Publications by authors named "Sandra L Talbot"

32 Publications

Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall's sheep.

BMC Res Notes 2021 May 7;14(1):173. Epub 2021 May 7.

School of Environmental and Forest Sciences, University of Washington, Seattle, USA.

Objectives: Dall's sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall's sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library will provide critical reference sequence data that will facilitate metabarcoding diet analysis of Dall's sheep and thus improve understanding of plant-animal interactions in a region undergoing rapid climate change.

Data Description: We provide sequences for the chloroplast rbcL gene of 16 arctic-alpine vascular plant species that are known to comprise the diet of Dall's sheep. These sequences contribute to a growing reference library that can be used in diet studies of arctic herbivores.
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http://dx.doi.org/10.1186/s13104-021-05590-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8103577PMC
May 2021

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini).

Mol Phylogenet Evol 2021 Aug 30;161:107164. Epub 2021 Mar 30.

US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA.

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species Φ > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.
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http://dx.doi.org/10.1016/j.ympev.2021.107164DOI Listing
August 2021

Isolation and characterization of microsatellite loci in merlins (Falco columbarius) and cross-species amplification in gyrfalcons (F. rusticolus) and peregrine falcons (F. peregrinus).

Mol Biol Rep 2020 Nov 24;47(11):8377-8383. Epub 2020 Oct 24.

U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA.

Merlins, Falco columbarius, breed throughout temperate and high latitude habitats in Asia, Europe, and North America. Like peregrine falcons, F. peregrinus, merlins underwent population declines during the mid-to-late twentieth century, due to organochlorine-based contamination, and have subsequently recovered, at least in North American populations. To better understand levels of genetic diversity and population structuring in contemporary populations and to assess the impact of the twentieth century decline, we used genomic data archived in public databases and constructed genomic libraries to isolate and characterize a suite of 17 microsatellite markers for use in merlins. We also conducted cross-amplification experiments to determine the markers' utility in peregrine falcons and gyrfalcons, F. rusticolus. These markers provide a valuable addition to marker suites that can be used to determine individual identity and conduct genetic analyses on merlins and congeners.
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http://dx.doi.org/10.1007/s11033-020-05842-4DOI Listing
November 2020

Identifying reliable indicators of fitness in polar bears.

PLoS One 2020 19;15(8):e0237444. Epub 2020 Aug 19.

U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America.

Animal structural body size and condition are often measured to evaluate individual health, identify responses to environmental change and food availability, and relate food availability to effects on reproduction and survival. A variety of condition metrics have been developed but relationships between these metrics and vital rates are rarely validated. Identifying an optimal approach to estimate the body condition of polar bears is needed to improve monitoring of their response to decline in sea ice habitat. Therefore, we examined relationships between several commonly used condition indices (CI), body mass, and size with female reproductive success and cub survival among polar bears (Ursus maritimus) measured in two subpopulations over three decades. To improve measurement and application of morphometrics and CIs, we also examined whether CIs are independent of age and structural size-an important assumption for monitoring temporal trends-and factors affecting measurement precision and accuracy. Maternal CIs and mass measured the fall prior to denning were related to cub production. Similarly, maternal CIs, mass, and length were related to the mass of cubs or yearlings that accompanied her. However, maternal body mass, but not CIs, measured in the spring was related to cub production and only maternal mass and length were related to the probability of cub survival. These results suggest that CIs may not be better indicators of fitness than body mass in part because CIs remove variation associated with body size that is important in affecting fitness. Further, CIs exhibited variable relationships with age for growing bears and were lower for longer bears despite body length being related to cub survival and female reproductive success. These results are consistent with findings from other species indicating that body mass is a useful metric to link environmental conditions and population dynamics.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237444PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437918PMC
October 2020

Conservation Genomics in a Changing Arctic.

Trends Ecol Evol 2020 02 5;35(2):149-162. Epub 2019 Nov 5.

Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.
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http://dx.doi.org/10.1016/j.tree.2019.09.008DOI Listing
February 2020

Coast to coast: High genomic connectivity in North American scoters.

Ecol Evol 2019 Jun 3;9(12):7246-7261. Epub 2019 Jun 3.

US Geological Survey Alaska Science Center, 4210 University Dr. Anchorage Alaska.

Dispersal shapes demographic processes and therefore is fundamental to understanding biological, ecological, and evolutionary processes acting within populations. However, assessing population connectivity in scoters ( sp.) is challenging as these species have large spatial distributions that span remote landscapes, have varying nesting distributions (disjunct vs. continuous), exhibit unknown levels of dispersal, and vary in the timing of the formation of pair bonds (winter vs. fall/spring migration) that may influence the distribution of genetic diversity. Here, we used double-digest restriction-associated DNA sequence (ddRAD) and microsatellite genotype data to assess population structure within the three North American species of scoter (black scoter, ; white-winged scoter, ; surf scoter, ), and between their European congeners (common scoter, ; velvet scoter, ). We uncovered no or weak genomic structure (ddRAD  < 0.019; microsatellite  < 0.004) within North America but high levels of structure among European congeners (ddRAD  > 0.155, microsatellite  > 0.086). The pattern of limited genomic structure within North America is shared with other sea duck species and is often attributed to male-biased dispersal. Further, migratory tendencies (east vs. west) of female surf and white-winged scoters in central Canada are known to vary across years, providing additional opportunities for intracontinental dispersal and a mechanism for the maintenance of genomic connectivity across North America. In contrast, the black scoter had relatively elevated levels of divergence between Alaska and Atlantic sites and a second genetic cluster found in Alaska at ddRAD loci was concordant with its disjunct breeding distribution suggestive of a dispersal barrier (behavioral or physical). Although scoter populations appear to be connected through a dispersal network, a small percentage (<4%) of ddRAD loci had elevated divergence which may be useful in linking areas (nesting, molting, staging, and wintering) throughout the annual cycle.
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http://dx.doi.org/10.1002/ece3.5297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662410PMC
June 2019

Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds.

Genes Genomics 2019 09 27;41(9):1015-1026. Epub 2019 May 27.

U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA.

Background: In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies.

Objectives: The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species.

Methods: We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland).

Results: Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci.

Conclusion: The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.
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http://dx.doi.org/10.1007/s13258-019-00819-5DOI Listing
September 2019

Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time.

Int J Parasitol 2018 11 11;48(13):1061-1070. Epub 2018 Oct 11.

US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA.

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at -80 °C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.
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http://dx.doi.org/10.1016/j.ijpara.2018.08.001DOI Listing
November 2018

Whole-genome analysis of finds that pulsed hybridization impacts evolution at high latitudes.

Commun Biol 2018 31;1:51. Epub 2018 May 31.

Department of Biological Sciences, University at Buffalo (SUNY), 109 Cooke Hall, Buffalo, NY, 14260, USA.

At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia-ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America's North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence.
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http://dx.doi.org/10.1038/s42003-018-0058-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123727PMC
May 2018

Flyway structure in the circumpolar greater white-fronted goose.

Ecol Evol 2018 Aug 30;8(16):8490-8507. Epub 2018 Jul 30.

Alaska Science Center U. S. Geological Survey Anchorage Alaska.

Dispersal and migratory behavior are influential factors in determining how genetic diversity is distributed across the landscape. In migratory species, genetic structure can be promoted via several mechanisms including fidelity to distinct migratory routes. Particularly within North America, waterfowl management units have been delineated according to distinct longitudinal migratory flyways supported by banding data and other direct evidence. The greater white-fronted goose () is a migratory waterfowl species with a largely circumpolar distribution consisting of up to six subspecies roughly corresponding to phenotypic variation. We examined the rangewide population genetic structure of greater white-fronted geese using mtDNA control region sequence data and microsatellite loci from 23 locales across North America and Eurasia. We found significant differentiation in mtDNA between sampling locales with flyway delineation explaining a significant portion of the observed genetic variation (~12%). This is concordant with band recovery data which shows little interflyway or intercontinental movements. However, microsatellite loci revealed little genetic structure suggesting a panmictic population across most of the Arctic. As with many high-latitude species, Beringia appears to have played a role in the diversification of this species. A common Beringian origin of North America and Asian populations and a recent divergence could at least partly explain the general lack of structure at nuclear markers. Further, our results do not provide strong support for the various taxonomic proposals for this species except for supporting the distinctness of two isolated breeding populations within Cook Inlet, Alaska () and Greenland (), consistent with their subspecies status.
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http://dx.doi.org/10.1002/ece3.4345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144976PMC
August 2018

Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides.

J Plant Res 2018 Sep 23;131(5):879-885. Epub 2018 Apr 23.

Biological Sciences Department, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, USA.

Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized novel microsatellite loci from H. peploides, using reads collected from whole genome shotgun sequencing on a 454 platform. The combined output from two shotgun runs yielded a total of 62,669 reads, from which 58 loci were screened. We identified 12 polymorphic loci that amplified reliably and exhibited disomic inheritance. Microsatellite data were collected and characterized for the 12 polymorphic loci in two Alaskan populations of H. peploides: Fossil Beach, Kodiak Island (n = 32) and Egg Bay, Atka Island (n = 29). The Atka population exhibited a slightly higher average number of alleles (3.9) and observed heterozygosity (0.483) than the Kodiak population (3.3 and 0.347, respectively). The overall probability of identity values for both populations was PID = 2.892e and PID = 3.361e. We also screened the 12 polymorphic loci in Wilhelmsia physodes (Fisch. ex Ser.) McNeill, the most closely related species to H. peploides, and only one locus was polymorphic. These microsatellite markers will allow future investigations into population genetic and colonization patterns of the beach dune ruderal H. peploides on new and recently disturbed islands.
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http://dx.doi.org/10.1007/s10265-018-1036-7DOI Listing
September 2018

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes.

PLoS One 2017 17;12(11):e0188185. Epub 2017 Nov 17.

Department of Plant and Wildlife Sciences and Monte L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America.

Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons-F. p. tundrius, anatum, and pealei-for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings-a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)-each comprised of discrete populations that are variously intra-regionally connected.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188185PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693296PMC
December 2017

Genetic structure among greater white-fronted goose populations of the Pacific Flyway.

Ecol Evol 2017 05 22;7(9):2956-2968. Epub 2017 Mar 22.

U.S. Geological Survey Alaska Science Center Anchorage AK USA.

An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.
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http://dx.doi.org/10.1002/ece3.2934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5415542PMC
May 2017

Legacy or colonization? Posteruption establishment of peregrine falcons () on a volcanically active subarctic island.

Ecol Evol 2017 Jan 12;7(1):107-114. Epub 2016 Dec 12.

US Geological Survey Alaska Science Center Anchorage AK USA.

How populations and communities reassemble following disturbances are affected by a number of factors, with the arrival order of founding populations often having a profound influence on later populations and community structure. Kasatochi Island is a small volcano located in the central Aleutian archipelago that erupted violently August 8, 2008, sterilizing the island of avian biodiversity. Prior to the eruption, Kasatochi was the center of abundance for breeding seabirds in the central Aleutian Islands and supported several breeding pairs of peregrine falcons (). We examined the reestablishment of peregrine falcons on Kasatochi by evaluating the genetic relatedness among legacy samples collected in 2006 to those collected posteruption and to other falcons breeding along the archipelago. No genotypes found in posteruption samples were identical to genotypes collected from pre-eruption samples. However, genetic analyses suggest that individuals closely related to peregrine falcons occupying pre-eruption Kasatochi returned following the eruption and successfully fledged young; thus, a genetic legacy of pre-eruption falcons was present on posteruption Kasatochi Island. We hypothesize that the rapid reestablishment of peregrine falcons on Kasatochi was likely facilitated by behavioral characteristics of peregrine falcons breeding in the Aleutian Islands, such as year-round residency and breeding site fidelity, the presence of an abundant food source (seabirds), and limited vegetation requirements by seabirds and falcons.
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http://dx.doi.org/10.1002/ece3.2631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215189PMC
January 2017

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Evol Appl 2016 Jul 3;9(6):805-17. Epub 2016 Jun 3.

Flathead Lake Biological StationUniversity of MontanaPolsonMTUSA; Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaMissoulaMTUSA.

Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.
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http://dx.doi.org/10.1111/eva.12389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908466PMC
July 2016

The Structure of Genetic Diversity in Eelgrass (Zostera marina L.) along the North Pacific and Bering Sea Coasts of Alaska.

PLoS One 2016 22;11(4):e0152701. Epub 2016 Apr 22.

Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America.

Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128-0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152701PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841600PMC
March 2017

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska.

Environ Microbiol 2016 Jan 22;18(1):146-58. Epub 2015 Jul 22.

Alaska Science Center, U. S. Geological Survey, Anchorage, AK, USA.

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.
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http://dx.doi.org/10.1111/1462-2920.12924DOI Listing
January 2016

Genetic Distinctiveness of Alexander Archipelago Wolves (Canis lupus ligoni).

J Hered 2015 Jul-Aug;106(4):412-4. Epub 2015 May 11.

From the Panthera, New York, NY 10018 (Weckworth); the College of Forestry and Conservation, University of Montana, Missoula, MT 59812 (Dawson); the U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508 (Talbot); and the Biology Department and Museum of Southwestern Biology, MSC03 2020, University of New Mexico Albuquerque, NM 87131-0001 (Cook).

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http://dx.doi.org/10.1093/jhered/esv026DOI Listing
August 2015

Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic.

PLoS One 2015 6;10(1):e112021. Epub 2015 Jan 6.

Alaska Science Center, US Geological Survey, Anchorage, Alaska, United States of America.

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1-3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112021PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285400PMC
January 2016

Accounting for rate variation among lineages in comparative demographic analyses.

Evolution 2014 Sep 21;68(9):2689-700. Epub 2014 Jul 21.

U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska, 99508.

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.
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http://dx.doi.org/10.1111/evo.12469DOI Listing
September 2014

Powassan virus in mammals, Alaska and New Mexico, U.S.A., and Russia, 2004-2007.

Emerg Infect Dis 2013 Dec;19(12):2012-6

Powassan virus is endemic to the United States, Canada, and the Russian Far East. We report serologic evidence of circulation of this virus in Alaska, New Mexico, and Siberia. These data support further studies of viral ecology in rapidly changing Arctic environments.
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http://dx.doi.org/10.3201/eid1912.130319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840874PMC
December 2013

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

Proc Natl Acad Sci U S A 2012 Sep 23;109(36):E2382-90. Epub 2012 Jul 23.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.
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http://dx.doi.org/10.1073/pnas.1210506109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437856PMC
September 2012

A climate for speciation: rapid spatial diversification within the Sorex cinereus complex of shrews.

Mol Phylogenet Evol 2012 Sep 29;64(3):671-84. Epub 2012 May 29.

Department of Biology and Museum of Southwestern Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, United States.

The cyclic climate regime of the late Quaternary caused dramatic environmental change at high latitudes. Although these events may have been brief in periodicity from an evolutionary standpoint, multiple episodes of allopatry and divergence have been implicated in rapid radiations of a number of organisms. Shrews of the Sorex cinereus complex have long challenged taxonomists due to similar morphology and parapatric geographic ranges. Here, multi-locus phylogenetic and demographic assessments using a coalescent framework were combined to investigate spatiotemporal evolution of 13 nominal species with a widespread distribution throughout North America and across Beringia into Siberia. For these species, we first test a hypothesis of recent differentiation in response to Pleistocene climate versus more ancient divergence that would coincide with pre-Pleistocene perturbations. We then investigate the processes driving diversification over multiple continents. Our genetic analyses highlight novel diversity within these morphologically conserved mammals and clarify relationships between geographic distribution and evolutionary history. Demography within and among species indicates both regional stability and rapid expansion. Ancestral ecological differentiation coincident with early cladogenesis within the complex enabled alternating and repeated episodes of allopatry and expansion where successive glacial and interglacial phases each promoted divergence. The Sorex cinereus complex constitutes a valuable model for future comparative assessments of evolution in response to cyclic environmental change.
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http://dx.doi.org/10.1016/j.ympev.2012.05.021DOI Listing
September 2012

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

Mol Ecol 2011 Oct 15;20(20):4346-70. Epub 2011 Sep 15.

Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.
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http://dx.doi.org/10.1111/j.1365-294X.2011.05226.xDOI Listing
October 2011

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

PLoS One 2011 May 4;6(5):e19582. Epub 2011 May 4.

Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019582PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087762PMC
May 2011

Adverse foraging conditions may impact body mass and survival of a high Arctic seabird.

Oecologia 2011 Sep 29;167(1):49-59. Epub 2011 Mar 29.

Environmental Science Department, Alaska Pacific University, Anchorage, AK 99508, USA.

Tradeoffs between current reproduction and future survival are widely recognized, but may only occur when food is limited: when foraging conditions are favorable, parents may be able to reproduce without compromising their own survival. We investigated these tradeoffs in the little auk (Alle alle), a small seabird with a single-egg clutch. During 2005-2007, we examined the relationship between body mass and survival of birds breeding under contrasting foraging conditions at two Arctic colonies. We used corticosterone levels of breeding adults as a physiological indicator of the foraging conditions they encountered during each reproductive season. We found that when foraging conditions were relatively poor (as reflected in elevated levels of corticosterone), parents ended the reproductive season with low body mass and suffered increased post-breeding mortality. A positive relationship between body mass and post-breeding survival was found in one study year; light birds incurred higher survival costs than heavy birds. The results of this study suggest that reproducing under poor foraging conditions may affect the post-breeding survival of long-lived little auks. They also have important demographic implications because even a small change in adult survival may have a large effect on populations of long-lived species.
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http://dx.doi.org/10.1007/s00442-011-1971-7DOI Listing
September 2011

The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America.

PLoS One 2010 Nov 18;5(11):e14042. Epub 2010 Nov 18.

Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA.

Background: Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F(ST) and D(EST)), and effective population size (N(e)). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions.

Methodology/principal Findings: The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N(e) were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods.

Conclusions/significance: These results, including those from simulations to assess the power of each method to estimate N(e), suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014042PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987794PMC
November 2010

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani.

BMC Evol Biol 2010 Jul 22;10:224. Epub 2010 Jul 22.

Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA.

Background: Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.

Results: To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism.

Conclusions: These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.
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http://dx.doi.org/10.1186/1471-2148-10-224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927923PMC
July 2010

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.

Proc Natl Acad Sci U S A 2010 Mar 1;107(11):5053-7. Epub 2010 Mar 1.

Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.
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http://dx.doi.org/10.1073/pnas.0914266107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841953PMC
March 2010

Genetic variation, relatedness, and effective population size of polar bears (Ursus maritimus) in the southern Beaufort Sea, Alaska.

J Hered 2009 Nov-Dec;100(6):681-90. Epub 2009 Jul 24.

School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, Palmer, AK 99645, USA.

Polar bears (Ursus maritimus) are unique among bears in that they are adapted to the Arctic sea ice environment. Genetic data are useful for understanding their evolution and can contribute to management. We assessed parentage and relatedness of polar bears in the southern Beaufort Sea, Alaska, with genetic data and field observations of age, sex, and mother-offspring and sibling relationships. Genotypes at 14 microsatellite DNA loci for 226 bears indicate that genetic variation is comparable to other populations of polar bears with mean number of alleles per locus of 7.9 and observed and expected heterozygosity of 0.71. The genetic data verified 60 field-identified mother-offspring pairs and identified 10 additional mother-cub pairs and 48 father-offspring pairs. The entire sample of related and unrelated bears had a mean pairwise relatedness index (r(xy)) of approximately zero, parent-offspring and siblings had r(xy) of approximately 0.5, and 5.2% of the samples had r(xy) values within the range expected for parent-offspring. Effective population size (N(e) = 277) and the ratio of N(e) to total population size (N(e)/N = 0.182) were estimated from the numbers of reproducing males and females. N(e) estimates with genetic methods gave variable results. Our results verify and expand field data on reproduction by females and provide new data on reproduction by males and estimates of relatedness and N(e) in a polar bear population.
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http://dx.doi.org/10.1093/jhered/esp061DOI Listing
March 2010
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