Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

Dynamic landscapes in northwestern North America structured populations of wolverines (Gulo gulo)

Cyclic climatic and glacial fluctuations of the Late Quaternary produced a dynamic biogeographic history for high latitudes. To refine our understanding of this history in northwestern North America, we explored geographic structure in a wide-ranging carnivore, the wolverine (Gulo gulo). We examined genetic variation in populations across mainland Alaska, coastal Southeast Alaska, and mainland western Canada using nuclear microsatellite genotypes and sequence data from the mitochondrial DNA (mtDNA) control region and Cytochrome b (Cytb) gene. Data from maternally inherited mtDNA reflect stable populations in Northwest Alaska, suggesting the region harbored wolverine populations since at least the Last Glacial Maximum (LGM; 21 Kya), consistent with their persistence in the fossil record of Beringia. Populations in Southeast Alaska are characterized by minimal divergence, with no genetic signature of long-term refugial persistence (consistent with the lack of pre-Holocene fossil records there). The Kenai Peninsula population exhibits mixed signatures depending on marker type: mtDNA data indicate stability (i.e., historical persistence) and include a private haplotype, whereas biparentally inherited microsatellites exhibit relatively low variation and a lack of private alleles consistent with a more recent Holocene colonization of the peninsula. Our genetic work is largely consistent with the early 20th century taxonomic hypothesis that wolverines on the Kenai Peninsula belong to a distinct subspecies. Our finding of significant genetic differentiation of wolverines inhabiting the Kenai Peninsula, coupled with the peninsula’s burgeoning human population and the wolverine’s known sensitivity to anthropogenic impacts, provides valuable foundational data that can be used to inform conservation and management prescriptions for wolverines inhabiting these landscapes.

Genetic structure of a widespread alpine shrub Rhododendron aureum (Ericaceae) across East Asia

The vast territory of East Asia, including southwestern Beringia, is considered to have been almost ice free during the Pleistocene. Cold-resistant flora may have persisted in this region expanding or contracting its range during the climate cooling. Only a few plant genera have been studied with a sampling area across their entire geographic range in East Asia; therefore, the understanding of the biogeographic history of alpine flora in this region remains limited. In the present study, genetic variation and population structure in 21 populations of the alpine shrub Rhododendron aureum across its range in East Asia were assessed using 18 microsatellite loci. Phylogenetic analyses revealed three main genetic groups: Siberia, Northeast, and North Pacific. According to the geographical pattern of genetic diversity, the North Pacific group includes populations from Kamchatka, south of Russian Far East, and territories close to central Japan. This group is the most diverse and likely diverged earlier than the Siberia and Northeast groups. Ecological niche modeling predicts range expansion of this species during the period of cooling and, together with demographic history, suggests that the divergence between the three main genetic groups predated the Last Glacial Maximum. Similar to other cold-resistant species such as Larix sibirica and Juniperus communis, the pattern of genetic diversity of R. aureum supports the survival of the species at high latitudes during the Pleistocene with limited contribution of the southern populations to expansion of the species range to the Northeast region and Siberia.

Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high-latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high-latitude species.

Evolutionary history and phylogeographic relationships of shrews from Sorex araneus group

Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species. These processes were additionally complicated by introgressions of mitochondrial DNA, which made the evolutionary history of this group quite complex and difficult to infer. To tackle the problem, we performed multi-method phylogenetic analyses based on mitochondrial cytochrome b that is considered a good molecular marker available for many representatives of Sorex. The results were compared with phylogenies based on chromosomal rearrangement data and put into temporal and spatial context using molecular dating and historical biogeography methods. We complemented the study with the estimation of diversification rates within the S. araneus group as well as comparing the results with paleontological records and climatic oscillations within the last 4 million years. Based on the gathered data, we proposed a hypothetical scenario for the evolution and geographic dispersion of species belonging to the S. araneus group. The shrews began to diversify about 2.7 million years ago in Eurasia and then migrated at least twice to North America. The evolution of shrews was driven by Pleistocene glacial and interglacial cycles, which increased their speciation rate and the emergence of new lineages. The migrations of populations were accompanied by introgressions of mitochondrial DNA into native shrews and occurred at least twice.

Phylogeographic structure in long-tailed voles (Rodentia: Arvicolinae) belies the complex Pleistocene history of isolation, divergence, and recolonization of Northwest North America's fauna

Quaternary climate fluctuations restructured biodiversity across North American high latitudes through repeated episodes of range contraction, population isolation and divergence, and subsequent expansion. Identifying how species responded to changing environmental conditions not only allows us to explore the mode and tempo of evolution in northern taxa, but also provides a basis for forecasting future biotic response across the highly variable topography of western North America. Using a multilocus approach under a Bayesian coalescent framework, we investigated the phylogeography of a wide‐ranging mammal, the long‐tailed vole, Microtus longicaudus. We focused on populations along the North Pacific Coast to refine our understanding of diversification by exploring the potentially compounding roles of multiple glacial refugia and more recent fragmentation of an extensive coastal archipelago. Through a combination of genetic data and species distribution models (SDMs), we found that historical climate variability influenced contemporary genetic structure, with multiple isolated locations of persistence (refugia) producing multiple divergent lineages (Beringian or northern, southeast Alaska or coastal, and southern or continental) during glacial advances. These vole lineages all occur along the North Pacific Coast where the confluence of numerous independent lineages in other species has produced overlapping zones of secondary contact, collectively a suture zone. Finally, we detected high levels of neoendemism due to complex island geography that developed in the last 10,000 years with the rising sea levels of the Holocene.

First record of the Holarctic least shrew (Sorex minutissimus) and associated helminths from Canada: new light on northern Pleistocene refugia

We report the first Canadian record of the Holarctic least shrew (Sorex minutissimus Zimmermann, 1780) and associated helminth worms, collected along the Dempster Highway in central Yukon in 2014. We identify the specimen based on morphological characters, characterize the habitat, report other mammals and helminth species associated with this specimen, and use mitochondrial DNA sequences to place the specimen within a phylogenetic context and address Pleistocene refugial hypotheses. Although long considered an Eurasian endemic, the diminutive least shrew was first reported from Alaska in 1994. Our new record for Canada indicates that the species may occur at least as far east as the MacKenzie River and DNA variation suggests this species persisted only in the Beringian refugium in North America during the Last Glacial Maximum. The discovery of a new mammal and associated parasites for Canada points to the urgent need for more detailed information on high-latitude biotas in North America, data that are best obtained through museum-based field surveys, particularly for small, cryptic species.

Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid-adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid-adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial-interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.

Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity

We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sampling and genetic analyses. We aimed to identify and explain potential general patterns of genetic discontinuity/connectivity and diversity, and to compare our findings with previously published hypotheses. We collected and analyzed 7707 samples of 17 widespread arctic-alpine plant species for amplified fragment length polymorphisms (AFLPs). Genetic structure, diversity and distinctiveness were analyzed for each species, and extrapolated to cover the geographic range of each species. The resulting maps were overlaid to produce metamaps. The Arctic and Atlantic Oceans, the Greenlandic ice cap, the Urals, and lowland areas between southern mountain ranges and the Arctic were the strongest barriers against gene flow. Diversity was highest in Beringia and gradually decreased into formerly glaciated areas. The highest degrees of distinctiveness were observed in Siberia. We conclude that large-scale general patterns exist in the Arctic, shaped by the Pleistocene glaciations combined with long-standing physical barriers against gene flow. Beringia served as both refugium and source for interglacial (re)colonization, whereas areas further west in Siberia served as refugia, but less as sources for (re)colonization.

Effects of late quaternary climate change on Palearctic shrews

The Late Quaternary was a time of rapid climatic oscillations and drastic environmental changes. In general, species can respond to such changes by behavioral accommodation, distributional shifts, ecophenotypic modifications (nongenetic), evolution (genetic) or ultimately face local extinction. How those responses manifested in the past is essential for properly predicting future ones especially as the current warm phase is further intensified by rising levels of atmospheric carbon dioxide. Here, we use ancient DNA (aDNA) and morphological features in combination with ecological niche modeling (ENM) to investigate genetic and nongenetic responses of Central European Palearctic shrews to past climatic change. We show that a giant form of shrew, previously described as an extinct Pleistocene Sorex species, represents a large ecomorph of the common shrew (Sorex araneus), which was replaced by populations from a different gene-pool and with different morphology after the Pleistocene Holocene transition. We also report the presence of the cold-adapted tundra shrew (S. tundrensis) in Central Europe. This species is currently restricted to Siberia and was hitherto unknown as an element of the Pleistocene fauna of Europe. Finally, we show that there is no clear correlation between climatic oscillations within the last 50 000 years and body size in shrews and conclude that a special nonanalogous situation with regard to biodiversity and food supply in the Late Glacial may have caused the observed large body size.

Using genetic variation to infer associations with climate in the common frog, Rana temporaria

Recent and historical species' associations with climate can be inferred using molecular markers. This knowledge of population and species-level responses to climatic variables can then be used to predict the potential consequences of ongoing climate change. The aim of this study was to predict responses of Rana temporaria to environmental change in Scotland by inferring historical and contemporary patterns of gene flow in relation to current variation in local thermal conditions. We first inferred colonization patterns within Europe following the last glacial maximum by combining new and previously published mitochondrial DNA sequences. We found that sequences from our Scottish samples were identical to (92%), or clustered with, the common haplotype previously identified from Western Europe. This clade showed very low mitochondrial variation, which did not allow inference of historical colonization routes but did allow interpretation of patterns of current fine-scale population structure without consideration of confounding historical variation. Second, we assessed fine-scale microsatellite-based patterns of genetic variation in relation to current altitudinal temperature gradients. No population structure was found within altitudinal gradients (average FST=0.02), despite a mean annual temperature difference of 4.5 °C between low- and high-altitude sites. Levels of genetic diversity were considerable and did not vary between sites. The panmictic population structure observed, even along temperature gradients, is a potentially positive sign for R. temporaria persistence in Scotland in the face of a changing climate. This study demonstrates that within taxonomic groups, thought to be at high risk from environmental change, levels of vulnerability can vary, even within species.

Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Pacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

Inferring recent historic abundance from current genetic diversity

Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.