haplotypes were detected. Genetic variation within each of the four regions corresponded to that expected from the palaeontologically based model. Beringian populations were the most genetically diverse. In contrast, no restriction site variation was observed in populations from the Hudson Bay region. Intermediate amounts of variation were observed in alpine populations of the Rocky and Appalachian Mountains. Maximum parsimony and cluster analysis provide evidence that at least two ancestral haplotypes existed in the Southern refugium from which the Rocky and the Appalachian Mountains populations were founded. Main conclusions The genetic results are generally consistent with the palaeontologically based model. The diversity of Beringian populations is consistent with this region having been continuously inhabited by Amara alpina throughout the Pleistocene. The Hudson Bay region was not deglaciated until about 6000 years, and its populations have no restriction site variation. The molecular genetic data support the interpretation that the Hudson Bay region was colonized from Beringia based on the occurrence of the same haplotype in both regions.     

Genetic consequences of glacial survival: the late Quaternary history of balsam poplar (Populus balsamifera L.) in North America

Aim Beringia, the unglaciated region encompassing the former Bering land bridge, as well as the land between the Lena and Mackenzie rivers, is recognized as an important refugium for arctic plants during the last ice age. Compelling palaeobotanical evidence also supports the presence of small populations of boreal trees within Beringia during the Last Glacial Maximum. The occurrence of balsam poplar (Populus balsamifera) in Beringia provides a unique opportunity to assess the implications of persistence in a refugium on present‐day genetic diversity for this boreal tree species. Location North America. Methods We sequenced three variable non‐coding regions of the chloroplast genome (cpDNA) from 40 widely distributed populations of balsam poplar across its North American range. We assessed patterns of genetic diversity, geographic structure and historical demography between glaciated and unglaciated regions of the balsam poplar’s range. We also utilized a coalescent model to test for divergence between regions. Results Levels of genetic diversity were consistently greater for populations at the southern margin (θ_W = 0.00122) than in the central (θ_W = 0.00086) or northern (θ_W = 0.00034) regions of the current distribution of balsam poplar, and diversity decreased with increasing latitude (R² = 0.49, P < 0.01). We detected low, but significant, structure (F_CT = 0.05, P = 0.05), among regions of P. balsamifera’s distribution. The cpDNA genealogy was shallow, however, showing an absence of highly differentiated chloroplast haplotypes. Coalescent analyses supported a model of divergence between the southern ice margin and the northern unglaciated region of balsam poplar’s distribution, but analyses of other regional comparisons did not converge. Main conclusions The palaeobotanical record supports the presence of a Beringian refugium for balsam poplar, but we were unable to definitively identify the presence of known refugial populations based on genetic data alone. Balsam poplar populations from Beringia are not a significant reservoir of cpDNA diversity today. Unique alleles that may have been present in the small, isolated populations that survived within Beringia were probably lost through genetic drift or swamped by post‐glacial, northward migration from populations south of the ice sheets.     

Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice‐free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross‐species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south‐central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.     

Repeatedly out of Beringia: Cassiope tetragona embraces the Arctic

Aim Eric Hultén hypothesized that most arctic plants initially radiated from Beringia in the Late Tertiary and persisted in this unglaciated area during the Pleistocene glaciations, while their distribution ranges were repeatedly fragmented and reformed elsewhere. Whereas taxonomic and fossil evidence suggest that Cassiope tetragona originated in Beringia and expanded into the circumarctic area before the onset of the glaciations, lack of chloroplast DNA (cpDNA) variation may suggest that colonization was more recent. We address these contradictory scenarios using high‐resolution nuclear markers. Location Circumpolar Arctic. Methods The main analysis was by amplified fragment‐length polymorphism (AFLP), while sequences of chloroplast DNA verified the use of Cassiope mertensiana as an outgroup for C. tetragona. Data were analysed using Bayesian clustering, principal coordinates analyses, parsimony and neighbour‐joining, and measures of diversity and differentiation were calculated. Results The circumpolar C. tetragona ssp. tetragona was well separated from the North American C. tetragona ssp. saximontana. The genetic structure in ssp. tetragona showed a strong east–west trend, with the Beringian populations in an intermediate position. The highest level of diversity was in Beringia, while the strongest differentiation in the data set was found between the populations from the Siberian Arctic west of Beringia and the remainder. Main conclusions The results are consistent with a Beringian origin of the species, but the levels and geographical patterns of differentiation and gene diversity suggest that the latest expansion from Beringia into the circumarctic was recent, possibly during the current interglacial. The results are in accordance with a recent leading‐edge mode of colonization, particularly towards the east throughout Canada/Greenland and across the North Atlantic into Scandinavia and Svalbard. As fossils demonstrate the presence of the species in North Greenland 2.5–2.0 Ma, as well as in the previous interglacial, we conclude that C. tetragona expanded eastwards from Beringia several times and that the earlier emigrants of this woody species became extinct. The last major westward expansion from Beringia seems older, and the data suggest a separate Siberian refugium during at least one glaciation.     

Polymorphisms in the Extracellular Region of Dopamine Receptor D4 Within and Among Avian Orders

Polymorphisms in the dopamine receptor D4 gene (DRD4) have been widely investigated to assess their correlation with variations in animal behavior. We precisely examined polymorphisms in the extracellular region of DRD4 in 75 avian species belonging to 16 orders and detected high degrees of polymorphism at inter- and intraordinal levels. The existence of a variable number of proline repeats (2 to 12 times) in the extracellular region was a common feature in all Neognathae, and a strong codon bias at synonymous sites was found among Passeriformes, Galliformes, and other non-passerine Neoaves. Furthermore, significantly higher values of the pairwise disparity index were detected in Passeriformes, suggesting either a substantial difference in the evolutionary processes or a higher level of mutation rate in the passerine clade. The differences in both codon bias and other genetic parameters among avian taxa would be explained by different levels of selective pressure on the extracellular region of DRD4. Our study suggested that different conformations determined in a sequence-dependent manner at the extracellular region could be one of the key factors affecting the efficiency and accuracy of DRD4 expression. Our findings further imply a possibility that behavioral diversity, which would be important during the processes of adaptive radiation, may be enhanced by the selection acting on indels or single-nucleotide substitutions in the extracellular region of DRD4.     

Late Pleistocene beetle faunas of Beringia: where east met west

Aim   To examine the issue of Beringian steppe-tundra from an entomological standpoint, using fossil beetle data collected from late Pleistocene sites.
Location   North-eastern Siberia (Western Beringia), the Bering Land Bridge (Central Beringia), and Alaska and the Yukon Territory (Eastern Beringia).
Methods   Analysis of habitat preferences of beetle species found in fossil assemblages, leading to classification of major habitat types characterized by the faunal assemblages.
Results   Fossil beetle assemblages indicative of steppe-tundra are found mainly in the interior regions of Eastern Beringia, whereas these assemblages dominate nearly all late Pleistocene fossil sites in Western Beringia. Eastern Beringian faunas contain a much larger proportion of mesic to hygrophilous species and very few arid-habitat species. In contrast to this, the habitat requirements of the Western Beringian faunas are more evenly spread across the moisture spectrum.
Main conclusions   The taxonomic patterns of the two sets of fossil assemblages are remarkably different. Eastern Beringian faunal assemblages contain substantial numbers of mesic tundra and riparian rove beetles (Staphylinidae); this element is almost entirely lacking in the Western Beringian fossil assemblages. Taphonomic bias tends to overemphasize moisture-loving species at the expense of dry, upland species in the fossil record. Both Western and Eastern Beringian landscapes undoubtedly contained mosaics of habitats ranging from dry uplands (steppe-tundra) through mesic tundra to bogs and riparian corridors.     

Comparative Phylogeography Highlights the Double-Edged Sword of Climate Change Faced by Arctic- and Alpine-Adapted Mammals

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.     

Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia

Repeated glacial events during the Pleistocene fragmented and displaced populations throughout the northern continents. Different models of the effects of these climate-driven events predict distinct phylogeographic and population genetic outcomes for high-latitude faunas. The role of glaciations in (i) promoting intraspecific genetic differentiation and (ii) influencing genetic diversity was tested within a phylogeographic framework using the rodent Microtus oeconomus. The spatial focus for the study was Beringia, which spans eastern Siberia and northwestern North America, and was a continental crossroads and potential high arctic refugium during glaciations. Variation in mitochondrial DNA (cytochrome b and control region; 214 individuals) and nuclear DNA (ALDH1 intron; 63 individuals) was investigated across the Beringian region. Close genetic relationships among populations on either side of the Bering Strait are consistent with a history of periodic land connections between North America and Asia. A genetic discontinuity observed in western Beringia between members of a Central Asian clade and a Beringian clade is geographically congruent with glacial advances and with phylogeographic discontinuities identified in other organisms. Divergent island populations in southern Alaska were probably initially isolated by glacial vicariance, but subsequent differentiation has resulted from insularity. Tests of the genetic effects of postglacial colonization were largely consistent with expansion accompanied by founder effect bottlenecking, which yields reduced diversity in populations from recently deglaciated areas. Evidence that populations in the Beringian clade share a history of expansion from a low-diversity ancestral population suggests that Beringia was colonized by a small founder population from central Asia, which subsequently expanded in isolation.     

MITOCHONDRIAL DNA HOMOGENEITY IN THE PHENOTYPICALLY DIVERSE REDPOLL FINCH COMPLEX (AVES: CARDUELINAE: CARDUELIS FLAMMEA-HORNEMANNI)

Breeding redpoll finches (Aves: Carduelinae) show extensive plumage and size variability and, in many cases, a plumage polymorphism that is not related to age or sex. This has been ascribed to extreme phenotypic variation within a single taxon or to moderate variability within distinct taxa coupled with hybridization. The predominant view favors the recognition of two largely sympatric species: Carduelis flammea, comprised of four well-marked subspecies—flammea, cabaret, islandica, and rostrata; and C. hornemanni, comprised of two subspecies—hornemanni and exilipes. We studied representative samples of these putative subspecies (except islandica) for variation in mitochondrial DNA (mtDNA). Using 20 informative restriction enzymes that recognized 124 sites (642 base pairs [bp] of sequence or ≈ 3.7% of the molecule), we identified 17 RFLP haplotypes in the 31 individuals surveyed. The haplotypes formed a simple phylogenetic network with most clones diverging by a single site difference from a common haplotype found in almost half of the individuals. Within populations and taxa, levels of mtDNA diversity were similar to those observed in other avian species. The pattern of mtDNA divergence among populations was statistically unrelated to their geographic or traditional taxonomic relationships, and the estimated distance between the two traditionally recognized species was very small relative to those typically observed among avian sister species.     

Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds

Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.     

Niche divergence promotes rapid diversification of East African sky island white‐eyes (Aves: Zosteropidae)

The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species‐rich white‐eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1–2.5 Ma) during the fluctuating Plio‐Pleistocene climate, which may have provided the primary driver for lineage diversification.     

Temporal,spatial and ecological dynamics of speciation among amphi‐Beringian small mammals

Aim

Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

Location

Beringia, the nexus of the northern continents.

Methods

We used approximate Bayesian computation methods to test for simultaneous divergence among eight pairs of taxa, using cytochrome b gene sequences. We calculated coalescence times for eastern and western components of each pair and for the combined pairs, and relate dates to Quaternary climatic periodicity and combinations of environmental events and physical barriers. Population growth and expansion statistics were used to test evolutionary responses among taxa, including range shifts, persistence or periodic extirpation. Species distribution models (SDMs) for each taxon were used to predict their geographical ranges during the present interglacial, Last Glacial Maximum and previous interglacial.

Results

Multiple divergence events across Beringia were primarily coincident with extreme glacial cycles of the late Quaternary. Structure within Beringia is spatially consistent with at least three environmental barriers arising at different times: the Kolyma Uplands, Bering Strait and portions of the Bering Isthmus. Levels of divergence varied substantially, indicating evolutionary processes spanning deep and shallow time‐scales. The different demographics among taxa reflect their distinct ecological responses. SDMs predicted regional distributional changes through time and different spatial responses among taxa.

Main conclusions

Beringia predominantly constituted a dispersal corridor during the early Quaternary and a major centre of endemism in the late Quaternary. Coincident with severe glacial cycles, small mammal species were ‘caught’ in Beringia and diversified over multiple climatic phases. Relative genetic differentiation across Beringia appears to be related to ecological differences reflecting a gradual adaptation to Beringian environments through time. Some methodological constraints associated with resolving recent (late Quaternary) isolation events or drawing inferences from a single locus are discussed.     

Eastern Beringian biogeography: historical and spatial genetic structure of singing voles in Alaska

Aim  Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high‐latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high‐latitude arvicoline rodents. Location  Continental Alaska (alpine and arctic tundra) and the St Matthew Archipelago (Bering Sea). Methods  We generated and analysed cytochrome b sequences of 97 singing and insular voles (M. miurus and M. abbreviatus) from Alaska. Deep evolutionary structure was inferred by phylogenetic analysis using parsimony, maximum likelihood and Bayesian approaches; the geographical structure of genetic diversity was assessed using analysis of molecular variance and network analysis; ages of cladogenetic and coalescent events were estimated using a relaxed molecular clock model with Bayesian approximation. Results  Regional nucleotide diversity in singing voles is higher than in other high‐latitude arvicoline species, but intra‐population diversity is within the observed range of values for arvicolines. Microtus abbreviatus specimens are phylogenetically nested within M. miurus. Molecular divergence date estimates indicate that current genetic diversity was formed in the last glacial (Wisconsinan) and previous interglacial (Sangamonian) periods, with the exception of a Middle Pleistocene split found between samples collected in the Wrangell Mountains region and all other singing vole samples. Main conclusions  High levels of phylogenetic and spatial structure are observed among analysed populations. This pattern is consistent with that expected for a taxon with a long history in Beringia. The spatial genetic structure of continental singing voles differs in its northern and southern ranges, possibly reflecting differences in habitat distribution between arctic and alpine tundra. Our phylogenetic results support the taxonomic inclusion of M. miurus in its senior synonym, M. abbreviatus.     

Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences

The glacial-interglacial cycles of the upper Pleistocene have had a major impact on the recent evolutionary history of Arctic species. To assess the effects of these large-scale climatic fluctuations to a large, migratory Arctic mammal, we assessed the phylogeography of reindeer (Rangifer tarandus) as inferred from mitochondrial DNA (mtDNA) sequence variation in the control region. Phylogenetic relationships among haplotypes seem to reflect historical patterns of fragmentation and colonization rather than clear-cut relationships among extant populations and subspecies. Three major haplogroups were detected, presumably representing three separate populations during the last glacial. The most influential one has contributed to the gene pool of all extant subspecies and seems to represent a large and continuous glacial population extending from Beringia and far into Eurasia. A smaller, more localized refugium was most likely isolated in connection with ice expansion in western Eurasia. A third glacial refugium was presumably located south of the ice sheet in North America, possibly comprising several separate refugial populations. Significant demographic population expansion was detected for the two haplogroups representing the western Eurasian and Beringian glacial populations. The former apparently expanded when the ice cap retreated by the end of the last glacial. The large continuous one, in contrast, seems to have expanded by the end of the last interglacial, indicating that the warm interglacial climate accompanied by marine transgression and forest expansion significantly confined population size on the continental mainland. Our data demonstrate that the current subspecies designation does not reflect the mtDNA phylogeography of the species, which in turn may indicate that morphological differences among subspecies have evolved as adaptive responses to postglacial environmental change.     

The Linnean shortfall in oceanic island biogeography: a case study in the Azores

Aim Speciation processes on islands are still poorly understood. Previous studies based on the analysis of distribution data from checklists found that the flora of the Azores archipelago differs from other island floras in the exceptionally low number of radiations and the low number of single‐island endemics. The general mechanism(s) responsible for these apparently unique patterns remained unclear. One possible explanation for the distinctiveness of the Azorean endemic flora is the lack of a consistent and critical taxonomic framework for the floras of the Atlantic archipelagos. In this study, molecular variation within a range of Azorean endemic plant lineages was analysed to determine whether inadequacies in the current taxonomy of endemics might be an explanation for the unusual diversity patterns observed in the endemic flora of the Azores. Location Azores archipelago. Method Sixty‐nine populations of eight endemic species or subspecies belonging to five genetic lineages were sampled from all Azorean islands but one. Nuclear and plastid DNA regions were sequenced, and relationships among internal transcribed spacer (ITS) region ribotypes established using statistical parsimony. Results Molecular diversity patterns differ from current taxonomic groupings, with all lineages comprising previously overlooked genetic entities. Main conclusions Recognition as distinct taxa of the genetically distinct entities discovered in this study would drastically change the diversity patterns and make them more similar to those of other Atlantic archipelagos. The results serve to highlight that current knowledge of endemic diversity on oceanic islands may be far from complete, even in relatively well‐known groups such as angiosperms. This limitation is rarely considered in macroecological and evolutionary studies that make use of data from taxonomic checklists to draw inferences about oceanic island biogeographic processes.