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At least 775 records · Page 43Linked to original sources

USGS2009

Fine-scale population genetic structure in Alaskan Pacific halibut ( Hippoglossus stenolepis )

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine microsatellite loci, significant heterogeneity was detected between Aleutian Island Pacific halibut and fish from the other two regions ( F ST range = 0.007–0.008). Significant F ST values represent the first genetic evidence of divergent groups of halibut in the central and western Aleutian Archipelago. No significant genetic differences were found between Pacific halibut in the Gulf of Alaska and the Bering Sea leading to questions about factors contributing to separation of Aleutian halibut. Previous studies have reported Aleutian oceanographic conditions at deep inter-island passes leading to ecological discontinuity and unique community structure east and west of Aleutian passes. Aleutian Pacific halibut genetic structure may result from oceanographic transport mechanisms acting as partial barriers to gene flow with fish from other Alaskan waters.

Alaska↗

USGS2010

Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): Implications for the conservation of frogs and rivers

Genetic data are increasingly being used in conservation planning for declining species. We sampled both the ecological and distributional limits of the foothill yellow-legged frog, Rana boylii to characterize mitochondrial DNA (mtDNA) variation in this declining, riverine amphibian. We evaluated 1525 base pairs (bp) of cytochrome b and ND2 fragments for 77 individuals from 34 localities using phylogenetic and population genetic analyses. We constructed gene trees using maximum likelihood and Bayesian inference, and quantified genetic variance (using AMOVA and partial Mantel tests) within and among hydrologic regions and river basins. Several moderately supported, geographically-cohesive mtDNA clades were recovered for R. boylii. While genetic variation was low among populations in the largest, most inclusive clade, samples from localities at the edges of the geographic range demonstrated substantial genetic divergence from each other and from more central populations. Hydrologic regions and river basins, which represent likely dispersal corridors for R. boylii, accounted for significant levels of genetic variation. These results suggest that both rivers and larger hydrologic and geographic regions should be used in conservation planning for R. boylii. ?? 2010 US Government.

Conservation Genetics↗

USGS2011

Genetic discontinuity among regional populations of Lophelia perfusa in the North Atlantic Ocean

Knowledge of the degree to which populations are connected through larval dispersal is imperative to effective management, yet little is known about larval dispersal ability or population connectivity in Lophelia pertusa, the dominant framework-forming coral on the continental slope in the North Atlantic Ocean. Using nine microsatellite DNA markers, we assessed the spatial scale and pattern of genetic connectivity across a large portion of the range of L. pertusa in the North Atlantic Ocean. A Bayesian modeling approach found four distinct genetic groupings corresponding to ocean regions: Gulf of Mexico, coastal southeastern U.S., New England Seamounts, and eastern North Atlantic Ocean. An isolation-by-distance pattern was supported across the study area. Estimates of pairwise population differentiation were greatest with the deepest populations, the New England Seamounts (average FST = 0.156). Differentiation was intermediate with the eastern North Atlantic populations (FST = 0.085), and smallest between southeastern U.S. and Gulf of Mexico populations (FST = 0.019), with evidence of admixture off the southeastern Florida peninsula. Connectivity across larger geographic distances within regions suggests that some larvae are broadly dispersed. Heterozygote deﬁciencies were detected within the majority of localities suggesting deviation from random mating. Gene ﬂow between ocean regions appears restricted, thus, the most effective management scheme for L. pertusa involves regional reserve networks

Conservation Genetics↗

USGS2011

Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae)

Imperiled Okaloosa darters ( Etheostoma okaloosae ) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom’s, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

Florida↗

USGS2011

Phylogeography of a vanishing North American songbird: The Painted Bunting (Passerina ciris)

The breeding distribution of Painted Buntings ( Passerina ciris ) is comprised of two allopatric populations separated by a 550-km distributional gap in the southeastern United States. Curiously, the boundary between the two recognized P. ciris subspecies does not separate the two allopatric breeding populations but instead runs roughly through the center of the interior population. Genetic relationships among these subspecies, and the allopatric breeding populations of Painted Bunting, have not been assessed. Given the recent decline in overall abundance of this species, such an assessment is warranted. We sampled birds from 15 localities (138 individuals) and identified 35 distinct haplotypes, six belonging to the Atlantic Coast population and 26 to the interior population, with three shared by both populations. AMOVA results showed that a significantly greater portion of the total genetic variance is explained when grouping birds by the interior and Atlantic Coast populations rather than by subspecies. Furthermore, our data indicate that the Atlantic Coast and interior populations represent independently evolving taxa, with no measureable gene flow between them. Although recently diverged (26,000–115,000 years ago), these isolated bunting populations represent incipient species. For development of conservation strategies, we suggest that the Atlantic Coast and interior populations be recognized as separate management units.

Conservation Genetics↗

USGS2011

Deltamethrin flea-control preserves genetic variability of black-tailed prairie dogs during a plague outbreak

Genetic variability and structure of nine black-tailed prairie dog (BTPD, Cynomys ludovicianus ) colonies were estimated with 15 unlinked microsatellite markers. A plague epizootic occurred between the first and second years of sampling and our study colonies were nearly extirpated with the exception of three colonies in which prairie dog burrows were previously dusted with an insecticide, deltamethrin, used to control fleas (vectors of the causative agent of plague, Yersinia pestis ). This situation provided context to compare genetic variability and structure among dusted and non-dusted colonies pre-epizootic, and among the three dusted colonies pre- and post-epizootic. We found no statistical difference in population genetic structures between dusted and non-dusted colonies pre-epizootic. On dusted colonies, gene flow and recent migration rates increased from the first (pre-epizootic) year to the second (post-epizootic) year which suggested dusted colonies were acting as refugia for prairie dogs from surrounding colonies impacted by plague. Indeed, in the dusted colonies, estimated densities of adult prairie dogs (including dispersers), but not juveniles (non-dispersers), increased from the first year to the second year. In addition to preserving BTPDs and many species that depend on them, protecting colonies with deltamethrin or a plague vaccine could be an effective method to preserve genetic variability of prairie dogs.

Montana↗

USGS2012

The genetic structure of a relict population of wood frogs

Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs ( Lithobates sylvatica ) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

Colorado↗

USGS2013

Severe reduction in genetic variation in a montane isolate: The endangered Mount Graham red squirrel (Tamiasciurus hudsonicus grahamensis)

The Mount Graham red squirrel ( Tamiasciurus hudsonicus grahamensis ; MGRS) is endemic to the Pinaleño Mountains of Arizona at the southernmost extent of the species’ range. The MGRS was listed as federally endangered in 1987, and is currently at high risk of extinction due to declining population size and increasing threats. Here we present a genetic assessment of the MGRS using eight nuclear DNA microsatellite markers and a 472 bp fragment of the mitochondrial cytochrome b gene. We analyzed 34 MGRS individuals and an additional 66 red squirrels from the nearby White Mountains, Arizona ( T. h. mogollonensis ). Both nuclear and mitochondrial DNA analyses revealed an extreme reduction in measures of genetic diversity relative to conspecifics from the White Mountains, suggesting that the MGRS has either experienced multiple bottlenecks, or a single long-term bottleneck. Additionally, we found a high degree of relatedness (mean = 0.75 ± 0.18) between individual MGRS. Our study implies that the MGRS may lack the genetic variation required to respond to a changing environment. This is especially important considering this region of the southwest United States is expected to experience profound effects from global climate change. The reduced genetic variability together with the high relatedness coefficients should be taken into account when constructing a captive population to minimize loss of the remaining genetic variation.

Conservation Genetics↗

USGS2014

Ephemeral stream reaches preserve the evolutionary and distributional history of threespine stickleback in the Santa Clara and Ventura River watersheds of southern California

Much remains to be understood about the evolutionary history and contemporary landscape genetics of unarmored threespine stickleback in southern California, where populations collectively referred to as Gasterosteus aculeatus williamsoni have severely declined over the past 70+ years and are now endangered. We used mitochondrial sequence and microsatellite data to assess the population genetics and phylogeography of unarmored populations sampled immediately downstream from the type locality of G. a. williamsoni in the upper Santa Clara River, and assessed their distinctiveness with respect to low-armor populations in the downstream sections of the river and the adjacent Ventura River. We also characterized the geographic limits of different plate morphs and evaluated the congruence of those boundaries with barriers to dispersal in both river systems and to neutral genetic variation. We show substantial population structuring within the upper reach of the Santa Clara River, but little partitioning between the lower Santa Clara and Ventura Rivers—we attribute these patterns to different ancestry between spatially subdivided populations within the same drainage, a predominance of downstream gene flow, and ability for coastal dispersal between the Santa Clara and Ventura Rivers. We also show that alleles from introduced low-plate stock have infiltrated a native population in at least one upper Santa Clara River tributary, causing this formerly unarmored population to become gradually low-plated over a 30 + year time period. Measures of genetic diversity, census surveys, and severe habitat disturbance all indicate that unarmored stickleback near the type locality are currently at high risk of extinction.

California↗

USGS2015

A genetic discontinuity in moose ( Alces alces ) in Alaska corresponds with fenced transportation infrastructure

The strength and arrangement of movement barriers can impact the connectivity among habitat patches. Anthropogenic barriers (e.g. roads) are a source of habitat fragmentation that can disrupt these resource networks and can have an influence on the spatial genetic structure of populations. Using microsatellite data, we evaluated whether observed genetic structure of moose ( Alces alces ) populations were associated with human activities (e.g. roads) in the urban habitat of Anchorage and rural habitat on the Kenai Peninsula, Alaska. We found evidence of a recent genetic subdivision among moose in Anchorage that corresponds to a major highway and associated infrastructure. This subdivision is most likely due to restrictions in gene flow due to alterations to the highway (e.g. moose-resistant fencing with one-way gates) and a significant increase in traffic volume over the past 30 years; genetic subdivision was not detected on the Kenai Peninsula in an area not bisected by a major highway. This study illustrates that anthropogenic barriers can substructure wildlife populations within a few generations and highlights the value of genetic assessments to determine the effects on connectivity among habitat patches in conjunction with behavioral and ecological data. .

Alaska↗

USGS2016

Can captive populations function as sources of genetic variation for reintroductions into the wild? A case study of the Arabian oryx from the Phoenix Zoo and the Shaumari Wildlife Reserve, Jordan

The Arabian oryx ( Oryx leucoryx ) historically ranged across the Arabian Peninsula and neighboring countries until its extirpation in 1972. In 1963–1964 a captive breeding program for this species was started at the Phoenix Zoo (PHX); it ultimately consisted of 11 animals that became known as the ‘World Herd’. In 1978 – 1979 a wild population was established at the Shaumari Wildlife Reserve (SWR), Jordan, with eight descendants from the World Herd and three individuals from Qatar. We described the mtDNA and nuclear genetic diversity and structure of PHX and SWR. We also determined the long-term demographic and genetic viability of these populations under different reciprocal translocation scenarios. PHX displayed a greater number of mtDNA haplotypes ( n = 4) than SWR ( n = 2). Additionally, PHX and SWR presented nuclear genetic diversities of N ¯ A N¯A = 2.88 vs. 2.75, H ¯ O H¯O = 0.469 vs. 0.387, and H ¯ E H¯E = 0.501 vs. 0.421, respectively. Although these populations showed no signs of inbreeding ( F ¯ IS F¯IS ≈ 0), they were highly differentiated ( G ′ ′ ST GST′′ = 0.580; P < 0.001). Migration between PHX and SWR ( Nm = 1, 4, and 8 individuals/generation) increased their genetic diversity in the short-term and substantially reduced the probability of extinction in PHX during 25 generations. Under such scenarios, maximum genetic diversities were achieved in the first generations before the effects of genetic drift became predominant. Although captive populations can function as sources of genetic variation for reintroduction programs, we recommend promoting mutual and continuous gene flow with wild populations to ensure the long-term survival of this species.

Conservation Genetics↗

USGS2016

Integration of genetic and demographic data to assess population risk in a continuously distributed species

The identification and demographic assessment of biologically meaningful populations is fundamental to species’ ecology and management. Although genetic tools are used frequently to identify populations, studies often do not incorporate demographic data to understand their respective population trends. We used genetic data to define subpopulations in a continuously distributed species. We assessed demographic independence and variation in population trends across the distribution. Additionally, we identified potential barriers to gene flow among subpopulations. We sampled greater sage-grouse ( Centrocercus urophasianus ) leks from across their range (≈175,000 Km 2 ) in Wyoming and amplified DNA at 14 microsatellite loci for 1761 samples. Subsequently, we assessed population structure in unrelated individuals ( n = 872) by integrating results from multiple Bayesian clustering approaches and used the boundaries to inform our assessment of long-term population trends and lek activity over the period of 1995–2013. We identified four genetic clusters of which two northern ones showed demographic independence from the others. Trends in population size for the northwest subpopulation were statistically different from the other three genetic clusters and the northeast and southwest subpopulations demonstrated a general trend of increasing proportion of inactive leks over time. Population change from 1996 to 2012 suggested population growth in the southern subpopulations and decline, or neutral, change in the northern subpopulations. We suggest that sage-grouse subpopulations in northern Wyoming are at greater risk of extirpation than the southern subpopulations due to smaller census and effective population sizes and higher variability within subpopulations. Our research is an example of incorporating genetic and demographic data and provides guidance on the identification of subpopulations of conservation concern.

Conservation Genetics↗

USGS2017

Molecular systematics of the critically-endangered North American spinymussels (Unionidae: Elliptio and Pleurobema ) and description of Parvaspina gen. nov.

Despite being common in numerous marine bivalve lineages, lateral spines are extremely rare among freshwater bivalves (Bivalvia: Unionidae), with only three known species characterized by the presence of spines: Elliptio spinosa, Elliptio steinstansana , and Pleurobema collina . All three taxa are endemic to the Atlantic Slope of southeastern North America, critically endangered, and protected by the US Endangered Species Act. Currently, these species are recognized in two genera and remain a source of considerable taxonomic confusion. Because spines are rare in freshwater mussels and restricted to a small region of North America, we hypothesized that spinymussels represent a monophyletic group. We sequenced two mtDNA gene fragments ( COI and ND1 ) and a fragment of the nuclear ITS-1 locus from >70 specimens. Bayesian and maximum-likelihood phylogenetic reconstructions suggest that the spinymussels do not comprise a monophyletic group. Elliptio steinstansana is sister to P. collina , forming a monophyletic clade that was estimated to have diverged from its most recent ancestor in the late Miocene and is distinct from both Elliptio and Pleurobema ; we describe a new genus ( Parvaspina gen. nov.) to reflect this relationship. Additionally, E. spinosa forms a monophyletic clade that diverged from members of the core Elliptio lineage in the mid-Pliocene. Furthermore, E. spinosa is genetically divergent from the other spinymussel species, suggesting that spines, while extremely rare in freshwater mussels worldwide, may have evolved independently in two bivalve lineages. Recognizing the genetic distinctiveness and inter-generic relationships of the spinymussels is an important first step towards effectively managing these imperiled species and lays the groundwork for future conservation genetics studies.

Conservation Genetics↗

USGS2017

Small-scale genetic structure in an endangered wetland specialist: possible effects of landscape change and population recovery

The effects of anthropogenic landscape change on genetic population structure are well studied, but the temporal and spatial scales at which genetic structure can develop, especially in taxa with high dispersal capabilities like birds, are less well understood. We investigated population structure in the Hawaiian gallinule ( Gallinula galeata sandvicensis ), an endangered wetland specialist bird on the island of O`ahu (Hawai`i, USA). Hawaiian gallinules have experienced a gradual population recovery from near extinction in the 1950s, and have recolonized wetlands on O`ahu in the context of a rapidly urbanizing landscape. We genotyped 152 Hawaiian gallinules at 12 microsatellite loci and sequenced a 520 base-pair fragment of the ND2 region of mitochondrial DNA (mtDNA) from individuals captured at 13 wetland locations on O`ahu in 2014–2016. We observed moderate to high genetic structuring (overall microsatellite F ST = 0.098, mtDNA F ST = 0.248) among populations of Hawaiian gallinules occupying wetlands at very close geographic proximity (e.g., 1.5–55 km). Asymmetry in gene flow estimates suggests that Hawaiian gallinules may have persisted in 2–3 strongholds which served as source populations that recolonized more recently restored habitats currently supporting large numbers of birds. Our results highlight that genetic structure can develop in taxa that are expanding their range after severe population decline, and that biologically significant structuring can occur over small geographic distances, even in avian taxa.

Hawai'i↗

USGS2019

Isolation by a hydroelectric dam induces minimal impacts on genetic diversity and population structure in six fish species

Reduced connectivity created by artificial barriers can influence the genetic integrity of isolated subpopulations by reducing local population sizes and altering patterns of gene flow. We investigated the genetic impacts of one such barrier, the Prairie du Sac dam, Wisconsin, USA, using microsatellite data from six fish species with varying life history traits sampled above and below the dam. Contrary to many past studies in other systems, we did not detect any significant differences in genetic diversity between populations found above and below the Prairie du Sac dam. Our results also revealed low genetic differentiation ( F ST = 0–0.008) between populations above and below the dam for all species. In fact, we found that more genetic variation was partitioned among sampling years than between above and below dam populations for all but one of the species. Results from coalescent simulations designed to model our study system indicated that the genetic impacts of the dam will likely be detectable approximately 40–60 generations after the dam was constructed, and that it is possible to largely mitigate these impacts with a fish passage strategy that facilitates a migration rate of ≥ 1% between above and below dam populations. In summary, our findings suggest the genetic impacts of dams can be relatively minimal on short time scales, and that fish passage strategies can significantly reduce genetic impacts if designed appropriately.

Wisconsin↗

USGS2021

Genetic structure and population history in two critically endangered Kaua‘i honeycreepers

Population sizes of endemic songbirds on Kaua‘i have decreased by an order of magnitude over the past 10–15 years to dangerously low numbers. The primary cause appears to be the ascent of invasive mosquitoes and Plasmodium relictum , the agent of avian malaria, into elevations formerly free of introduced malarial parasites and their vectors. Given that these declines in native bird populations appear to be continuing, last resort measures to save these species from extinction, such as conservation breeding, are being implemented. Using 200–1439 SNPs from across the genome, we assessed kinship among individuals, levels of genetic variation, and extent of population decline in wild birds of the two most critically endangered Kaua‘i endemic species, the ‘akikiki ( Oreomystis bairdi ) and ‘akeke‘e ( Loxops caeruleirostris ). We found relatively high genomic diversity within individuals and little evidence of spatial population genetic structure. Populations displayed genomic signatures of declining population size, but individual inbreeding coefficients were universally negative, likely indicating inbreeding avoidance. Diversity within the founding conservation breeding population largely mirrored that in the wild, indicating that genetic variation in the conservation breeding population is representative of the wild population and suggesting that the current breeding program captures existing variation. Thus, although existing genetic diversity is likely lower than in historical populations, contemporary variation has been retained through high gene flow and inbreeding avoidance. Nonetheless, current effective population size for both species was estimated at fewer than 20 individuals, highlighting the urgency of management actions to protect these species.

Hawaii↗

USGS2021

Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue

Functional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue ( Penstemon grahamii ), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.

Conservation Genetics↗

USGS2021

Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose ( Alces alces ) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.

Conservation Genetics↗