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USGS2017

The Southern Appalachian Brook Trout management conundrum: What should restoration look like in the 21st Century?

Brook Trout Salvelinus fontinalis in the southern Appalachian portion of their range have been isolated in remote headwater systems for millennia. Recent genetic investigations indicate extremely low allelic diversity, heterozygosity and effective population sizes in many streams. In populations restored using multiple source stocks, limited introgression has been observed despite source stocks being collected from streams within the same subwatershed. It remains unclear if pre- and/or post-reproductive isolating mechanisms are restricting effective gene flow among source stocks in restored streams. Objectives of this study were to: 1) identify environmental variables contributing to assortative mating, and 2) use common garden crossings to determine if wild type brood stock crossings resulted in physiologically viable offspring. We observed markedly different fertilization success rates within-population (66.7%) and betweenpopulation (91.7%) from the 42 crosses (N=18 control, N=24 treatment). Moreover, we observed significant (P < 0.05) differences between within-population and between-population groups in each of our linear mixed effects global models for each trial stage of development (i.e., fertilization rate, eyed egg rate, and hatch rates). Tukey’s HSD comparisons revealed only one significantly (P < 0.003) different fertilization rate among the forty five pairwise comparisons in each of our three stages of trails. In addition, we observed differential peaks of gamete production within and among source stream brood stock, despite common garden conditions, that appeared to have limited fertilization success rates between interstream and control groups. Despite differential peak gamete timing, intrastream crosses performed equally, and, in some instances, better than those between control groups. Our results suggest differential responses to shared environmental conditions (i.e., temperature and/or photoperiod) may contribute to mismatched spawning phenology (i.e., gamete production timing) among restoration founder stocks leading to introgression (i.e., genetic admixture). The application of contemporary genetic techniques could help determine if these possible local adaptations are genetically fixed or may break down over time in restored populations with mixed source stocks. These findings demonstrate the need to apply contemporary conservation genetics tools to future wild trout restoration projects using translocated source stock towards the goal of “genetically-robust”, naturally reproducing populations with the ability to cope with current and future perturbations.

North Carolina, Tennessee↗

USGS2012

Yellowstone bison genetics: let us move forward

White and Wallen (2012) disagree with the conclusions and suggestions made in our recent assessment of population structure among Yellowstone National Park (YNP) bison based on 46 autosomal microsatellite loci in 661 animals (Halbert et al. 2012). First, they suggest that "the existing genetic substructure (that we observed) was artificially created." Specifically, they suggest that the substructure observed between the northern and central populations is the result of human activities, both historical and recent. In fact, the genetic composition of all known existing bison herds was created by, or has been influenced by, anthropogenic activities, although this obviously does not reduce the value of these herds for genetic conservation (Dratch and Gogan 2010). As perspective, many, if not most, species of conservation concern have been influenced by human actions and as a result currently exist as isolated populations. However, it is quite difficult to distinguish between genetic differences caused by human actions and important ancestral variation contained in separate populations without data from early time periods. Therefore, to not lose genetic variation that may be significant or indicative of important genetic variation, the generally acceptable management approach is to attempt to retain this variation based on the observed population genetic subdivision (Hedrick et al. 1986).

Yellowstone National Park↗

USGS2004

An animal location-based habitat suitability model for bighorn sheep and wild horses in Bighorn Canyon National Recreation Area and the Pryor Mountain Wild Horse Range, Montana, and Wyoming

The purpose of this habitat suitability model is to provide a tool that will help managers and researchers better manage bighorn sheep and wild horses in the Bighorn Canyon National Recreation Area (BICA) and Pryor Mountain Wild Horse Range (PMWHR). A concern in the management of the Pryor Mountain wild horse population is whether or not the wild horses compete with bighorn sheep for available forage or available space. Two studies have been conducted that have shown no obvious, convincing competition between the two species. A study of diets and habitat-use of both species revealed substantial diet overlap only during some seasons, but there were considerable spatial and habitat separations between wild horses and bighorns during all seasons (Kissell and others, 1996). This empirical data was then used in a modeling exercise that predicted that neither the current (about 160 horses at the time of the analysis) nor larger numbers of wild horses on the area (e.g., about 200 horses) would result in reduced numbers or condition of bighorn sheep (Coughenour 1999). But competition is a very complex biological process to document. Bighorns might have already been spatially avoiding wild horses when these studies were conducted. A second concern for managers is that earlier studies suggest both species are not using many areas of the range that appear to be suitable (Gudorf and others, 1996; Kissell and others, 1996). A primary goal for the management of both species is to increase their numbers for purposes of genetic conservation and viability. The bighorn sheep population declined during the mid-1990’s from a peak of about 211 animals to ~ 100 animals at present. Absolute minimum goals for genetic viability in the bighorn sheep herd (genetic effective population size of N >50) suggest at least 150 animals should be present, while studies of persistence suggest populations of 250+ are e more likely to recover rapidly and persist should the population experience an epizootic die-off (Singer and others, 2001). Since all bighorn sheep populations are potentially vulnerable to disease epizootics, managing for larger populations of 200–300 animals appears to increase the potential for long-term persistence (Berger, 1990; Singer and others, 2001). Wild horses are not prone to rapid disease die-offs. However, minimum goals for genetic viability in the Pryor Mountain wild horses ( Ne > 50) require that at least 160 animals be present on the range (Singer and others, 2000). Since the Ne > 50 goal is set for the breeding of domestic animals, and since the vagaries of drought, severe winters, predation, and other stochastic events cause stress in wild animals, larger goals for Ne (e.g. Ne > 100) for wild horses are even more desirable (USDI, BLM, 1999; Gross, 2000). Expanding the area of the wild horse range is one option, but the prospects for expanding the range do not appear to be great (L. Coates-Markle, BLM, oral comm.). A second option would be to increase the amount of useable habitat for horses on the existing range. One goal of this modeling effort was to use GIS-based habitat analyses to determine the reason wild horses are not using some areas of the range, and to explore the potential for making some of these areas useable. The National Park Service (NPS) has shown considerable interest in management actions within BICA that will increase the range, useable habitat, and population size of bighorn sheep. There has also been interest expressed by the Bureau of Land Management (BLM) and wild horse advocates to improve the useable habitat for wild horses and to possibly increase the size of the horse range.

Report↗

USGS2016

Loss of genetic diversity and increased subdivision in an endemic Alpine Stonefly threatened by climate change

Much remains unknown about the genetic status and population connectivity of high-elevation and high-latitude freshwater invertebrates, which often persist near snow and ice masses that are disappearing due to climate change. Here we report on the conservation genetics of the meltwater stonefly Lednia tumana (Ricker) of Montana, USA, a cold-water obligate species. We sequenced 1530 bp of mtDNA from 116 L. tumana individuals representing “historic” (>10 yr old) and 2010 populations. The dominant haplotype was common in both time periods, while the second-most-common haplotype was found only in historic samples, having been lost in the interim. The 2010 populations also showed reduced gene and nucleotide diversity and increased genetic isolation. We found lower genetic diversity in L. tumana compared to two other North American stonefly species, Amphinemura linda (Ricker) and Pteronarcys californica Newport. Our results imply small effective sizes, increased fragmentation, limited gene flow, and loss of genetic variation among contemporary L. tumana populations, which can lead to reduced adaptive capacity and increased extinction risk. This study reinforces concerns that ongoing glacier loss threatens the persistence of L. tumana, and provides baseline data and analysis of how future environmental change could impact populations of similar organisms.

Montana↗

USGS2026

Genomic structural variation rescues a classic biological invader from a population bottleneck

Invasion genetics presents a classic paradox: how do species successfully spread despite severe population bottlenecks? The brown treesnake ( Boiga irregularis ) in Guam represents a striking example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for ‘rescuing’ the population from inbreeding-driven declines. Structural variant density was highest in gene promoters, where recombination and DNA repair often occur, providing a mechanism for rapid evolution of gene-linked diversity. This diversity is enriched in genes vital for adaptive immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners.

BioRxiv↗

USGS2021

Genomic comparison of carbapenem-resistant Enterobacteriaceae from humans and gulls in Alaska

Objectives Wildlife may harbor clinically important antimicrobial resistant (AMR) bacteria, but the role of wildlife in the epidemiology of AMR bacterial infections in humans is largely unknown. In this study, we aimed to assess dissemination of the bla KPC carbapenemase gene among humans and gulls in Alaska. Methods We performed whole genome sequencing to determine the genetic context of bla KPC in bacterial isolates from all four human carbapenemase-producing Enterobacteriaceae (CPE) infections reported in Alaska between 2013–2018 and to compare sequences to seven previously reported CPE isolates from gull feces within the same region and time period. Results Genomic analysis of CPE isolates suggested independent acquisition events among humans with no evidence for direct transmission of bla KPC between people and gulls. However, some isolates shared conserved genetic elements surrounding bla KPC , suggesting possible exchange between species. Conclusions Our results highlight the genomic plasticity associated with bla KPC and demonstrate that sampling of wildlife may be useful for identifying clinically relevant antimicrobial resistance not observed through local passive surveillance in humans.

Alaska↗

USGS2020

A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye ( Sander vitreus ), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.

Minnesota, Wisconsin↗

USGS2000

Application of a PCR-based approach to identify sex in Hawaiian honeycreepers (Drepanidinae)

The application of molecular techniques to conservation genetics issues can provide important guidance criteria for management of endangered species. The results from this study establish that PCR-based approaches for sex determination developed in other bird species (Griffiths and Tiwari 1995; Griffiths et al. 1996, 1998; Ellegren 1996) can be applied with a high degree of confidence to at least four species of Hawaiian honeycreepers. This provides a rapid, reliable method with which population managers can optimize sex ratios within populations of endangered species that are subject to artificial manipulation through captive breeding programmes or geographic translocation.

Hawai'i↗

USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗

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↗

USGS2023

A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus).

The Lesser Prairie-Chicken ( Tympanuchus pallidicinctus ; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays. Unfortunately, the species has disappeared across much of its historical range, with corresponding precipitous declines in contemporary population abundance, largely due to climatic and anthropogenic factors. These declines led to a 2022 US Fish and Wildlife decision to identify and list two distinct population segments (DPSs; i.e., northern and southern DPSs) as threatened or endangered under the 1973 Endangered Species Act. Herein, we describe an annotated reference genome that was generated from a LEPC sample collected from the southern DPS. We chose a representative from the southern DPS because of the potential for introgression in the northern DPS, where some populations hybridize with the Greater Prairie-Chicken ( Tympanuchus cupido ). This new LEPC reference assembly consists of 206 scaffolds, an N50 of 45 Mb, and 15,563 predicted protein-coding genes. We demonstrate the utility of this new genome assembly by estimating genome-wide heterozygosity in a representative LEPC and in related species. Heterozygosity in a LEPC sample was 0.0024, near the middle of the range (0.0003–0.0050) of related species. Overall, this new assembly provides a valuable resource that will enhance evolutionary and conservation genetic research in prairie grouse.

Genome Biology and Evolution↗

USGS2024

Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework

Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of the taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.

Ecology Letters↗

USGS2020

Bot fly parasitism of Allegheny woodrats (Neotoma magister) in Virginia

The Allegheny woodrat ( Neotoma magister ) is a species of high conservation concern and relatively well-studied with respect to habitat use/associations, food habits, conservation genetics, and population trends. However, with the exception of raccoon roundworm ( Baylisascaris procyonis ) occurrence and etiology in woodrats, most disease and parasite ecology aspects for the woodrat are unknown. Herein, we examined the prevalence of bot flies ( Cuterebra ) over nearly three decades of woodrat surveys (1990–2018) in the central Appalachian Mountains of western Virginia. We use genetic analyses to identify recent bot fly specimen collections from a woodrat captured in 2017. Though highly variable from year to year, the overall prevalence of parasitism was low (typically < 4% of captures). As such, bot flies do not appear to be a widespread parasitic burden to Allegheny woodrats in Virginia. Genetic analysis of four collected bot fly larvae was inconclusive, as the genetic signature of these woodrat bots did not match any of the six bot species known to parasitize rodents and lagomorphs in the eastern United States. Further collections and genetic analyses will be needed to determine if the genetic database is incomplete or incorrect, or if our find is a new species of bot fly not yet taxonomically recognized.

Virginia↗

USGS2018

Shoal bass hybridization in the Chattahoochee River Basin near Atlanta, Georgia

The shoal bass (Micropterus cataractae) is a sportfish endemic to the Apalachicola-Chattahoochee-Flint Basin of the southeastern United States. Introgression with several non-native congeners poses a pertinent threat to shoal bass conservation, particularly in the altered habitats of the Chattahoochee River. Our primary objective was to characterize hybridization in shoal bass populations near Atlanta, Georgia, including a population inhabiting Big Creek and another in the main stem Chattahoochee River below Morgan Falls Dam (MFD). A secondary objective was to examine the accuracy of phenotypic identifications below MFD based on a simplified suite of characters examined in the field. Fish were genotyped with 16 microsatellite DNA markers, and results demonstrated that at least four black bass species were involved in introgressive hybridization. Of 62 fish genotyped from Big Creek, 27% were pure shoal bass and 65% represented either F1 hybrids of shoal bass x smallmouth bass (M. dolomieu) or unidirectional backcrosses towards shoal bass. Of 29 fish genotyped below MFD and downstream at Cochran Shoals, 45% were pure shoal bass. Six hybrid shoal bass included both F1 hybrids and backcrosses with non-natives including Alabama bass (M. henshalli), spotted bass (M. punctulatus), and smallmouth bass. Shoal bass alleles comprised only 21% of the overall genomic composition in Big Creek and 31% below MFD (when combined with Cochran Shoals). Phenotypic identification below MFD resulted in an overall correct classification rate of 86% when discerning pure shoal bass from all other non-natives and hybrids. Results suggest that although these two shoal bass populations feature some of the highest introgression rates documented, only a fleeting opportunity may exist to conserve pure shoal bass in both populations. Continued supplemental stocking of pure shoal bass below MFD appears warranted to thwart increased admixture among multiple black bass taxa, and a similar stocking program could benefit the Big Creek population. Further, selective removal of non-natives and hybrids, which appears to be practical with phenotypic identification, may provide increased benefits towards conserving genetic integrity of these shoal bass populations.

Journals of the Southeastern Association of Fish a↗

USGS2020

Malaclemys terrapin (Diamondback terrapin) Lepadomorph epibionts

Diamondback terrapins (Malaclemys terrapin) are distributed along the Atlantic and Gulf of Mexico (GoM) coasts of the U.S.A. (Hart et al. 2014. Conserv. Genet. DOI 10.1007/s10592-014-0563-6). Under consideration for listing in Florida and proposed for Appendix II listing by the U.S. at CoP16 (CITES), terrapin populations are declining in many parts of their range due to drowning in crab pots, road mortality, exploitation by the pet trade and habitat loss. The species has been divided into seven subspecies based on morphometric and geographic variations: M.t. terrapin, M.t. centrata, M.t. tequesta, M.t. rhizophorarum, M.t. macrospilota, M.t. pileata, and M.t. littoralis. (Ernst and Lovich 2009). Terrapins in the northern GoM are comprised primarily of the Mississippi (M.t. pileata) and ornate subspecies (M.t. macrospilota) which inhabit salt marshes across the region from approximately the Texas/Louisiana border to Naples, Florida.

Alabama, Florida, Louisiana, Mississippi, Texas↗

USGS2005

Population genetic structure and conservation of marbled murrelets ( Brachyramphus marmoratus )

Marbled murrelets ( Brachyramphus marmoratus ) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among 194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ??ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.

Conservation Genetics↗

USGS1999

The evolutionary history of steelhead ( Oncorhynchus mykiss ) along the US Pacific Coast: Developing a conservation strategy using genetic diversity

Changes in genetic variation across a species range may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer and thus provide insight into evolutionary development. Genetic data is used, drawn from 11 microsatellite loci amplified from anadromous steelhead ( Oncorhynchus mykiss ) sampled throughout its range in the eastern Pacific Ocean, to explore population structure at the southern edge in California. Steelhead populations in this region represent less than 10% of their reported historic abundance and survive in very small populations found in fragmented habitats. Genetic data derived from three independent molecular systems (allozymes, mtDNA, and microsatellites) have shown that the southernmost populations are characterized by a relatively high genetic diversity. Two hypothetical models supporting genetic population substructure such as observed were considered: (1) range expansion with founder-flush effects and subsequent population decline; (2) a second Pleistocene radiation from the Gulf of California. Using genetic and climatic data, a second Pleistocene refugium contributing to a southern ecotone seems more feasible. These data support strong conservation measures based on genetic diversity be developed to ensure the survival of this uniquely diverse gene pool.

ICES Journal of Marine Science↗

USGS2016

Genetic status and conservation of Westslope Cutthroat Trout in Glacier National Park

Invasive hybridization is one of the greatest threats to the persistence of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi . Large protected areas, where nonhybridized populations are interconnected and express historical life history and genetic diversity, provide some of the last ecological and evolutionary strongholds for conserving this species. Here, we describe the genetic status and distribution of Westslope Cutthroat Trout throughout Glacier National Park, Montana. Admixture between Westslope Cutthroat Trout and introduced Rainbow Trout O. mykiss and Yellowstone Cutthroat Trout O. clarkii bouvieri was estimated by genotyping 1,622 fish collected at 115 sites distributed throughout the Columbia, Missouri, and South Saskatchewan River drainages. Currently, Westslope Cutthroat Trout occupy an estimated 1,465 km of stream habitat and 45 lakes (9,218 ha) in Glacier National Park. There was no evidence of introgression in samples from 32 sites along 587 km of stream length (40% of the stream kilometers currently occupied) and 17 lakes (2,555 ha; 46% of the lake area currently occupied). However, nearly all (97%) of the streams and lakes that were occupied by nonhybridized populations occurred in the Columbia River basin. Based on genetic status (nonnative genetic admixture ≤ 10%), 36 Westslope Cutthroat Trout populations occupying 821 km of stream and 5,482 ha of lakes were identified as “conservation populations.” Most of the conservation populations ( N = 27; 736 km of stream habitat) occurred in the Columbia River basin, whereas only a few geographically restricted populations were found in the South Saskatchewan River ( N = 7; 55 km) and Missouri River ( N = 2; 30 km) basins. Westslope Cutthroat Trout appear to be at imminent risk of genomic extinction in the South Saskatchewan and Missouri River basins, whereas populations in the Columbia River basin are widely distributed and conservation efforts are actively addressing threats from hybridization and other stressors. A diverse set of pro-active management approaches will be required to conserve, protect, and restore Westslope Cutthroat Trout populations in Glacier National Park throughout the 21st century.

Glacier National Park↗