Phylogeographical analysis of mtDNA data indicates postglacial expansion from multiple glacial refugia in woodland caribou (Rangifer tarandus caribou)

Genomic population structure and inbreeding history of Lake Superior caribou

Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), 1 of the 12 Designatable Units, has lost approximately half of its historic range in the last 150 years, particularly along the southern edge of its distribution. Despite this overall northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the continuous boreal caribou range in Ontario, along the coast and nearshore islands of Lake Superior. The population history of caribou along Lake Superior remains unclear. It appears that these caribou likely represent a remnant distribution at the trailing edge of the receding population of boreal caribou, but they may also exhibit local adaptation to the coastal environment. A better understanding of the population structure and history of caribou along Lake Superior is important for their conservation and management. Here, we use high-coverage whole genomes (N = 20) from boreal, eastern migratory, and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate population structure and inbreeding histories. We discovered that caribou from the Lake Superior range form a distinct group but also found some evidence of gene flow with the continuous boreal caribou range. Notably, caribou along Lake Superior demonstrated relatively high levels of inbreeding (measured as runs of homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between ranges. Despite inbreeding, caribou along Lake Superior retained high heterozygosity, particularly in genomic regions without ROH. These results suggest that they present distinct genomic characteristics but also some level of gene flow with the continuous range. Our study provides key insights into the genomics of the southernmost range of caribou in Ontario, beginning to unravel the evolutionary history of these small, isolated caribou populations.

Pleistocene-Holocene vicariance, not Anthropocene landscape change, explains the genetic structure of American black bear (Ursus americanus) populations in the American Southwest and northern Mexico

The phylogeography of the American black bear (Ursus americanus) is characterized by isolation into glacial refugia, followed by population expansion and genetic admixture. Anthropogenic activities, including overharvest, habitat loss, and transportation infrastructure, have also influenced their landscape genetic structure. We describe the genetic structure of the American black bear in the American Southwest and northern Mexico and investigate how prehistoric and contemporary forces shaped genetic structure and influenced gene flow. Using a suite of microsatellites and a sample of 550 bears, we identified 14 subpopulations organized hierarchically following the distribution of ecoregions and mountain ranges containing black bear habitat. The pattern of subdivision we observed is more likely a product of postglacial habitat fragmentation during the Pleistocene and Holocene, rather than a consequence of contemporary anthropogenic barriers to movement during the Anthropocene. We used linear mixed-effects models to quantify the relationship between landscape resistance and genetic distance among individuals, which indicated that both isolation by resistance and geographic distance govern gene flow. Gene flow was highest among subpopulations occupying large tracts of contiguous habitat, was reduced among subpopulations in the Madrean Sky Island Archipelago, where montane habitat exists within a lowland matrix of arid lands, and was essentially nonexistent between two isolated subpopulations. We found significant asymmetric gene flow supporting the hypothesis that bears expanded northward from a Pleistocene refugium located in the American Southwest and northern Mexico and that major highways were not yet affecting gene flow. The potential vulnerability of the species to climate change, transportation infrastructure, and the US-Mexico border wall highlights conservation challenges and opportunities for binational collaboration.

The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act

More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.

Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies

Advancements in molecular and phylogenetic analysis have revealed the need for greater taxonomic resolution since Rangifer (Reindeer and caribou: Cervidae) was last revised in 1961. Recent literature shows that many of the subspecies and several species synonymised out of existence are, in fact, valid, some names have been misapplied, and new subspecies-level clades are in need of description. This paper reviews available names for recently defined ecotypes of reindeer and caribou in compliance with ICZN rules for zoological nomenclature.

Whole genome sequences from non-invasively collected caribou faecal samples

Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

Population dynamics of caribou shaped by glacial cycles before the last glacial maximum

Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.

Phylogeography of Cedros and Tiburón Island Mule Deer in North America's Desert Southwest

Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, habitat loss, unregulated hunting, and other factors have reduced their historical range in México. Two of the 6 putative subspecies inhabiting México's deserts and Baja California peninsula are of conservation concern, occupying islands in the Pacific Ocean (Odocoileus hemionus cerrosensis on Cedros Island: endangered) and Sea of Cortés (Odocoileus hemionus sheldoni on Tiburón Island: threatened). Focusing on the desert southwest (n = 448), we sampled Tiburón (n = 22) and Cedros (n = 15) Island mule deer using contemporary samples and natural history museum specimens to complete a phylogeographic evaluation of the species complex, and assess the phylogeography of these insular subspecies. Both insular subspecies formed endemic haplotype lineages, consistent with island biogeographic theory. Bayesian skyline plots were consistent with Holocene demographic expansion. Cedros Island deer were genetically most similar to adjacent mainland Baja California deer, but exhibited a suite of unique haplotypes and reduced genetic variation. Tiburón Island deer haplotypes unexpectedly nested within a mainland lineage found in distant New Mexico, rather than the adjacent mainland Sonoran lineage. Such findings suggest the importance of postglacial climate fluctuations and biotic community turnover in the phylogeographic history of mule deer in the desert southwest. Our genetic data corroborates cultural, archaeological, and phenotypic evidence supporting Cedros and Tiburón deer endemicity and subspecies status. Reduced genetic variation, divergence from mainland populations, and demographic trends on both islands indicate that conservation, monitoring, and management are critical to ensure persistence of these endemic insular subspecies.

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units

Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole-genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.

Post-glacial phylogeography and variation in innate immunity loci in a sylvatic rodent, bank vole Myodes glareolus

In the northern hemisphere, the spatial structure of many taxa has been shaped by migration patterns after the last glaciation, and phylogeography based on mtDNA variation may reflect the post-glacial demography. The mtDNA lineages are expected to differ in their adaptations to local conditions but little is known about the impact of these conditions on functional genetic variation. Here, we answer this question through an analysis of geographic variation and selection patterns in seven innate immunity genes in free-living bank voles Myodes glareolus from 10 localities across species range assigned to different lineages based on mtDNA. We found clear discrepancies between population structure in mtDNA and each of the studied innate immunity genes. There was no uniform pattern of spatial variation at immunity loci, they differed in the levels of polymorphism, and the results of neutrality tests were not consistent over loci. Each locus comprised a few common haplotypes shared between mitochondrial lineages and studied locations, plus numerous haplotypes unique for each studied site. Our results suggest that the diversity of innate immunity genes cannot be explained solely in terms of demographic processes, and that the observed polymorphism may be attributed to local selection. The strength and direction of selection differed between loci, even within the same gene family, which underlines how crucial it is to take a complex approach while studying the selection patterns acting on immune-related genes.

The biogeography of the caribou lungworm, Varestrongylus eleguneniensis (Nematoda: Protostrongylidae) across northern North America

Varestrongylus eleguneniensis (Nematoda; Protostrongylidae) is a recently described species of lungworm that infects caribou (Rangifer tarandus), muskoxen (Ovibos moschatus) and moose (Alces americanus) across northern North America. Herein we explore the geographic distribution of V. eleguneniensis through geographically extensive sampling and discuss the biogeography of this multi-host parasite. We analyzed fecal samples of three caribou subspecies (n = 1485), two muskox subspecies (n = 159), and two moose subspecies (n = 264) from across northern North America. Protostrongylid dorsal-spined larvae (DSL) were found in 23.8%, 73.6%, and 4.2% of these ungulates, respectively. A portion of recovered DSL were identified by genetic analyses of the ITS-2 region of the nuclear rDNA or the cytochrome oxidase c subunit I (COI) region of the mtDNA. We found V. eleguneniensis widely distributed among caribou and muskox populations across most of their geographic prange in North America but it was rare in moose. Parelaphostrongylus andersoni was present in caribou and moose and we provide new geographic records for this species. This study provides a substantial expansion of the knowledge defining the current distribution and biogeography of protostrongylid nematodes in northern ungulates. Insights about the host and geographic range of V. eleguneniensis can serve as a geographically extensive baseline for monitoring current distribution and in anticipating future biogeographic scenarios under a regime of accelerating climate and anthropogenic perturbation.

Phylogeography of moose in western North America

Subspecies designations within temperate species’ ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids. We used genetics and the fossil record to study the phylogeography of three moose subspecies (Alces alces andersoni, A. a. gigas, and A. a. shirasi) in western North America. We sequenced the complete mitochondrial genome (16,341 base pairs; n = 60 moose) and genotyped 13 nuclear microsatellites (n = 253) to evaluate genetic variation among moose samples. We also reviewed the fossil record for detections of all North American cervids to comparatively assess the evidence for the existence of a southern refugial population of moose corresponding to A. a. shirasi during the last glacial maximum of the Pleistocene. Analysis of mtDNA molecular variance did not support distinct clades of moose corresponding to currently recognized subspecies, and mitogenomic haplotype phylogenies did not consistently distinguish individuals according to subspecies groupings. Analysis of population structure using microsatellite loci showed support for two to five clusters of moose, including the consistent distinction of a southern group of moose within the range of A. a. shirasi. We hypothesize that these microsatellite results reflect recent, not deep, divergence and may be confounded by a significant effect of geographic distance on gene flow across the region. Review of the fossil record showed no evidence of moose south of the Wisconsin ice age glaciers ≥ 15,000 years ago. We encourage the integration of our results with complementary analyses of phenotype data, such as morphometrics, originally used to delineate moose subspecies, for further evaluation of subspecies designations for North American moose.

Origins of Chinese reindeer (Rangifer tarandus) based on mitochondrial DNA analyses

The most southern population of reindeer (Rangifer tarandus) inhabits northeastern China, but the migration route and origin of this population have not been confirmed. The sequences of mitochondrial DNA control regions from domestic and wild herds from Eurasia and China were analysed. The results showed that the Chinese reindeer population originated independently from north-central Russian domestic herds, belonging to a large reindeer population that was present across Beringia during the last glacial period. Some studies have reported that the Chinese reindeer population is closely related to wild forest reindeer herds in Russia. Our results, however, indicate that wild forest reindeer herds of southeastern Russia contributed little or nothing to the Chinese reindeer herd gene pool. Chinese reindeer herds have a much greater genetic similarity to more northerly distributed tundra-type herds that inhabit open areas. The present findings will be essential for future conservation planning for Chinese reindeer.

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R ST and F ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad-scale patterns of genetic structure and closely aligned with the R ST network. The F ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.

Partitioning drivers of spatial genetic variation for a continuously distributed population of boreal caribou: Implications for management unit delineation

Isolation by distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using nonspatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1,221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies, and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation, and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.

Parallel evolution of site-specific changes in divergent caribou lineages

The parallel evolution of phenotypes or traits within or between species provides important insight into the basic mechanisms of evolution. Genetic and genomic advances have allowed investigations into the genetic underpinnings of parallel evolution and the independent evolution of similar traits in sympatric species. Parallel evolution may best be exemplified among species where multiple genetic lineages, descended from a common ancestor, colonized analogous environmental niches, and converged on a genotypic or phenotypic trait. Modern North American caribou (Rangifer tarandus) originated from three ancestral sources separated during the Last Glacial Maximum (LGM): the Beringian-Eurasian lineage (BEL), the North American lineage (NAL), and the High Arctic lineage (HAL). Historical introgression between the NAL and the BEL has been found throughout Ontario and eastern Manitoba. In this study, we first characterized the functional differentiation in the cytochrome-b (cytB) gene by identifying nonsynonymous changes. Second, the caribou lineages were used as a direct means to assess site-specific parallel changes among lineages. There was greater functional diversity within the NAL despite the BEL having greater neutral diversity. The patterns of amino acid substitutions occurring within different lineages supported the parallel evolution of cytB amino acid substitutions suggesting different selective pressures among lineages. This study highlights the independent evolution of identical amino acid substitutions within a wide-ranging mammal species that have diversified from different ancestral haplogroups and where ecological niches can invoke parallel evolution.

Population structure and dispersal routes of an invasive parasite, Fascioloides magna, in North America and Europe

Background

Fascioloides magna (Trematoda: Fasciolidae) is an important liver parasite of a wide range of free-living and domestic ruminants; it represents a remarkable species due to its large spatial distribution, invasive character, and potential to colonize new territories. The present study provides patterns of population genetic structure and admixture in F. magna across all enzootic regions in North America and natural foci in Europe, and infers migratory routes of the parasite on both continents.

Methods

In total, 432 individuals from five North American enzootic regions and three European foci were analysed by 11 microsatellite loci. Genetic data were evaluated by several statistical approaches: (i) the population genetic structure of F. magna was inferred using program STRUCTURE; (ii) the genetic interrelationships between populations were analysed by PRINCIPAL COORDINATES ANALYSIS; and (iii) historical dispersal routes in North America and recent invasion routes in Europe were explored using MIGRATE.

Results

The analysis of dispersal routes of the parasite in North America revealed west-east and south-north lineages that partially overlapped in the central part of the continent, where different host populations historically met. The exact origin of European populations of F. magna and their potential translocation routes were determined. Flukes from the first European focus, Italy, were related to F. magna from northern Pacific coast, while parasites from the Czech focus originated from south-eastern USA, particularly South Carolina. The Danube floodplain forests (third and still expanding focus) did not display relationship with any North American population; instead the Czech origin of the Danube population was indicated. A serial dilution of genetic diversity along the dispersion route across central and eastern Europe was observed. The results of microsatellite analyses were compared to previously acquired outputs from mitochondrial haplotype data and correlated with past human-directed translocations and natural migration of the final cervid hosts of F. magna.

Conclusions

The present study revealed a complex picture of the population genetic structure and interrelationships of North American and European populations, global distribution and migratory routes of F. magna and an origin of European foci.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1811-z) contains supplementary material, which is available to authorized users.

Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus)

Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer.

The eastern migratory caribou: the role of genetic introgression in ecotype evolution

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada's Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.

Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)

The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.

Varestrongylus eleguneniensis sp. n. (Nematoda: Protostrongylidae): a widespread, multi-host lungworm of wild North American ungulates, with an emended diagnosis for the genus and explorations of biogeography

BACKGROUND

A putative new species of Varestrongylus has been recently recognized in wild North American ungulates based on the ITS-2 sequences of larvae isolated from feces during a wide geographic survey. No taxonomic description was provided, as adult specimens were not examined.

METHODS

Lungworm specimens were collected in the terminal bronchioles of muskoxen from Quebec, and a woodland caribou from central Alberta, Canada. The L3 stage was recovered from experimentally infected slugs (Deroceras spp.). Description of specimens was based on comparative morphology and integrated approaches. Molecular identity was determined by PCR and sequencing of the ITS-2 region of the nuclear ribosomal DNA, and compared to other protostrongylids.

RESULTS

Varestrongylus eleguneniensis sp. n. is established for a recently discovered protostrongylid nematode found in caribou (Rangifer tarandus), muskoxen (Ovibos moschatus) and moose (Alces americanus); hosts that collectively occupy an extensive geographic range across northern North America. Adults of Varestrongylus eleguneniensis are distinguished from congeners by a combination of characters in males (distally bifurcate gubernaculum, relatively short equal spicules not split distally, a strongly elongate and bifurcate dorsal ray, and an undivided copulatory bursa) and females (reduced provagina with hood-like fold extending ventrally across prominent genital protuberance). Third-stage larvae resemble those found among other species in the genus. The genus Varestrongylus is emended to account for the structure of the dorsal ray characteristic of V. eleguneniensis, V. alpenae, V. alces and V. longispiculatus.

CONCLUSIONS

Herein we describe and name V. eleguneniensis, a pulmonary protostrongylid with Rangifer tarandus as a primary definitive host, and which secondarily infects muskoxen and moose in areas of sympatry. Biogeographic history for V. eleguneniensis and V. alpenae, the only two endemic species of Varestrongylus known from North America, appears consistent with independent events of geographic expansion with cervid hosts from Eurasia into North America during the late Pliocene and Quaternary.

A walk on the tundra: Host-parasite interactions in an extreme environment

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Climate change is altering host–parasite interactions in the Arctic.

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Changing ecological barriers reflect climate warming.

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Metabolic Theory of Ecology advances understanding of host–parasite interactions.

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Diversity emerges from host/parasite biogeographic/ecologic history.

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Insights gained from the Arctic apply to more complex systems.

Climate change is occurring very rapidly in the Arctic, and the processes that have taken millions of years to evolve in this very extreme environment are now changing on timescales as short as decades. These changes are dramatic, subtle and non-linear. In this article, we discuss the evolving insights into host–parasite interactions for wild ungulate species, specifically, muskoxen and caribou, in the North American Arctic. These interactions occur in an environment that is characterized by extremes in temperature, high seasonality, and low host species abundance and diversity. We believe that lessons learned in this system can guide wildlife management and conservation throughout the Arctic, and can also be generalized to more broadly understand host–parasite interactions elsewhere. We specifically examine the impacts of climate change on host–parasite interactions and focus on: (I) the direct temperature effects on parasites; (II) the importance of considering the intricacies of host and parasite ecology for anticipating climate change impacts; and (III) the effect of shifting ecological barriers and corridors. Insights gained from studying the history and ecology of host–parasite systems in the Arctic will be central to understanding the role that climate change is playing in these more complex systems.

Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution

Interglacial-glacial cycles of the Quaternary are widely recognized in shaping phylogeographic structure. Patterns from cold adapted species can be especially informative - in particular, uncovering additional glacial refugia, identifying likely recolonization patterns, and increasing our understanding of species' responses to climate change. We investigated phylogenetic structure of the wolverine, a wide-ranging cold adapted carnivore, using a 318 bp of the mitochondrial DNA control region for 983 wolverines (n=209 this study, n=774 from GenBank) from across their full Holarctic distribution. Bayesian phylogenetic tree reconstruction and the distribution of observed pairwise haplotype differences (mismatch distribution) provided evidence of a single rapid population expansion across the wolverine's Holarctic range. Even though molecular evidence corroborated a single refugium, significant subdivisions of population genetic structure (0.01< ΦST <0.99, P<0.05) were detected. Pairwise ΦST estimates separated Scandinavia from Russia and Mongolia, and identified five main divisions within North America - the Central Arctic, a western region, an eastern region consisting of Ontario and Quebec/Labrador, Manitoba, and California. These data are in contrast to the nearly panmictic structure observed in northwestern North America using nuclear microsatellites, but largely support the nuclear DNA separation of contemporary Manitoba and Ontario wolverines from northern populations. Historic samples (c. 1900) from the functionally extirpated eastern population of Quebec/Labrador displayed genetic similarities to contemporary Ontario wolverines. To understand these divergence patterns, four hypotheses were tested using Approximate Bayesian Computation (ABC). The most supported hypothesis was a single Beringia incursion during the last glacial maximum that established the northwestern population, followed by a west-to-east colonization during the Holocene. This pattern is suggestive of colonization occurring in accordance with glacial retreat, and supports expansion from a single refugium. These data are significant relative to current discussions on the conservation status of this species across its range.