NORTH AMERICAN BLACK BEAR mtDNA PHYLOGEOGRAPHY: IMPLICATIONS FOR MORPHOLOGY AND THE HAIDA GWAII GLACIAL REFUGIUM CONTROVERSY

The controversial role of Haida Gwaii (Queen Charlotte Islands) as a biological refugium on the northwestern coast of North America has been widely discussed for more than fifty years. The presence of morphologically divergent subspecies on Haida Gwaii is one of the major lines of evidence suggesting this archipelago's role as a refugium during the Wisconsin. However, since morphological distinction can be derived postglacially as well as in extended isolation, such evidence is ambiguous. To examine this question, we did a phylogenetic analysis of cytochrome b sequences (719 bp) of black bear (Ursus americanus), one of the distinctive endemics of Haida Gwaii, and compared these with conspecifics from across North America, focusing primarily on the northwestern coast. We found that the Haida Gwaii bear are indistinguishable from coastal bear of British Columbia and Vancouver Island, but are highly distinct from continental bear. Coastal and continental bears differ by 24 synapomorphies and an average sequence divergence of 3.6%. The coastal mitochondrial lineage occurs in each of the three recognized coastal subspecies suggesting that the morphological characteristics differentiating these taxa may be postglacially derived. The data are consistent with recent suggestions that a glacial refugium existed on the now submerged continental shelf connecting Haida Gwaii, Vancouver Island, and the coastal fringe of mainland British Columbia. This refugium would have been an additional source for postglacial recolonization of northwestern North America.     

Molecular markers provide insights into contemporary and historic gene flow for a non‐migratory species

Hairy woodpeckers Picoides villosus are a common, year round resident with distinct plumage and morphological variation across North America. We genotyped 335 individuals at six variable microsatellite loci and analyzed 322 mtDNA control region sequences in order to examine the role of contemporary and historical barriers to gene flow. In addition we combined genetic analyses with ecological niche modelling to test if hairy woodpeckers were isolated in northern refugia (Alaska, Newfoundland and the Queen Charlotte Islands) during the last glacial maximum. Genetic analyses revealed that gene flow among North American hairy woodpecker populations is restricted, but not to the extent predicted for a sedentary species. Populations clustered into two main genetic groups, east and west of the Great Plains in the south and the Rocky Mountains in the north. Contact zones between the two main genetic groups exist in central British Columbia and Washington, but are narrow. Within each group we found additional population structure with genetic breaks between subgroups in the geographic west corresponding to breaks in forested habitat and physical barriers like open expanses of water. Population genetic patterns for hairy woodpeckers have resulted from isolation in multiple southern refugia with the current distribution of genetic groups resulting from post‐glacial expansion and subsequent reduction in gene flow. While populations in Alaska, Newfoundland and the Queen Charlotte Islands are genetically distinct from other populations, we found no evidence of these areas acting as refugia throughout the Pleistocene. Atlantic Canada populations contained unique haplotypes raising the possibility of a separate colonization from the rest of eastern Canada. The endemic subspecies on the island of Newfoundland is not genetically distinct from their closest mainland population unlike the Queen Charlotte Island subspecies.     

A taxonomic study of campylopus schimperi and C. subulatus (Bryopsida: Dicranaceae) in North America

Campylopus schimperi is known in North America from Oaxaca, Colorado, British Columbia, Yukon, Alaska, Baffin Island, Gaspé Peninsula, and Newfoundland, and reported from Greenland. No specimens of the previously reported C. subulatus were found from North America and this species should be excluded from the North American bryophyte flora. A quantitative study and critical review of the characters distinguishing these two species indicate that leaf laminal cell shape and length, and costal anatomy are the most definitive taxonomic features. The distributional range of C. schimperi in North America suggests a close association with unglaciated areas and hypothesized glacial refugia.     

Going coastal: shared evolutionary history between coastal British Columbia and Southeast Alaska wolves (Canis lupus)

Background

Many coastal species occupying the temperate rainforests of the Pacific Northwest in North America comprise endemic populations genetically and ecologically distinct from interior continental conspecifics. Morphological variation previously identified among wolf populations resulted in recognition of multiple subspecies of wolves in the Pacific Northwest. Recently, separate genetic studies have identified diverged populations of wolves in coastal British Columbia and coastal Southeast Alaska, providing support for hypotheses of distinct coastal subspecies. These two regions are geographically and ecologically contiguous, however, there is no comprehensive analysis across all wolf populations in this coastal rainforest.

Methodology/Principal Findings

By combining mitochondrial DNA datasets from throughout the Pacific Northwest, we examined the genetic relationship between coastal British Columbia and Southeast Alaska wolf populations and compared them with adjacent continental populations. Phylogenetic analysis indicates complete overlap in the genetic diversity of coastal British Columbia and Southeast Alaska wolves, but these populations are distinct from interior continental wolves. Analyses of molecular variation support the separation of all coastal wolves in a group divergent from continental populations, as predicted based on hypothesized subspecies designations. Two novel haplotypes also were uncovered in a newly assayed continental population of interior Alaska wolves.

Conclusions/Significance

We found evidence that coastal wolves endemic to these temperate rainforests are diverged from neighbouring, interior continental wolves; a finding that necessitates new international strategies associated with the management of this species.     

Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.     

INTERCHANGE AND ISOLATION OF HUMPBACK WHALES OFF CALIFORNIA AND OTHER NORTH PACIFIC FEEDING GROUNDS

Humpback whales feed in several high-latitude areas of the North Pacific. We examined the interchange of humpback whales between one of these areas, off California, and those in other feeding grounds in the eastern North Pacific:. Fluke photographs of 597 humpback whales identified off California between 1986 and 1992 were compared with those off Oregon and Washington (29); British Columbia (81); southeastern Alaska (343); Prince William Sound, Alaska (141); Kodiak Island, Alaska (104); Shumagin Islands, Alaska (22); and in the Bering Sea (7). A high degree of interchange, both inter-and intrayear, was found among humpback whales seen off California, Oregon, and Washington., A low rate of interchange was found between British Columbia and California.: two whales seen near the British Columbia/Washington border were photographed off California in a different year, No interchange was found between California and the three feeding areas in Alaska. Humpback whales off California, Oregon, and Washington form a single intermixing feeding aggregation with only limited interchange with areas farther north. These findings are consistent with photographic identification studies in the North Atlantic and with genetic studies in both the North Atlantic and North Pacific.     

Historical biogeography of the North American glacier ice worm, Mesenchytraeus solifugus (Annelida: Oligochaeta: Enchytraeidae)

North American ice worms are the largest glacially-obligate metazoans, inhabiting coastal, temperate glaciers between southcentral Alaska and Oregon. We have collected ice worm specimens from 10 new populations, completing a broad survey throughout their geographic range. Phylogenetic analyses of 87 individuals using fragments of nuclear 18S rRNA, and mitochondrial 12S rRNA and cyctochrome c oxidase subunit 1 (CO1) identified 18 CO1 haplotypes with divergence values up to ~10%. Phylogeographic interpretations suggest a St. Elias Range, Alaskan ancestry from an aquatic mesenchytraeid oligochaete during the early-Pliocene. A gradual, northward expansion by active dispersal from the central St. Elias clade characterizes a northern clade that is confined to Alaska (with one exception on Vancouver Island, British Columbia), while a distinct southern clade representing worms from British Columbia, Washington and Oregon was likely founded by a passive dispersal event originating from a northern ancestor. The geographic boundary between central and southern clades coincides with an ice worm distribution gap located in southern Alaska, which appears to have restricted active gene flow throughout the species' evolutionary history.     

Muscleworms, Parelaphostrongylus andersoni (Nematoda: Protostrongylidae), discovered in Columbia white-tailed deer from Oregon and Washington: implications for biogeography and host associations

Parelaphostrongylus andersoni is considered a characteristic nematode infecting white-tailed deer (Odocoileus virginianus). Host and geographic distribution for this parasite, however, remain poorly defined in the region of western North America. Fecal samples collected from Columbia white-tailed deer (O. v. leucurus) in a restricted range endemic to Oregon and Washington, USA, were examined for dorsal-spined larvae characteristic of many protostrongylid nematodes. Multilocus DNA sequence data (internal transcribed spacer 2 and cytochrome c oxidase subunit 1) established the identity and a new record for P. andersoni in a subspecies of white-tailed deer previously unrecognized as hosts. Populations of P. andersoni are now recognized along the basin of the lower Columbia River in Oregon and Washington and from south-central Oregon on the North Umpqua River. Current data indicate a potentially broad zone of sympatry for P. andersoni and Parelaphostrongylus odocoilei in the western region of North America, although these elaphostrongylines seem to be segregated, respectively, in white-tailed deer or in black-tailed and mule deer (Odocoileus hemionus) at temperate latitudes. The geographic range for P. andersoni in white-tailed deer is extended substantially to the west of the currently defined limit in North America, and we confirm an apparently extensive range for this elpahostrongyline. These observations are explored in the broader context of host and geographic associations for P. andersoni and related elaphostrongylines in North American cervids.     

The biogeography of aquatic macrophytes in North America since the Last Glacial Maximum

Aim To document the post‐glacial migration of the major aquatic macrophytes of North America. Location North America north of Mexico. Methods Aquatic macrophyte pollen were extracted from the North American Pollen Database. The modern pollen distribution was mapped and related to the climate to document the geographical and climatic constraints on these taxa. The fossil pollen were mapped at 2‐ka intervals for the past 21 ka. Results Numerous genera were present in ice‐free Alaska during the Last Glacial Maximum, and south of the Laurentide Ice Sheet in the southeast. Those taxa with the widest modern climatic ranges migrated rapidly into ice‐marginal areas, first in the west and then in the east of North America. Subsequent changes in the range and abundance were smaller. Main conclusions There were four migration routes of aquatic macrophytes during the late‐glacial and post‐glacial periods: a southward migration from Alaska between 14–13 and ka, a northern migration in the west at the same time into the ice‐free Cordilleran region, and movements east and west of Appalachia as early as 19 ka for some taxa into the lower Mississippi and into the upper Mississippi and Great Lakes by 11 ka. As the Laurentide ice sheet wasted, aquatic taxa with the broadest contemporary temperature tolerances rapidly occupied ice‐marginal environments.     

Rapid divergence and postglacial colonization in western North American Steller's jays (Cyanocitta stelleri)

Post-Pleistocene avian colonization of deglaciated North America occurred from multiple refugia, including a coastal refugium in the northwest. The location of a Pacific Coastal refugium is controversial; however, multiple lines of evidence suggest that it was located near the Queen Charlotte Islands (also known as Haida Gwaii). The Queen Charlotte Islands contain a disproportionately large number of endemic plants and animals including the Steller's jay Cyanocitta stelleri carlottae. Using five highly variable microsatellite markers, we studied population structure among eight populations of Steller's jay (N = 150) from geographical areas representing three subspecies in western North America: C. s. carlottae, C. s. stelleri and C. s. annectens. Microsatellite analyses revealed genetic differentiation between each of the three subspecies, although more extensive sampling of additional C. s. annectens populations is needed to clarify the level of subspecies differentiation. High levels of population structure were found among C. s. stelleri populations with significant differences in all but two pairwise comparisons. A significant isolation by distance pattern was observed amongst populations in the Pacific Northwest and Alaska. In the C. s. carlottae population, there was evidence of reduced genetic variation, higher number of private alleles than northern C. s. stelleri populations and higher levels of divergence between Queen Charlotte Island and other populations. We were unable to reject the hypothesis that the Queen Charlotte Islands served as a refugium during the Pleistocene. Steller's jay may have colonized the Queen Charlotte Islands near the end of the last glaciation or persisted throughout the Pleistocene, and this subspecies may thus represent a glacial relic. The larger number of private alleles, despite reduced genetic variation, morphological distinctiveness and high divergence from other populations suggests that the Queen Charlotte Island colonization pre-dates that of the mainland. Furthermore, our results show rapid divergence in Steller's jay populations on the mainland following the retreat of the ice sheets.     

Freshwater littoral copepods of British Columbia and Alberta (Canada)

This is part of an ongoing study on the freshwater littoral copepods of northwestern North America, comprising Alaska, Yukon, western Northwest Territories, British Columbia, Alberta, and Saskatchewan. In this paper we report 13 species of calanoids and 16 species of cyclopoids found in 142 samples collected from northern British Columbia and Alberta on either side of the Rocky mountains. We discuss morphology and distribution of some of these species.     

Population genetic isolation and limited connectivity in the purple finch (Haemorhous purpureus)

Using a combination of mitochondrial and z‐linked sequences, microsatellite data, and spatio‐geographic modeling, we examined historical and contemporary factors influencing the population genetic structure of the purple finch (Haemorhous purpureus). Mitochondrial DNA data show the presence of two distinct groups corresponding to the two subspecies, H. p. purpureus and H. p. californicus. The two subspecies likely survived in separate refugia during the last glacial maximum, one on the Pacific Coast and one east of the Rocky Mountains, and now remain distinct lineages with little evidence of gene flow between them. Southwestern British Columbia is a notable exception, as subspecies mixing between central British Columbia and Vancouver Island populations suggests a possible contact zone in this region. Z‐linked data support two mitochondrial groups; however, Coastal Oregon and central British Columbia sites show evidence of mixing. Contemporary population structure based on microsatellite data identified at least six genetic clusters: three H. p. purpureus clusters, two H. p. californicus clusters, and one mixed cluster, which likely resulted from high site fidelity and isolation by distance, combined with sexual selection on morphological characters reinforcing subspecies differences.     

Inferring the biogeographic origins of inter‐continental disjunct endemics using a Bayes‐DIVA approach

The arcto‐Tertiary relictual flora is comprised of many genera that occur non‐contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more‐continuous arcto‐Tertiary forest. The historical biogeographic events leading to the present‐day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes‐DIVA method handles both types of uncertainty. Thus, we used Bayes‐DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto‐Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present‐day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto‐Tertiary species endemic in the neotropics.     

The origin of unique diversity in deglaciated areas: traces of Pleistocene processes in north‐European endemics from the Galium pusillum polyploid complex (Rubiaceae)

The role of glacial oscillations in shaping plant diversity has been only rarely addressed in endemics of formerly glaciated areas. The Galium pusillum group represents a rare example of an ecologically diverse and ploidy‐variable species complex that exhibits substantial diversity in deglaciated northern Europe. Using AFLP and plastid and nuclear DNA sequences of 67 populations from northern, central, and western Europe with known ecological preferences, we elucidate the evolutionary history of lineages restricted to deglaciated areas and identify the eco‐geographic partitioning of their genetic variation. We reveal three distinct endemic northern lineages: (i) diploids from southern Sweden + the British Isles, (ii) tetraploids from southern Scandinavia and the British Isles that show signs of ancient hybridization between the first lineage and populations from unglaciated central Europe, and (iii) tetraploids from Iceland + central Norway. Available evidence supports a stepwise differentiation of these three lineages that started at least before the last glacial maximum by processes of genome duplication, interlineage hybridization and/or allopatric evolution in distinct periglacial refugia. We reject the hypothesis of more recent postglacial speciation. Ecological characteristics of the populations under study only partly reflect genetic variation and suggest broad niches of postglacial colonizers. Despite their largely allopatric modern distributions, the north‐European lineages of the G. pusillum group do not show signs of rapid postglacial divergence, in contrast to most other northern endemics. Our study suggests that plants inhabiting deglaciated areas outside the Arctic may exhibit very different evolutionary histories compared with their more thoroughly investigated high‐arctic counterparts.     

Minisatellite DNA variation and stock identification of coho salmon

Geographic variation in minisatellite DNA variation was examined in 18 stocks of coho salmon Oncorhynchus kisutch from British Columbia and three stocks from Kamchatka or Western Alaska. Genomic DNA was restricted with Mbo I or Hae III and hybridized with two minisatellite probes (p Ssa -A34, Ots PBS-1). Allele frequencies and DNA band counts derived from the two probes were combined with band counts from the probe Ssa to show a regional stock structure. In British Columbia, stocks from the Fraser River were distinct from those on Vancouver Island, and all were differentiated from those on the mainland of British Columbia. Average heterozygosity at the Ssa -A34 locus was 71%. Compared with a previous study of British Columbia coho salmon population structure in which variation at 26 allozyme loci was examined, greater population differentiation and higher heterozygosity were observed at minisatellite loci. Estimated stock compositions of simulated mixtures of fishery samples from British Columbia stocks were accurate and precise, with the potential of identifying stocks within the drainage basin of a major river, the Fraser River. Minisatellite DNA variation may provide accurate and precise estimates of stock composition in actual fishery applications, and has the potential of identifying individual fish to region or stock of origin.     

Divergence in an archipelago and its conservation consequences in Aleutian Island rock ptarmigan

The identification and assessment of island endemics is a conservation priority. We genotyped 115 rock ptarmigan from five insular populations in the Aleutian-Commander archipelago and two Alaska mainland populations to identify conservation units, assess genetic diversity and gene flow, and to determine whether populations have declined over time. We found four distinct populations that appear to be completely isolated and which correspond closely to recognized subspecies. The most geographically isolated populations also have the lowest genetic diversity. Three populations (Attu Island, Rat Islands, and Adak Island), which each experienced historic introductions of an exotic predator, showed genetic signals of declines, but the timing did not correspond with the introduction. We recommend management of each endemic group as a unique conservation unit.     

Beringia as a high-latitude engine of avian speciation

Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting–reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such ‘losses’ could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.     

Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from Southeast Asia

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.     

TWO NEW SPECIES OF TAYLORIELLA (RHODOMELACEAE,RHODOPHYTA) FROM THE NORTHEASTERN NORTH PACIFIC1

Two new species are recognized in the rhodomelacean genus Tayloriella Kylin: T. divaricata sp. nov. and T. abyssalis sp. nov. These two taxa are distributed in the northeastern North Pacific, the former ranging from Amchitka Island in the Aleutians through southcentral Alaska to northern British Columbia, and the latter ranging also from Amchitka Island through southcentral Alaska and British Columbia into northern Washington. A characteristic of these two species shared with the type of Tayloriella is that the abaxial lateral always overtops the monopodially developed axes in every order of branching. The laterals have little congenital fusion with the parent axes. A common feature in these two species is that the laterals are terminated in a relatively long monosiphonous portion (usually 6 or 7 cells). The relationship of Tayloriella to Pterosiphonia and Pterosiphoniella is discussed.     

Ice‐age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long‐distance postglacial migration from south of the ice sheets resulted in the modern‐day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long‐term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range‐wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long‐term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern‐day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.