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Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse (Reithrodontomys raviventris), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and ΦST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise. [ABSTRACT FROM AUTHOR]

Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization. [ABSTRACT FROM AUTHOR]

Island populations may have a higher extinction risk due to reduced genetic diversity and need to be managed effectively in order to reduce the risk of biodiversity loss. The Eurasian red squirrels (Sciurus vulgaris) in the south of England only survive on three islands (the Isle of Wight, Brownsea and Furzey islands), with the Isle of Wight harbouring the largest population in the region. Fourteen microsatellites were used to determine the genetic structure of red squirrel populations on the Isle of Wight, as well as their relatedness to other populations of the species. Our results demonstrated that squirrels on these islands were less genetically diverse than those in Continental mainland populations, as would be expected. It also confirmed previous results from mitochondrial DNA which indicated that the squirrels on the Isle of Wight were relatively closely related to Brownsea island squirrels in the south of England. Importantly, our findings showed that genetic mixing between squirrels in the east and west of the Isle of Wight was very limited. Given the potential deleterious effects of small population size on genetic health, landscape management to encourage dispersal of squirrels between these populations should be a priority. [ABSTRACT FROM AUTHOR]

The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns. [ABSTRACT FROM AUTHOR]

The European whitefish Coregonus lavaretus complex represents one of the most diverse radiations within salmonids, with extreme morphological and genetic differentiation across its range. Such variation has led to the assignment of many populations to separate species. In Great Britain, the seven native populations of C. lavaretus (two in Scotland, four in England, one in Wales) were previously classified into three species, and recent taxonomic revision resurrected the previous nomenclature. Here we used a dataset of 15 microsatellites to: (1) investigate the genetic diversity of British populations, (2) assess the level of population structure and the relationships between British populations. Genetic diversity was highest in Welsh (HO = 0.50, AR = 5.29), intermediate in English (HO = 0.41–0.50, AR = 2.83–3.88), and lowest in Scottish populations (HO = 0.28–0.35, AR = 2.56–3.04). Population structure analyses indicated high genetic differentiation (global FST = 0.388) between all populations but for the two Scottish populations (FST = 0.063) and two English populations (FST = 0.038). Principal component analysis and molecular ANOVA revealed separation between Scottish, English, and Welsh populations, with the Scottish populations being the most diverged. We argue that the data presented here are not sufficient to support a separation of the British European whitefish populations into three separate species, but support the delineation of different ESUs for these populations. [ABSTRACT FROM AUTHOR]

San Bernardino kangaroo rat (Dipodomys merriami parvus; SBKR), an endangered subspecies, faces ongoing anthropogenic threats such as habitat loss. Their habitat has undergone strong human-mediated fragmentation, resulting in extinction of some local populations and dramatic size reduction of the remaining populations. We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented. Clear population structure and low level of haplotype sharing suggests that there has been no recent gene flow among populations, except in the case of human mediated gene flow as a result of a single translocation event. Diversity levels are on par with other species with fragmented distributions. Further, shallow phylogenetic divergence suggests the populations have not been diverged long enough to detect phylogenetic structure and separation is likely recent. Given the limited gene flow, low numbers of SBKR as evident by low return on trapping efforts, and low effective population size, habitat restoration and translocations may be warranted to maintain levels of diversity in a declining metapopulation. [ABSTRACT FROM AUTHOR]

After decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes. [ABSTRACT FROM AUTHOR]

Species that inhabit fragmented habitats are expected to exhibit spatial genetic structure with respect to geographic distance and landscape features. These patterns are also shaped by a variety of temporal processes, namely post-glacial recolonization, and those operating at more contemporary scales, such as sex-biased dispersal. We quantified the spatial population genetic structure of mountain goats (Oreamnos americanus) in northern British Columbia (BC). We observed little genetic differentiation among mountain ranges across northern BC, suggesting a panmictic subpopulation. Genetic diversity values increased slightly with latitude, while bottleneck signatures were strongest in the south; these signatures are indicative of southward post-glacial colonization consistent with a northern glacial refugium. Mountain ranges were the most important predictor of genetic relatedness, suggesting large valleys impeded gene flow, and specific landscape features were not correlated to genetic variation. We used a case study in the Skeena region of BC to show how these data can directly inform local management recommendations. This study provides insight and much needed clarification of the genetic population structure of North American mountain goats and illustrates the limited impact of geographic distance and landscape features on gene flow in the northern half of the range. [ABSTRACT FROM AUTHOR]

Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species' ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment efforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, salt marsh bird's-beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration efforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the range of this subspecies in southern California, and three additional occurrences from Baja California, Mexico. We used flow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found five distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These findings can bolster management and restoration efforts by identifying potentially isolated occurrences and areas that are the richest sources of allelic diversity, and by providing insight into the amount of genetic differentiation across the taxon's range. [ABSTRACT FROM AUTHOR]

The endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is strongly linked ecologically to xeric areas with high abundance of kangaroo rats. Endemic to the San Joaquin Desert of central California, the elusive nature of SJKF, coupled with steady habitat loss and lack of comprehensive surveys, has precluded efforts to quantify the species' population size and distribution, especially in the central and northern parts of its range. Because the Ciervo-Panoche Natural Area contains the largest area of high-quality habitat in this central/northern region, we conducted systematic transect surveys for SJKF scats with professionally trained dog-handler teams throughout the area during 2009–2011. We collected almost 600 scats over 473 km of transects, documenting the freshness and location of each scat. Using molecular methods, we identified 93 SJKF individuals (56 males and 37 females) from 332 samples. Half of the individuals carried a mtDNA haplotype with a 16 bp deletion that had not been previously detected in other areas surveyed. Four individuals were recaptured in 2010 and five in 2011, including one female that was captured every year. We documented a unique mtDNA haplotype and more individuals across a wider area of the Ciervo-Panoche Natural Area than expected. Population analyses revealed two distinct subpopulations, with low connectivity between foxes in the Panoche Valley that are separated by hills with unsuitable habitat from those on the adjacent valley floor next to a major Interstate highway (I-5). While individuals detected within 6 km of each other were closely related, overall relatedness within each subpopulation approached zero. Genetic population models indicated a conservative population estimate of 90 kit foxes in total, with 60–90 individuals in the Panoche Valley and 17–27 individuals in the I-5 area. These results will help to inform management of the SJKF and identify areas that may be important to maintaining connectivity between populations. [ABSTRACT FROM AUTHOR]

Understanding genetic structure and diversity underpins the management of isolated populations. Small populations confined to islands may require effective genetic management for population persistence due to inbreeding and reduced genetic diversity. Endemic to the offshore islands of mainland Mauritius, the Bojer's skink (Gongylomorphus bojerii) has previously been managed as two genetic units due to divergence between populations to the north and south-east. In 2009, a few individuals were discovered on the south-eastern island Ile de la Passe (IDLP), an island within its former range where the species was believed to have gone extinct. This island was later supplemented with translocations from other south-eastern islands, but individual geographic origin and the genetic consequences of these translocations remains unknown. Demographic population history and translocation events were reconstructed using a suite of microsatellite markers and the mitochondrial DNA cytochrome b gene, assessing two northern and three south-eastern populations to infer the geographic origin of the IDLP individuals, and to assess the population's genetic diversity and structure. Although IDLP showed significant differentiation from all other populations, all analyses indicated a south-eastern origin, possibly founded by a single gravid female. Subsequent translocations have so far failed to ameliorate IDLP's genetic diversity. In addition, admixture analysis was used to track translocation and gene-flow in IDLP. We recommend using additional translocations from other south-eastern islands to further genetically support IDLP. Our study highlights the need to clarify cryptic population structure and utilise post-translocation genetic monitoring among similarly managed populations, particularly endangered island populations. [ABSTRACT FROM AUTHOR]

The Cascade red fox (CRF) occurred historically throughout subalpine and alpine habitats in the Cascade Range of Washington and southernmost British Columbia, but now appears to be extremely rare. Causes for its apparent decline are unknown, as is the current distribution and connectivity of its populations. Additionally, the introduction of nonnative (fur-farm) red foxes to surrounding lowland areas during the past century raises concerns about their expansion to higher elevations and potential hybridization with the CRF. We conducted noninvasive genetic sampling and analyses of CRFs in a 5575 km2 region in the southern portion of its range, which is thought to contain a significant proportion of the current population. We obtained 154 mitochondrial DNA sequences and microsatellite genotypes for 51 individuals to determine trends in genetic diversity, assess evidence for nonnative introgression, and describe population structure. Although heterozygosity (He = 0.60, SE = 0.03) was only slightly lower than an estimate obtained from samples collected during the 1980s (He = 0.64, SE = 0.05), genetic effective size of the current population based on a one-sample estimate was very small (Ne = 16.0, 95% CI 13.3-19.4), suggesting a loss of genetic diversity and the potential for inbreeding depression in future decades. Genetic connectivity was high and we found no evidence for hybridization with nonnative lowland red foxes. Thus, although a small effective population size indicates the possibility of inbreeding depression and loss of evolutionary potential, high connectivity and genetic integrity could mitigate this to some extent, indicating that the population could respond to conservation efforts. Ultimately, successful conservation of this species depends on a better understanding of the factors that originally contributed to its decline and that currently limit its growth. [ABSTRACT FROM AUTHOR]

Climate change accelerates biodiversity alterations in northern ecosystems. A prevalent example is that tundra regions are invaded by boreal species. This impacts negatively on native species through competition, predation and transmission of zoonoses. Scandinavian red foxes ( Vulpes vulpes) have emerged into the tundra and have altered the structure and function of the tundra community. For instance, they threaten persistence of the endangered Swedish Arctic fox ( Vulpes lagopus). County board administrations implement control of the tundra red foxes, but little is known about the underlying expansion dynamics. A broad-scale study revealed high connectivity where northern areas were supplemented with red foxes from surrounding population. However, red fox expansion is most prevalent in tundra regions and the fine-scaled expansion dynamics in these areas have not yet been disseminated. With the aim of identifying the invasive pathways of tundra red foxes, we present microsatellite data for 205 Swedish red foxes and mitochondrial sequence variation in 102 foxes sampled across the historical boreo-nemoral distribution and recently colonized tundra regions. Genetic structuring was low with high levels of ongoing, asymmetric dispersal from surrounding boreal zones into tundra habitats causing high genetic admixture. In both tundra and boreo-nemoral regions, inter-individual relatedness decreased with increasing geographic distance and data suggests male-biased dispersal patterns. Overall, fine-scaled expansion patterns were affected by multiple factors and we discuss its implications for future red fox management. [ABSTRACT FROM AUTHOR]

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway's rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities. [ABSTRACT FROM AUTHOR]

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species endemic to the San Francisco Bay region of California, USA, where habitat loss and fragmentation over the past century have reduced the mouse's distribution to <25 % of its historical range. To aid in conservation prioritization, we first investigated the possibility of hybridization with the morphologically similar western harvest mouse (WHM, R. megalotis) in areas of sympatry and developed genetic tools to differentiate the two species. We then investigated the phylogeography and genetic structure of the SMHM, including support for currently recognized SMHM subspecies designations. Lastly, we evaluated the morphological criteria currently used for the identification of species in the field. Analyses using mtDNA cytochrome b sequences and 11 microsatellites from 142 mice indicated complete and substantial separation of the SMHM and WHM, with no evidence of hybridization. These genetic markers as well as the mtDNA control region also identified a deep genetic division within the SMHM concordant with the current subspecies designations, R. r. raviventris and R. r. halicoetes. We identified the lowest genetic diversity within the southern subspecies, which inhabits a much reduced and highly fragmented portion of the species range. Morphological field identification of harvest mouse species was more successful at identifying SMHM (92 %) than WHM (44 %), with a large portion of WHM being incorrectly identified as SMHM. Field identification of harvest mouse species in the range of the southern SMHM subspecies was just above 50 %, indicating that current methods for morphological differentiation of species in that area are insufficient. Our confirmation of genetically distinct SMHM subspecies highlights the importance of determining the status and genetic composition of relict populations in the remaining patches of marshland in the central San Francisco Bay where the two subspecies may occur, as well as developing better tools for the discrimination of species, particularly in the range of the southern subspecies [ABSTRACT FROM AUTHOR]

Introgression and admixture from domestic or foreign conspecifics into wild populations are of great concern in wildlife conservation. The issue is of particular interest in ungulates where translocations and re-introductions have been common practice. In Europe, the only large remaining wild populations of reindeer ( Rangifer tarandus L.) are found in the mountainous habitats of southern Norway. These populations have during the last centuries been exposed to extensive habitat modifications and periods of contact with domestic reindeer. Through analyses of ancient and extant mitochondrial DNA (mtDNA) we document extensive intra- and inter-population genetic changes during the last millennium. Our data indicate population reduction within a short time interval during the 11th-12th century during a period when mass trapping of reindeer was common. Significant differentiation between the ancient herds suggests an ancient genetic structuring of the reindeer herds in southern Norway, although not as strong as between modern herds. Two different mtDNA lineages characterized the ancient herds. A Bayesian approach to reconstruct the recent evolutionary history suggests that the reindeer herds in southern Norway originate from two populations separated in different refugia during the last glacial period. The presence of two additional extant lineages, characteristic of domestic herds, suggests substantial introgression into the native wild reindeer. The putatively different refugial origins of the lineages represented by the extant herds in Rondane/Dovre, Hardangervidda and those with a mainly domestic origin may well reflect different adaptations to environmental conditions, including degree of human interference. Further research on this issue would provide important insights for conservation priorities and a sustainable and flexible management strategy for the remaining wild reindeer herds in the Scandinavian mountains. [ABSTRACT FROM AUTHOR]

We investigated the origins and persistence of European pine marten ( Martes martes) populations across the British Isles by identifying mitochondrial DNA (mtDNA) sequences from contemporary populations (sampled since 1981) and comparing these with those of older 'historical' museum specimens (pre-1981) originally collected from the same geographic areas. Excluding Scotland, where the haplotype composition of populations appears to be unchanged, haplotypes found in contemporary and historical marten populations elsewhere differed both temporally and geographically. While these data suggest that the contemporary Irish population is descended from a relict population that passed through an early to mid 1900s bottleneck, the historical and contemporary English and Welsh populations differ in their abundance of specific mtDNA control region haplotypes. These data appear to suggest that particular haplotypes may have been lost from England and Wales at some point in the early to mid 1900s, but further nuclear DNA work is required to determine whether this shift has occurred by rapid genetic drift in the mtDNA control region or whether relict populations have been replaced by pine martens from elsewhere. If the reported shifts in mtDNA haplotypes reflect population extirpation events, historical pine marten populations of England and Wales would appear to have become extinct in the twentieth century (in Wales after 1950 and in England after 1924). Additionally, the recent occurrence of haplotypes originating from continental Europe, and of M. americana, suggest that relict populations of England and Wales have been replaced by, or hybridised with, occasional released, escaped and/or translocated animals. The implications of these results for pine marten conservation, and particularly reintroduction, are discussed. [ABSTRACT FROM AUTHOR]