Search USGSSearch

SEARCH · Search USGS

Results for “Conservation Genetics”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

Isolation and characterization of eight novel microsatellite loci in the double-crested cormorant ( Phalacrocorax auritus )

We describe the isolation and characterization of eight microsatellite loci from the double-crested cormorant ( Phalacrocorax auritus ). Genetic variability was assessed using 60 individuals from three populations. All loci were variable with the number of alleles ranging from two to 17 per locus, and observed heterozygosity varying from 0.05 to 0.89. No loci showed signs of linkage disequilibrium and all loci conformed to Hardy–Weinberg equilibrium frequencies. Further, all loci amplified and were polymorphic in two related Phalacrocorax species. These loci should prove useful for population genetic studies of the double-crested cormorant and other pelecaniform species.

Conservation Genetics Resources

Genetics as a tool for conservation and management of West Indian manatee populations in Brazil

A study conducted by the National Center for Research and Conservation of Aquatic Mammals (CMA), United States Geological Survey Wetland and Aquatic Research Center, and partner researchers found that the marine Antillean manatee ( Trichechus manatus manatus ) has low genetic diversity in regions where there are territorial interfaces with the Amazonian manatee ( Trichechus inunguis ). The study was published as an article in the journal, Frontiers in Marine Science.

Sirenews

Genetic structure in a previously extirpated population of gray wolves following reintroduction and natural recolonization

Genetic structuring in wildlife populations is driven by barriers that restrict gene flow as well as the history of population demography. Mechanisms driving genetic structuring can be nuanced in group-living species, such as gray wolves ( Canis lupus ). Behavioral factors, such as social affiliation and resistance, natal habitat imprinting, and trade-offs between dispersal from natal packs and territorial biding, affect habitat selection of wolves despite landscape barriers providing little resistance to their extensive dispersal capabilities. Wolves were previously extirpated from Idaho, USA, and current populations are the result of both reintroductions in 1995 and 1996 and natural dispersal from Canada. In this context we examined genetic structure of wolves in Idaho using 101 individuals genotyped at 18 nuclear DNA microsatellite loci and a subset of 38 individuals genotyped at 1019 single nucleotide polymorphism markers. We hypothesized panmictic (i.e., random mating) genetic structure in Idaho due to the long-distance dispersal abilities of gray wolves. Contrary to our hypothesis, we found three genetic clusters of gray wolves in Idaho, primarily supported by SNP markers. Microsatellite data suggested similar patterns, but permutation tests indicated these differences were not statistically significant. The extent of differentiation and evidence of gene flow, however, suggests that the three genetic clusters are not wholly isolated from one another. The distinctions between clusters spatially align with areas of reintroduction into central Idaho and Yellowstone National Park, as well ongoing natural recolonization from adjacent populations in Canada and Montana. Wolves at the periphery of analysis areas showed more admixture than those in the core, consistent with territoriality and mating behaviors contributing to genetic structuring. We demonstrate how management history, including reintroduction efforts, and animal behavior may interact and contribute to patterns of genetic structure in wild populations.

Idaho, Montana, Wyoming

PumaPlex100: An expanded tool for puma SNP genotyping with low-yield DNA

The original PumaPlex is a high-throughput assay developed to genotype 25 single nucleotide polymorphisms (SNPs) in pumas ( Puma concolor ). Here, we describe the development of PumaPlex100 – an expanded version of the original assay that now genotypes > 100 SNPs. We tested 142 candidate SNPs and developed a panel of 101 polymorphic loci, which are spread across four multiplexes and suitable for genotyping of non-invasive samples. This panel will provide researchers a set of standardized markers, that can be analyzed with minimal bioinformatic skills, for the assessment of population structure and genetic diversity. These SNPs will serve as an important resource for the continued genetic monitoring of this species, especially monitoring through non-invasive sampling.

Sonora

Concordant signal of genetic variation across marker densities in the desert annual Chylismia brevipes is linked with timing of winter precipitation

Climate change coupled with large-scale surface disturbances necessitate active restoration strategies to promote resilient and genetically diverse native plant communities. However, scarcity of native plant materials hinders restoration efforts, leading practitioners to choose from potentially viable but nonlocal seed sources. Genome scans for genetic variation linked with selective environmental gradients have become a useful tool in such efforts, allowing rapid delineation of seed transfer zones along with predictions of genomic vulnerability to climate change. When properly applied, genome scans can reduce the risk of maladaptation due to mismatches between seed source and planting site. However, results are rarely replicated among complimentary data sources. Here, we compared RAD-seq datasets with 819 and 2699 SNPs (in 625 and 356 individuals, respectively) from the Mojave Desert winter annual Chylismia brevipes . Overall, we found that the datasets consistently characterized both neutral population structure and genetic–environmental associations. Ancestry analyses indicated consistent spatial genetic structuring into four regional populations. We also detected a marked signal of isolation by resistance (IBR), wherein spatial genetic structure was better explained by habitat resistance than by geographic distance. Potentially adaptive loci identified from genome scans were associated with the same environmental gradients—fall precipitation, winter minimum temperature, and precipitation timing—regardless of dataset. Paired with our finding that habitat resistance best explained genetic divergence, our results suggest that isolation of populations within environmentally similar habitats—and subsequent local adaption along gradients parallel to these habitats—drive genome-wide divergence in this species. Moreover, strong genetic associations with winter precipitation timing, along with forecasted shifts in precipitation regime due to midcentury climate change, could impact future population dynamics, habitat distribution, and genetic connectivity for C. brevipes populations within the Mojave Desert.

Arizona, California, Nevada

Genes in space: What Mojave desert tortoise genetics can tell us about landscape connectivity

Habitat loss and fragmentation in the Mojave Desert have been increasing, which can create barriers to movement and gene flow leading to decreased populations of native species. Disturbance and degradation of Mojave desert tortoise habitat includes linear features (e.g. highways, railways, and a network of dirt roads), urbanized areas, and their associated infrastructure, mining activities, energy distribution systems, and most recently, utility-scale solar facilities. To evaluate the spatial genetic structure of tortoises in an area experiencing rapid habitat loss, we conducted field surveys from 2015-2017 and genotyped 299 tortoises at 20 microsatellite loci within and around Ivanpah Valley along the California/Nevada border. We used a Bayesian clustering analysis to examine population genetic structure across valley and mountain pass habitat. Spatial principal components analysis was included to further investigate population genetic structure with isolation-by-distance. To explicitly incorporate landscape features (e.g. habitat and anthropogenic linear barriers) we used maximum likelihood population effects. We assessed recent gene flow on the landscape through maximum likelihood pedigree analyses of relatedness. We detected three to four genetic clusters with high levels of admixture that generally corresponded to three valleys separated by mountain ranges, and a genetically distinguishable population in one mountain pass. Pedigree analyses showed second order relationships up to 60 km apart suggesting a greater range of interactions and inter-relatedness between individuals than previously suspected. Our results support historical gene flow with isolation-by-resistance, and reveal a genetic signal indicative of reduction in genetic connectivity across two parallel linear features (a railway and a highway). This work demonstrates the value of protecting connected tracts of functional habitat and the importance of connectivity research in conservation.

California, Nevada

Stock composition of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) encountered in marine and estuarine environments on the U.S. Atlantic Coast

Atlantic sturgeon ( Acipenser oxyrinchus oxyrinchus ) is a large, anadromous fish native to the Atlantic Coast of North America. Although this species once supported important fisheries, centuries of exploitation and habitat degradation have resulted in dramatic declines, presumed extirpation in some rivers, and ultimately listing under the U.S. Endangered Species Act (ESA). Under the ESA, Atlantic sturgeon are listed as five separate Distinct Population Segments (DPSs), which form the basis for federal management. Despite state and federal protections Atlantic sturgeon still face significant threats to their recovery, including fisheries bycatch mortality, marine construction, dredging, dams, and vessel strikes. However, because subadult and adult Atlantic sturgeon migrate extensively across estuarine and marine environments and frequently form mixed-stock aggregations in non-natal habitats, it can be difficult to determine how these threats impact specific populations and DPSs. To better understand ontogenetic shifts in habitat use and stock-specific exposure to anthropogenic threats, we performed a mixed-stock analysis of 1704 Atlantic sturgeon encountered across the U.S. Atlantic Coast. Collections made north of Cape Cod, MA and south of Cape Hatteras, NC were dominated by individuals from regional stocks; however, we found extensive stock mixing in the mid-Atlantic region, particularly in coastal environments where individuals from all five DPSs were commonly observed. Subadults and adults that were encountered in offshore environments had moved, on average, 277 km from their natal source; however, 23% were sampled over 500 km from their natal river suggesting long-distance movements are relatively common in these age classes. Overall, our work highlights that Atlantic sturgeon populations are vulnerable to threats over vast areas and emphasizes the need for continued genetic monitoring to track recovery progress.

Atlantic Coast

Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.

Journal of Great Lakes Research

Characterization of ten microsatellite loci in midget faded rattlesnake (Crotalus oreganus concolor)

Primers for 10 microsatellite loci were developed for midget faded rattlesnake ( Crotalus oreganus concolor ), a small bodied subspecies of the Western Rattlesnake, which is found in the Colorado Plateau of eastern Utah, western Colorado and southwestern Wyoming. In a screen of 23 individuals from the most northern portion of the subspecies range in southwestern Wyoming, the 10 loci were found to have levels of variability ranging from 4 to 11 alleles. No loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses, which will ultimately aid in management efforts for this rare subspecies of rattlesnake.

Conservation Genetics Resources

An amplicon genotyping panel suitable for species identification and population genetics in sauger (Sander canadensis) and walleye (Sander vitreus)

Sauger ( Sander canadensis ) and walleye ( Sander vitreus ) are closely related North American fish species that are often managed by fishery agencies throughout their ranges. However, genotyping resources for sauger are presently limited to a small set of microsatellite loci. We evaluated whether primers in an existing walleye genotyping-in-thousands panel could amplify single nucleotide polymorphism loci (SNPs) in sauger. We identified 71 primer pairs that amplify 118 SNPs in both species. Allele frequency differences were large enough to confidently distinguish the species and identify hybrids. Additionally, we identified 41 loci with observed heterozygosity > 0.1 in sauger; these markers may be useful for simple population genetic analyses and parentage analysis when few contributors are present and for differentiating highly structured populations.

Minnesota, Wisconsin

Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

Journal of Biodiversity & Endangered Species

Genetic swamping and species collapse: Tracking introgression between the native Candy Darter and introduced Variegate Darter

Candy Darters ( Etheostoma osburni ) and Variegate Darters (E. variatum ) are both native to West Virginia and Virginia. The geographic ranges of these two species were historically separated by Kanawha Falls, a natural barrier to fish dispersal located at Glen Ferris, WV. In the early 1980s, Variegate Darters or putative hybrids ( E. osburni × E. variatum ) were first collected at locations upstream of Kanawha Falls, and have since undergone range expansion. Hybridization with the Variegate Darter was one of the threats that led to the Candy Darter being proposed for listing under the U.S. Endangered Species Act in 2017. Genetic and morphologic data were examined for individuals from the New, Gauley, and Greenbrier river drainages. Individuals were genotyped using a suite of 5 diagnostic microsatellite loci to investigate potential hybridization. Widespread hybridization was found throughout populations of Candy Darters, with the geographic range of hybridization expanding from 2004 to 2014. A hybrid zone was observed, with the highest levels of Variegate Darter introgression representing the kernel within this zone and the locations of first-generation (F1) hybrids at the periphery. F1 hybrids were morphologically intermediate within and across characters for parental species. Introgressive hybridization threatens the genetic integrity of the Candy Darter, and may lead to population extirpation or extinction.

West Virginia

Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace ( Tribolodon hakonensis )

Twenty one polymorphic microsatellite loci for the Japanese dace ( Tribolodon hakonensis ) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.

Conservation Genetics Resources

Molecular status of the dusky Canada goose (Branta canadensis occidentalis): A genetic assessment of a translocation effort

Until recently, the dusky Canada goose ( Branta canadensis occidentalis ) was managedas one breeding population from the CopperRiver Delta (CRD), Alaska. Population numberson the CRD have declined precipitously over thelast three decades, due in part to changes inhabitat. In 1981, a pair of Canada geese,presumably B.c. occidentalis , wasreported nesting on Middleton Island (MID), inthe Gulf of Alaska. Numbers of Canada geese onthe island increased in the decade subsequentto a translocation of geese from CRD to MID,but it is unclear whether the increase isattributable to the translocation effort. Weused genetic data derived from three classes ofgenetic markers to clarify relationships ofCanada geese breeding in south-coastal Alaska. Geese were sampled from 5 populations: CRD,MID, Anchorage (ANC), Admiralty Island (ADM) insoutheastern Alaska, and Green Island (GRN) inPrince William Sound (PWS). Mitochondrial DNAanalyses demonstrate Canada geese from MID arenearly monomorphic for a unique haplotype fixedon GRN but not found in CRD or any otherbreeding population. Furthermore, nuclearmarkers consistently cluster MID with GRN tothe exclusion of CRD. We suggest the currentpopulation on MID is not derived from birdstranslocated from CRD, but rather that MID wasmost likely colonised by birds inhabiting otherisland habitats within the PWS. Furthermore,since geese from the CRD share mtDNA haplotypeswith geese from other breeding locales, theyapparently share recent common ancestry and/orgene flow with populations representing othersubspecies. Our genetic data raise questionsabout the validity of current management unitsof Canada geese.

Conservation Genetics

Genetic variation in steelhead ( Salmo gairdneri ) from the north coast of Washington

Steelhead ( Salmo gairdneri ) collected from various sites in nine drainages in northwestern Washington were genetically characterized at 65 protein-coding loci by starch-gel electrophoresis. Genetic differentiation within and among drainages was not significant, and genetic variation among drainages was much less than that reported in British Columbia; these results may be the consequence of gene flow from hatchery stocks that have been released in Washington since the 1940's. Allele frequencies varied significantly among year-classes (hence, genetic characterization studies must include data from several year-classes), and also between hatchery fish (including a stock developed with local wild fish) and wild fish, indicating that few wild fish have been successfully and routinely included in hatchery brood stocks. Conservation of genetic diversity along the north coast of Washington should be facilitated by reducing the numbers of hatchery fish that spawn in streams and by including wild fish in hatchery brood stocks.

Washington

Gunnison sage-grouse lek site suitability modeling

In order to better understand and protect species with minimal or decreasing populations, it is imperative to determine their actual existing population size. The focal species for this project is the Gunnison sage-grouse (GUSG), which became a proposed endangered species under the Endangered Species Act, thus confirming the need for better population estimates. Lek site counting during mating season has historically been the primary method for estimating population size since the grouse are very difficult to count at other times of the year. The objective of this project was to use historical data and available technology to identify additional potential lekking sites. This was done by determining areas throughout the study area that have the same landscape characteristics as those where known lekking activities occur. More accurate population counts could be the outcome of locating more lek sites. One of the remaining seven GUSG populations, the Crawford population (estimated at 128 individuals) exists in an area that includes the Gunnison Gorge National Conservation Area and the northern portion of the Black Canyon of the Gunnison National Park (our study area). While the Crawford population is small, it is still considered a self-sustaining population; the persistence and growth of this population directly contribute to genetic diversity conservation of this declining species. To date, only observational and anecdotal information about the Crawford population’s range, movements, and seasonal habitat use exist. From 1978 to the present, GUSG population monitoring has been accomplished through annual lek counts conducted each spring during GUSG mating season. Although this method has provided information on GUSG population trends, it is somewhat limited because counts are based only on known lekking sites and historically minimal efforts have been made to identify additional lek sites. To meet the objective of locating more potential lekking sites, we used a suite of spatial data, geographic information system tools, and maximum entropy species distribution tools. Based on expert knowledge and landscape variables, the modeling process evolved into a hybrid approach for delineating areas that would have a significant probability for supporting GUSG lekking activities. Based on model results, a sampling protocol was developed for model verification. The results of this project provide wildlife managers with a more sophisticated methodology to evaluate GUSG habitat for potential lekking sites.

Colorado

Utilization of genetic data to inform native Brook Trout conservation in North Carolina

As North Carolina’s only native salmonid, Brook Trout Salvelinus fontinalis is a fish of considerable ecological and cultural significance in the state, but anthropogenic alterations to the landscape and introductions of nonnative salmonids have fragmented and reduced its native range. As a result, the North Carolina Wildlife Resources Commission (NCWRC) has enacted numerous efforts to help conserve the species. Annual demographic surveys of self-sustaining Brook Trout populations have been on-going since 1978, which have also included successful efforts to document previously unidentified populations. Beginning in earnest during the 1990s, allozyme testing was used to assess patterns of hatchery introgression, with over 480 collections genotyped at the creatine kinase locus. In 2010, the NCWRC began using microsatellite markers to conduct an extensive survey of Brook Trout genetic diversity and variation. To date, 541 Brook Trout collections representing 11,090 individuals have been genotyped at 12 microsatellite loci. These data have provided insights into evolutionary relationships among populations, spatial patterns of genetic diversity, and the extent of hatchery introgression within populations. Ultimately, increased understanding of genetic diversity and relatedness have been informative for determining that Brook Trout management in North Carolina is likely best enacted at the level of individual populations. Moreover, we have used these data to actively guide stream restoration and population reintroduction activities. Over the last 15 years, NCWRC and its partners have used genetic data to prioritize habitat enhancement activities and guide 17 Brook Trout population reintroduction projects. In the future, we plan to continue expanding the microsatellite genetic baseline while also exploring the utility of phylogenomic analyses to inform Brook Trout conservation activities. Genetic and genomic approaches have great potential to improve the efficacy of conservation actions for Brook Trout in North Carolina and throughout its native range.

North Carolina

Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (Centrocercus urophasianus phaios) subspecies of Sage-grouse using mitochondrial control-region sequence data

The status of Sage-grouse ( Centrocercus urophasianus ) is of increasing concern, as populations throughout its range have contracted as a result of habitat loss and degradation. Historically, Sage-grouse were classified into two subspecies: eastern( C. u. urophasianus ) and western Sage-grouse ( C. u. phaios ) based on slight differences in coloration noted among eight individuals sampled from Washington, Oregon, and California. We sequenced a rapidly evolving portion of the mitochondrial control region in 332 birds from 16 populations. Although our sampling area covers the proposed boundary between the eastern and western subspecies, no genetic evidence to support the delineation of these subspecies was found. However, a population straddling southwestern Nevada and eastern California was found to contain an unusually high proportion of unique haplotypes, consistent with its genetic isolation from other Sage-grouse populations. Of additional interest was the lack of diversity in the two populations sampled from Washington, one of which contained only a single haplotype. We suggest that multiple lines of evidence are valuable for the formulation of conservation strategies and hence the southwestern Nevada/eastern California population merits further morphological, behavioral, and molecular investigation.

Conservation Genetics