[Show abstract][Hide abstract] ABSTRACT: 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
[Show abstract][Hide abstract] ABSTRACT: Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.
No preview · Article · Aug 2014 · Conservation Genetics
[Show abstract][Hide abstract] ABSTRACT: Increased global temperature and associated changes to Arctic habitats will likely result in the northward advance of species, including an influx of pathogens novel to the Arctic. How species respond to these immunological challenges will depend in part on the adaptive potential of their immune response system. We compared levels of genetic diversity at a gene associated with adaptive immune response [Class II major histocompatibility complex (MHC), DQB exon 2] between populations of walrus (Odobenus rosmarus), a sea ice-dependent Arctic species. Walrus was represented by only five MHC DQB alleles, with frequency differences observed between Pacific and Atlantic populations. MHC DQB alleles appear to be under balancing selection, and most (80 %; n = 4/5) of the alleles were observed in walruses from both oceans, suggesting broad scale differences in the frequency of exposure and diversity of pathogens may be influencing levels of heterozygosity at DQB in walruses. Limited genetic diversity at MHC, however, suggests that walrus may have a reduced capacity to respond to novel immunological challenges associated with shifts in ecological communities and environmental stressors predicted for changing climates. This is particularly pertinent for walrus, since reductions in summer sea ice may facilitate both northward expansion of marine species and associated pathogens from more temperate regions, and exchange of marine mammals and associated pathogens through the recently opened Northwest Passage between the Atlantic and Pacific Oceans in the Canadian high Arctic.
[Show abstract][Hide abstract] ABSTRACT: Shorebirds are exceptionally diverse in their social mating systems, and genetic analyses of a few species have revealed further variation in genetic mating systems. The ecological and evolutionary causes of this variation are largely unknown. We studied the mating system of American Golden-Plovers (Pluvialis dominica) at Barrow, Alaska, between 2004 and 2009. In this arctic population, birds bred in socially monogamous pairs, as has been seen in other populations, yet rates of philopatry and mate fidelity were low. We used microsatellite DNA markers to analyze parentage and found that most offspring originated from monogamous matings, but 8% of 131 offspring and 16% of 37 nests were the result of nonmonogamous matings. One nest was ambiguous; it was either a full clutch sired through extra-pair copulation or represented an instance of social polygyny. Despite wide variation in synchrony of breeding and density of nesting both within and among breeding seasons, these ecological variables were unrelated to mating patterns. We speculate that the low rate of pair fidelity and the high rate of extra-pair paternity are linked, because the lack of familiarity between partners reduces benefits of monogamy. Further study of breeding behavior and rates of philopatry are needed to understand why, among socially monogamous shorebirds, the American Golden-Plover has high rates of extra-pair paternity.
Las aves playeras son excepcionalmente diversas en sus sistemas de apareamiento social y los análisis genéticos de unas pocas especies han revelado una mayor variación en los sistemas de apareamiento genético. Las causas ecológicas y evolutivas de esta variación son en gran medida desconocidas. Estudiamos el sistema de apareamiento de Pluvialis dominica en Barrow, Alaska, entre 2004 y 2009. En esta población ártica, las aves crían en parejas socialmente monógamas, como ha sido registrado en otras poblaciones, aunque las tasas de filopatría y de fidelidad a la pareja fueron bajas. Usamos marcadores de ADN micro satelital para analizar el parentesco y encontramos que la mayoría de las crías se originaron a partir de parejas monógamas, pero 8% de las 131 crías y 16% de los 37 nidos fueron el resultado de apareamientos no monógamos. Un nido fue ambiguo; fue o una nidada completa engendrada por copulación extra pareja, o representó un caso de poliginia social. A pesar de la amplia variación en la sincronía de la cría y en la densidad de nidificación tanto dentro como entre estaciones reproductivas, estas variables ecológicas no estuvieron relacionadas con los parones de apareamiento. Especulamos que la baja tasa de fidelidad de pareja y la alta tasa de paternidad extra pareja están vinculadas, debido a que la falta de familiaridad entre los compañeros reduce los beneficios de la monogamia. Se necesita un estudio posterior del comportamiento reproductivo y de las tasas de filopatría para entender porque, entre las aves playeras socialmente monógamas, P. dominica tiene altas tasas de paternidad extra pareja.
[Show abstract][Hide abstract] ABSTRACT: Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We developed sixteen polymorphic microsatellites from the Alaska blackfish (Dallia pectoralis) to study genetic diversity in Dallia. Genotypes from two populations, Denali (n = 31) and Bethel (n = 35), demonstrated the usefulness of the loci for population-level investigation. Observed and expected heterozygosity averaged 18.6 and 19.8 % in Denali and 61.1 and 63.7 % in Bethel. Number of alleles at each locus averaged 3.50 in Denali and 9.63 in Bethel. The observed signature of variability and structuring between populations is consistent with mitochondrial data.
No preview · Article · Jun 2013 · Conservation Genetics Resources
[Show abstract][Hide abstract] ABSTRACT: Human activities and global warming are driving major modifications in the world’s ecosystems; the coastal zone being one of the most damaged because less attention. Seagrass meadows constitute coastal communities that have experienced great losses worldwide but remains as one of the most productive. The dominant seagrass in the meadows of the coastal lagoons at Mexican Pacific coast is Zostera marina L. and represent the southern boundary of the species in the northeast Pacific. This species is heavily damaged by human activities mainly fisheries trawling and the lack of an appropriate legal protection and no management plan available. Even when seagrasses are considered as part of the Mexican Official Norm (NOM-022-SEMARNAT-2003) who protects mainly mangrove and wetlands in general and brief mention of seagrasses is made. They are not considered in the species endanger list (NOM-ECOL-059). Pacific coast populations of Z. marina are not only separated geographically but also genetically from populations in the Gulf of California. They are also exposed to different current regimes and environmental conditions. As part of a long term studies of demographic, ecophysiological and phylogeographic studies of Z. marina we are presenting here a review of the conservational status of the populations along the Mexican Pacific over the last 2 decades. Population studies have shown that Z. marina has a mixture of perennial and annual populations around the area but most of historically known sites have started to decline or completely disappear. At least 50% of the historically known sites are not longer present and the other 40% have strong impacts with reduction of their area and density causing severe pressure in the trophic structure. Severe cases, as San Ignacio Lagoon in the Pacific Coast of Baja California and the case of coastal lagoons of the eastern Gulf of California are presented as case study. Zostera marina also displays significant interpopulation differences in morphology, biochemical composition and depth distribution along this coastline that appear to be promoted by variation in climatic conditions. Furthermore, Z. marina displays restricted pollen and seed dispersal, even in areas with strong tidal currents (50 cm s-1). Analyses of molecular variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using ST values, was observed among all populations. The test for isolation by distance showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation events along the Pacific coast. Because of that we strongly suggest that special areas for conservation of Z. marina should be declared along the Mexican Pacific with the development of a management plan based on a scientific agenda.
[Show abstract][Hide abstract] ABSTRACT: Multiple species of large octopus are known from the north Pacific waters around Japan, however only one large species is known in the Gulf of Alaska (the giant Pacific octopus, Enteroctopus dofleini). Current taxonomy of E. dofleini is based on geographic and morphological characteristics, although with advances in genetic technology that is changing. Here, we used two mitochondrial genes (cytochrome b and cytochrome oxidase I), three nuclear genes (rhodopsin, octopine dehydrogenase, and paired-box 6), and 18 microsatellite loci for phylogeographic and phylogenetic analyses of octopuses collected from across southcentral and the eastern Aleutian Islands (Dutch Harbor), Alaska. Our results suggest the presence of a cryptic Enteroctopus species that is allied to, but distinguished from E. dofleini in Prince William Sound, Alaska. Existence of an undescribed and previously unrecognized taxon raises important questions about the taxonomy of octopus in southcentral Alaska waters.
No preview · Article · Dec 2012 · Conservation Genetics
[Show abstract][Hide abstract] ABSTRACT: 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 (Φ ST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (Φ ST = 0.336—0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite F ST = 0.019; mtDNA Φ ST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite F ST = 0.019—0.035; mtDNA Φ ST = 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.
No preview · Article · Dec 2012 · Journal of Mammalogy
[Show abstract][Hide abstract] ABSTRACT: North American caribou (Rangifer tarandus) herds commonly exhibit little nuclear genetic differentiation among adjacent herds, although available evidence supports strong demographic separation, even for herds with seasonal range overlap. During 1997—2003, we studied the Mentasta and Nelchina caribou herds in south-central Alaska using radiotelemetry to determine individual movements and range overlap during the breeding season, and nuclear and mitochondrial DNA (mtDNA) markers to assess levels of genetic differentiation. Although the herds were considered discrete because females calved in separate regions, individual movements and breedingrange overlap in some years provided opportunity for male-mediated gene flow, even without demographic interchange. Telemetry results revealed strong female philopatry, and little evidence of female emigration despite overlapping seasonal distributions. Analyses of 13 microsatellites indicated the Mentasta and Nelchina herds were not significantly differentiated using both traditional population-based analyses and individual-based Bayesian clustering analyses. However, we observed mtDNA differentiation between the 2 herds (F ST =0.041, P < 0.001). Although the Mentasta and Nelchina herds exhibit distinct population dynamics and physical characteristics, they demonstrate evidence of gene flow and thus function as a genetic metapopulation.
No preview · Article · Oct 2012 · Journal of Mammalogy
[Show abstract][Hide abstract] ABSTRACT: Northern Goshawks occupying the Alexander Archipelago, Alaska, and coastal British Columbia nest primarily in old-growth and mature forest, which results in spatial heterogeneity in the distribution of individuals across the landscape. We used microsatellite and mitochondrial data to infer genetic structure, gene flow, and fluctuations in population demography through evolutionary time. Patterns in the genetic signatures were used to assess predictions associated with the three population models: panmixia, metapopulation, and isolated populations. Population genetic structure was observed along with asymmetry in gene flow estimates that changed directionality at different temporal scales, consistent with metapopulation model predictions. Therefore, Northern Goshawk assemblages located in the Alexander Archipelago and coastal British Columbia interact through a metapopulation framework, though they may not fit the classic model of a metapopulation. Long-term population sources (coastal mainland British Columbia) and sinks (Revillagigedo and Vancouver islands) were identified. However, there was no trend through evolutionary time in the directionality of dispersal among the remaining assemblages, suggestive of a rescue–effect dynamic. Admiralty, Douglas, and Chichagof island complex appears to be an evolutionarily recent source population in the Alexander Archipelago. In addition, Kupreanof island complex and Kispiox Forest District populations have high dispersal rates to populations in close geographic proximity and potentially serve as local source populations. Metapopulation dynamics occurring in the Alexander Archipelago and coastal British Columbia by Northern Goshawks highlight the importance of both occupied and unoccupied habitats to long-term population persistence of goshawks in this region.
No preview · Article · Aug 2012 · Conservation Genetics
[Show abstract][Hide abstract] ABSTRACT: 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.
Full-text · Article · Jul 2012 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: The major histocompatibility complex (MHC), which harbours the most polymorphic vertebrate genes, plays a critical role in the host-pathogen coevolutionary arms race. However, the extent to which MHC diversity determines disease susceptibility and long-term persistence of populations is currently under debate, as recent studies have demonstrated that low MHC variability does not necessarily hamper population viability. However, these studies typically assayed small and decimated populations in species with restricted distribution, thereby making inferences about the evolutionary potential of these populations difficult. Here, we show that MHC impoverishment has not constrained the ecological radiation and flourishing of falcons (Aves: Falconidae) worldwide. We found two remarkably different patterns of MHC variation within the genus Falco. Whereas MHC variation in kestrels (the basal group within the genus) is very high, falcons exhibit ancestrally low intra- and interspecific MHC variability. This pattern is not due to the inadvertent survey of paralogous genes or pseudogenes. Further, patterns of variation in mitochondrial or other nuclear genes do not indicate a generalized low level of genome-wide variability among falcons. Although a relative contribution of genetic drift cannot be completely ruled out, we propose the falcons went through an evolutionary transition, driven and maintained by natural selection, from primarily highly variable towards low polymorphic and slow-evolving MHC genes with a very specific immune function. This study highlights that the importance of MHC diversity cannot be generalized among vertebrates, and hints at the evolution of compensatory immune mechanisms in falcons to cope with emerging and continuously evolving pathogens.
[Show abstract][Hide abstract] ABSTRACT: The major histocompatibility complex (MHC), which harbours the most
polymorphic vertebrate genes, plays a critical role in the host–pathogen
coevolutionary arms race. However, the extent to which MHC diversity
determines disease susceptibility and long-term persistence of populations is
currently under debate, as recent studies have demonstrated that low MHC
variability does not necessarily hamper population viability. However, these
studies typically assayed small and decimated populations in species with
restricted distribution, thereby making inferences about the evolutionary
potential of these populations difficult. Here, we show that MHC impoverishment
has not constrained the ecological radiation and flourishing of falcons
(Aves: Falconidae) worldwide. We found two remarkably different patterns of
MHC variation within the genus Falco. Whereas MHC variation in kestrels (the
basal group within the genus) is very high, falcons exhibit ancestrally low
intra- and interspecific MHC variability. This pattern is not due to the
inadvertent survey of paralogous genes or pseudogenes. Further, patterns of
variation in mitochondrial or other nuclear genes do not indicate a generalized
low level of genome-wide variability among falcons. Although a relative
contribution of genetic drift cannot be completely ruled out, we propose the
falcons went through an evolutionary transition, driven and maintained by
natural selection, from primarily highly variable towards low polymorphic and
slow-evolving MHC genes with a very specific immune function. This study
highlights that the importance of MHC diversity cannot be generalized among
vertebrates, and hints at the evolution of compensatory immune mechanisms
in falcons to cope with emerging and continuously evolving pathogens.
[Show abstract][Hide abstract] ABSTRACT: We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.
Full-text · Article · Jun 2012 · Conservation Genetics Resources
[Show abstract][Hide abstract] ABSTRACT: We developed microsatellite loci for demographic assessments of shorebirds, a group with limited markers. First, we isolated five dinucleotide repeat microsatellite loci from the Black Oystercatcher (Haematopodidae: Haematopus bachmani), and three from the Bristle-thighed Curlew (Scolopacidae: Numenius tahitiensis); both species are of conservation concern. All eight loci were polymorphic in their respective target species. Hbaμ loci were characterized by two to three alleles with observed heterozygosity ranging from 0.07 to 0.33, and two to nine alleles were detected for Nut loci with observed heterozygosity ranging from 0.08 to 0.72. No linkage disequilibrium or departures from Hardy–Weinberg equilibrium were observed. The eight loci were also tested for cross-species amplification in 12 other species within Charadriidae and Scolopacidae, and the results demonstrated transferability across several genera. We further tested all 14 species at 12 additional microsatellite markers developed for other shorebirds: Dunlin (Calidris alpina; four loci) and Ruff (Philomachus pugnax; eight loci). Two markers (Hbaμ4 and Ruff6) were polymorphic in 13 species, while two (Calp6 and Ruff9) were monomorphic. The remaining eight markers revealed polymorphism in one to nine species each. Our results provide further evidence that locus Ruff10 is sex-linked, contrary to the initial description. These markers can be used to enhance our understanding of shorebird biology by, for example, helping to determine migratory connectivity among breeding and wintering populations and detecting relatedness among individuals.
[Show abstract][Hide abstract] ABSTRACT: We used feathers from adult Gyrfalcons (Falco rusticolus) molted in breeding territories and blood samples from nestlings to document nest-site fidelity and dispersal of breeding adults and juveniles at three areas 100– 350 km apart in Yukon Delta National Wildlife Refuge, Alaska, 2003–2007. We used genotypes from seven polymorphic microsatellite loci that provided a mean probability of identity of 0.91 × 10-5. Breeding Gyrfalcons were highly faithful to study area and territory; we documented no dispersals of breeding birds among study areas and only one dispersal between territories. But their fidelity to nest sites was low; 22% of birds returned to the same nest site the following year. Distance among alternate nests within a territory averaged 750 m and was similar for both sexes. Mean tenure in a territory was 2.8 years, similar for both sexes, and distributed bimodally with peaks at 1 and 4 years. Mean annual turnover rate at the Ingakslugwat Hills (Volcanoes) study area was 20%. We detected three young that established breeding territories at distances ranging from 0 to 254 km from their natal territory, representing 2.5% apparent recruitment. Gyrfalcons in the Askinuk Mountains study area were slightly but statistically significantly differentiated genetically from those in the Volcanoes and Kilbuck Mountain study areas. These data are the first published on the nest-site fidelity, breeding dispersal, and natal dispersal of the Gyrfalcon in North America and demonstrate the utility of noninvasive genetic sampling to greatly improve our understanding of avian dispersal and its underlying mechanisms.
[Show abstract][Hide abstract] ABSTRACT: Gene flow can have profound effects on the genetic diversity of a founding population depending on the number and relationship among colonizers and the duration of the colonization event. Here we used data from nuclear microsatellite and mitochondrial DNA control region loci to assess genetic diversity in golden eagles of the recently colonized Channel Islands, California. Genetic diversity in the Channel Island population was low, similar to signatures observed for other recent colonizing island populations. Differences in levels of genetic diversity and structure observed between mainland California and the islands suggests that few individuals were involved in the initial founding event, and may have comprised a family group. The spatial genetic structure observed between Channel Island and mainland California golden eagle populations across marker types, and genetic signature of population decline observed for the Channel Island population, suggest a single or relatively quick colonization event. Polarity in gene flow estimates based on mtDNA confirm an initial colonization of the Channel Islands by mainland golden eagles, but estimates from microsatellite data suggest that golden eagles on the islands were dispersing more recently to the mainland, possibly after reaching the carrying capacity of the island system. These results illustrate the strength of founding events on the genetic diversity of a population, and confirm that changes to genetic diversity can occur within just a few generations.
No preview · Article · Feb 2012 · Biological Conservation