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At least 91 records · Page 5Linked to original sources
USGS2022

Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation

Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica , is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. Lack of congruence among morphological subspecies hypotheses and lack of measurable genetic structure found in a few genetic markers led to questions about the validity of subspecies within P. californica and the listing status of the coastal California gnatcatcher, P. c. californica . As a U.S. federally threatened subspecies, P. c. californica is recognized as a flagship for coastal sage scrub conservation throughout southern California. We used restriction site-associated DNA sequencing to develop a genomic dataset for the California gnatcatcher. We sampled throughout the species' range, examined genetic structure, gene–environment associations, and demographic history, and tested for concordance between genetic structure and morphological subspecies groups. Our data support two distinct genetic groups with evidence of restricted movement and gene flow near the U.S.- Mexico international border. We found that climate-associated outlier loci were more strongly differentiated than climate neutral loci, suggesting that local climate adaptation may have helped to drive differentiation after Holocene range expansions. Patterns of habitat loss and fragmentation are also concordant with genetic substructure throughout the southern California portion of the range. Finally, our genetic data supported the morphologically defined P. c. californica as a distinct group, but there was little evidence of genetic differentiation among other previously hypothesized subspecies in Baja California. Our data suggest that retaining and restoring connectivity, and protecting populations, particularly at the northern range edge, could help preserve existing adaptive potential to allow for future range expansion and long-term persistence of the California gnatcatcher.

California↗
USGS2005

Patterns of genetic differentiation and conservation of the slabside pearlymussel, Lexingtonia dolabelloides (Lea, 1840) in the Tennessee River drainage

The restoration and recovery of imperiled mussel species will require the re-establishment of populations into historically occupied habitats. The possible existence of genetic differentiation among populations should be considered before inter-basin transfers are made. Eighty individuals of the federal candidate species Lexingtonia dolabelloides were sampled from populations in the North Fork Holston, Middle Fork Holston, Clinch, Paint Rock and Duck rivers of the Tennessee River basin in the southeastern United States. We sequenced 603 base-pairs of a mitochondrial DNA gene (ND-1) and 512 base-pairs of a nuclear DNA gene (ITS-1). Analyses of molecular variation (AMOVA) values for both genes indicated that the majority of variation in L. dolabelloides resided within populations (82.9-88.3%), with 11.7-17.1% of variation among populations. Haplotype frequencies differed significantly among populations for both genes sequenced. Clustering of haplotypes in minimum-spanning networks did not conform stringently to population boundaries, reflecting high within-population and low between-population variability. Maximum parsimony analysis did not identify any population as a monophyletic lineage. A Mantel test showed no significant correlation between geographical stream distance and genetic distance, thus not supporting a pattern of isolation-by-distance. Overall, results provided support to manage fragmented populations of L. dolabelloides in the Tennessee River drainage as two management units (MUs), but did not provide evidence for the existence of ESUs following published molecular criteria. ?? The Author 2005. Published by Oxford University Studies on behalf of The Malacological Society of London, all rights reserved.

Journal of Molluscan Studies↗
USGS2007

Where the buffalo roam: The role of history and genetics in the conservation of bison on U.S. federal lands

As an emblem of the Great Plains, American Indians, and wildlife conservation, the American bison ( Bison bison ) is one of the most visible and well-known of wildlife species in North America (fig. 1, above). Species of the genus Bison originally entered the continent via the Bering land bridge from northern Eurasia in the Illinoian glacial period of the Pleistocene epoch (125,000–500,000 years ago). Bison are the largest species in North America to have survived the late Pleistocene–early Holocene megafauna extinction period (around 9,000–11,000 years ago), but likely experienced a dramatic population reduction triggered by environmental changes and increased human hunting pressures around this time (Dary 1989; McDonald 1981). The modern American bison species ( Bison bison ) emerged and expanded across the grasslands of North America around 4,000–5,000 years ago (McDonald 1981). As the major grazer of the continent, bison populations ranged from central Mexico to northern Canada and nearly from the east to west coasts ( fig. 2; McDonald 1981), with 25–40 million bison estimated to have roamed the Great Plains prior to the 19th century (Flores 1991; McHugh 1972; Shaw 1995).

Park Science↗
USGS2021

Genetic structure and diversity of the endemic Carolina Madtom and conservation implications

Identification and conservation of genetic diversity within and among freshwater fish populations are important to better manage and conserve imperiled species. The Carolina Madtom Noturus furiosus is a small, nongame catfish that is endemic to the Tar and Neuse River basins of North Carolina. Genetic structure has not been studied in the species, and given recent population declines in both basins, identification of remaining genetic diversity within the species is vital for informing conservation efforts. To assess the status and trends of Carolina Madtom genetic structure, we analyzed genetic markers from 173 individuals to (1) define population genetic structure, (2) assess intra- and interbasin genetic differentiation in the Tar and Neuse River basins, and (3) present management implications to guide conservation efforts. Using 10 microsatellite primers developed for the related Yellowfin Madtom N. flavipinnis , we observed low genetic diversity in Carolina Madtoms. Genotype frequencies within samples were not in Hardy–Weinberg equilibrium, with a deficit of heterozygotes that could be due to family structure, inbreeding, or segregation of null alleles. Mean (±SD) M -ratios for the Tar River (0.414 ± 0.117) and Neuse River (0.117 ± 0.102) basin collections indicated that both populations have experienced recent demographic bottlenecks, with that in the Neuse River basin population being more severe. Effective population size estimates for the respective populations were small, on the order of tens of individuals, driving low genetic diversity within populations. However, the multilocus population differentiation metrics (mean ± SE = 0.135 ± 0.031) and D EST (0.125 ± 0.029) were significantly different from zero ( P < 0.001), indicating significant genetic differentiation between the Tar and Neuse River basin populations. Our findings will inform managers on the status of genetic variation in the Carolina Madtom and will guide conservation toward protective listing and management decisions to maintain the viability of this important endemic species.

North Carolina↗
USGS2023

Is now the time? Review of genetic rescue as a conservation tool for brook trout

Brook trout populations have been declining throughout their native range in the east coast of the United States. Many populations are now distributed in small, isolated habitat patches where low genetic diversity and high rates of inbreeding reduce contemporary viability and long-term adaptive potential. Although human-assisted gene flow could theoretically improve conservation outcomes through genetic rescue, there is widespread hesitancy to use this tool to support brook trout conservation. Here, we review the major uncertainties that have limited genetic rescue from being considered as a viable conservation tool for isolated brook trout populations and compare the risks of genetic rescue with other management alternatives. Drawing on theoretical and empirical studies, we discuss methods for implementing genetic rescue in brook trout that could yield long-term evolutionary benefits while avoiding negative fitness effects associated with outbreeding depression and the spread of maladapted alleles. We also highlight the potential for future collaborative efforts to accelerate our understanding of genetic rescue as a viable tool for conservation. Ultimately, while we acknowledge that genetic rescue is not without risk, we emphasize the merits that this tool offers for protecting and propagating adaptive potential and improving species' resilience to rapid environmental change.

Ecology and Evolution↗
USGS2011

Genetic applications in avian conservation

A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems.

The Auk↗
USGS2012

A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

Journal of Marine Animals and Their Ecology↗
USGS2019

Establishing genome sizes of focal fishery and aquaculture species along Baja California, Mexico

Genome size—the total haploid content of nuclear DNA— is constant in all cells in individuals within a species, but differs among species. Consequently, the genome size is a quantifiable genetic signature that not only characterizes a species, but it can reflect chromatin modifications, which play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. This characteristic makes the genome size a crucial parameter for genetic research on endemic aquatic species and for genetic manipulations in aquaculture species. Technologies for genetic assessments and improvements applied to fishery and aquaculture species use genome size values as a means by which hybrids, polyploids, and sex can be identified, when sex chromosomes exist. The objectives of this study were to determine genome sizes of aquatic species with economic and biological importance along the Pacific coast of Mexico, as well as to identify the appropriate reference standards for use in this study. Blood, hemolymph or milt were collected from 10 species occurring along the coast of Baja California: Sablefish Anoplopoma fimbria , Black Snapper Lutjanus novemfasciatus , California Halibut Paralichthys californicus , Pacific Sardine Sardinops sagax , Flag Rockfish Sebastes rubrivinctus , Starry Rockfish Sebastes constellatus, Totoaba Totoaba macdonaldi , Whiteleg Shrimp Litopenaeus vannamei and two Yellowtail Seriola lalandi and S. dorsalis . Nuclear DNA was stained with propidium iodide solution and the genome size was determined by flow cytometry, with results ranging from 0.61 pg (1.22 pg/diploid cell) to 2.59 pg (5.18 pg/diploid cell), with the smallest value in Sablefish and the largest in the Whiteleg Shrimp. No significant differences were detected ( P ≤ 0.05) among individuals of the same species; the likely reason behind any dissimilar DNA content values with those from the literature were differences in methodologies or variations in genetics. Red-ear Slider Turtle Trachemys scripta elegans 2.65 pg (5.30 pg/diploid cell) and Red Junglefowl Gallus gallus 1.27 pg (2.54 pg/diploid cell) were chosen as the standards for reference values. These results establish the basis for the Mexican National Aquatic Genetic Resources project supporting genetic improvements for aquaculture and conservation status parameters for fisheries species.

Baja California↗
USGS2019

Noninvasive identification of cryptic herpetofauna from fecal samples: A novel approach pairing conservation dog surveys and genetic analysis

Noninvasive fecal sampling combined with genetic analysis is a powerful technique allowing the study of elusive or otherwise difficult to monitor species without the need for direct contact. While this method is widely used in birds and mammals, it has never been successfully applied on a large scale in reptiles. The blunt-nosed leopard lizard (Gambelia sila) is an endangered species endemic to the San Joaquin Desert of California. Presently, acquiring data on G. sila for research and management involves more traditional methods such as live capture to obtain tissue samples for DNA analysis, or observation via visual surveys, which are also used for regulatory monitoring in accordance with wildlife agency protocols. Here we describe an innovative approach for gathering additional information, that combines use of conservation detection dogs trained to locate G. sila scat samples with genetic analysis for identifying and distinguishing among sympatric lizard species. We developed two PCR assays that produce fluorescently labelled amplicons of species-specific fragment length for six lizard species in the study area. Using these assays we genetically identifed to species 78% (255 of 327) of samples collected by dog-handler teams across four years. The majority of the genetically identifed samples (82.4%; 210 of 255) were confirmed as originating from G. sila. Beyond the immediate application of these techniques for the study and monitoring of G. sila, our ability to recover usable DNA and to differentiate among a diverse group of lizards highlights the broad potential of our methodology for noninvasive sampling in reptiles.

California↗
USGS2002

Genetic diversity in a morphologically conservative invasive taxon: Multiple introductions of swamp eels to the southeastern United States

Genetic analysis of introduced populations, especially in morphologically conservative taxa, can clarify introduction histories, identify management units and source populations, provide a more realistic estimate of the frequency of successful invasion, and suggest strategies for preventing further introductions. In the last 7 years, populations of swamp eels, referred to the Asian genus Monopterus (Family Synbranchidae) on the basis of external morphology, have been discovered in aquatic habitats near Atlanta, Georgia; Tampa, Florida; North Miami, Florida; and most recently in close proximity to Everglades National Park in Homestead, Florida. Swamp eels are large predators capable of dispersal over land and have the potential to disrupt already threatened ecosystems. We analyzed mitochondrial DNA sequences from four known populations in the continental United States and samples from Malaysia, Indonesia, Vietnam, and two locations in China to determine introduction histories, source populations, genetic diversity, and relationships among populations. Our results indicate that there have been at least three independent introductions of genetically distinct forms. Introduced populations in close proximity (separated by <40 km) are genetically distinct. The level of sequence difference among introduced populations reaches levels seen among sister families of teleost fishes for the same region of the mitochondrial genome. These genetically distinct introduced populations in all likelihood represent at least two and possibly three species. Regardless of species status, these genetically distinct lineages may be expected to vary in ecological or life-history traits, representing different potential threats to the ecosystems where they have been introduced. Given the success of swamp eels in invading many habitats around the world, further study of these eels is warranted to elucidate the characteristics of successful invaders and invasions.

Conservation Biology↗
USGS2025

A single nucleotide polymorphism panel for identifying North American species and hybrids in the genus Morone

Four species of the fish genus Morone exist in North America and are often the focus of management actions, including propagation and stocking of their hybrids. We have developed an amplicon-based single nucleotide polymorphism (SNP) genotyping panel that provides the ability to distinguish all four species and the commonly stocked M. chrysops x M. saxatilis hybrid using a set of 47 SNPs. This resource provides a means of cost effective, high confidence genetic species identification that may aid management and conservation efforts for North American Morone species.

North America↗
USGS1995

Genetic strategies for lake trout rehabilitation: a synthesis

The goal of lake trout rehabilitation efforts in the Great Lakes has been to reestablish inshore lake trout ( Salvelinus namaycush ) populations to self-sustaining levels. A combination of sea lamprey control, stocking of hatchery-reared lake trout, and catch restrictions were used to enhance remnant lake trout stocks in Lake Superior and reestablish lake trout in Lakes Michigan, Huron, Erie, and Ontario. Genetic diversity is important for the evolution and maintenance of successful adaptive strategies critical to population restoration. The loss of genetic diversity among wild lake trout stocks in the Great Lakes imposes a severe constraint on lake trout rehabilitation. The objective of this synthesis is to address whether the particular strain used for stocking combined with the choice of stocking location affects the success or failure of lake trout rehabilitation. Poor survival, low juvenile recruitment, and inefficient habitat use are three biological impediments to lake trout rehabilitation that can be influenced by genetic traits. Evidence supports the hypothesis that the choices of appropriate lake trout strain and stocking locations enhance the survival of lake trout stocked into the Great Lakes. Genetic strategies proposed for lake trout rehabilitation include conservation of genetic diversity in remnant stocks, matching of strains with target environments, stocking a greater variety of lake trout phenotypes, and rehabilitation of diversity at all trophic levels.

Journal of Great Lakes Research↗
USGS2018

Characterizing range-wide population divergence in an alpine-endemic bird: A comparison of genetic and genomic approaches

The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating “evolutionarily significant units,” but with recent advances in genomic technology, we now have an unprecedented ability to utilize information about neutral and adaptive variation across the entire genome. Here, we use traditional genetic markers (microsatellites) and a newer reduced-representation genomic approach (single nucleotide polymorphisms) to delineate distinct groups of white-tailed ptarmigan (Lagopus leucura), an alpine-obligate species that is distributed in naturally fragmented habitats from Alaska to New Mexico. Five subspecies of white-tailed ptarmigan are currently recognized but their distinctiveness has not been verified with molecular data. Based on analyses of 436 samples at 12 microsatellite loci and 95 samples at 14,866 single nucleotide polymorphism loci, we provide strong support for treating two subspecies as distinct intraspecific units—L. l. altipetens, found in Colorado and neighboring states; and L. l. saxatilis, found on British Columbia’s Vancouver Island—but our findings reveal more moderate patterns of divergence within the remainder of the species’ range. Results based on genetic and genomic datasets generally agreed with one another, indicating that in many cases microsatellite loci may be sufficient for describing major patterns of genetic structure across species’ ranges. This work will inform future conservation and management decisions for the white-tailed ptarmigan, a species that may be vulnerable to future changes in climate.

Conservation Genetics↗
USGS2020

The transformative impact of genomics on sage-grouse conservation and management

For over two decades, genetic studies have been used to assist in the conservation and management of both Greater Sage-grouse ( Centrocercus urophasianus ) and Gunnison Sage-grouse ( C. minimus ), addressing a wide variety of topics including taxonomy, parentage, population connectivity, and demography. The field of conservation genetics has been transformed by dramatic improvements in sequencing technology, facilitating genomic studies in many wildlife species. The quality and amount of data generated by genomic methods vastly exceed that of traditional genetic studies, allowing for increased precision in estimating genetic parameters of interest. Perhaps more importantly, genomic methods can provide insight into non-neutral evolution such as adaptive divergence. Here we recount the shift from genetic to genomic methods using two wildlife species of substantial conservation interest, focusing on the improved capabilities and advantages of genomic methods. For instance, reassessment of divergence in sage-grouse using genomic methods confirmed strong differentiation between the two species and revealed that a small population in the state of Washington was more genetically distinct than previously recognized. Further, new genomic resources and approaches have been used to identify a family of genes linked to local dietary adaptation suggesting that sage-grouse may possess digestive and metabolic adaptations that mitigate the effects of consuming plant secondary metabolites like those found in sagebrush. Genetic variation among populations in these gene regions is thought to be involved with local dietary adaptations, and therefore maintaining the tie between sage-grouse and the chemistry of local sagebrush may be an important management consideration. We posit that the integration of newly developed genomic resources combined with the vast wealth of ecological and behavioral data for sage-grouse has the potential to shed light on mechanistic relationships that ultimately are vital to the conservation and management of these species.

Book chapter↗
USGS2019

Signatures of adaptive divergence among populations of an avian species of conservation

Understanding the genetic underpinning of adaptive divergence among populations is a key goal of evolutionary biology and conservation. Gunnison sage‐grouse ( Centrocercus minimus ) is a sagebrush obligate species with a constricted range consisting of seven discrete populations, each with distinctly different habitat and climatic conditions. Though geographically close, populations have low levels of natural gene flow resulting in relatively high levels of differentiation. Here, we use 15,033 SNP loci in genomic outlier analyses, genotype–environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation in an avian species of conservation concern. We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. The identified gene set was enriched for cytochrome P450 gene family members (CYP4V2, CYP2R1, CYP2C23B, CYP4B1) and could impact metabolism of plant secondary metabolites, a critical challenge for sagebrush obligates. Additionally, the gene set was also enriched with members potentially involved in antiviral response (DEAD box helicase gene family and SETX). Our results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring. This information can be useful in managing this species of conservation concern, for example, to identify unique populations to conserve, avoid translocation or release of individuals that may swamp locally adapted genetic diversity, or guide habitat restoration efforts.

Arizona, Colorado, New Mexico, Utah↗
USGS2020

Development of genetic baseline information to support the conservation and management of wild Brook Trout in North Carolina

Following centuries of declines, there is growing interest in conserving extant wild populations and reintroducing Brook Trout ( Salvelinus fontinalis ) populations of native ancestry. A population genetic baseline can enhance conservation outcomes and promote restoration success. Consequently, it is important to document existing patterns of genetic variation across the landscape and translate these data into an approachable format for fisheries managers. We genotyped 9,507 Brook Trout representing 467 wild collections at 12 microsatellite loci to establish a genetic baseline for North Carolina, USA. Rarefied allelic richness and observed heterozygosity, which reflect within‐population diversity, were low to moderate relative to levels typically observed at higher latitudes (means = 3.12 and 0.42, respectively). Effective population sizes varied widely, but were often very low (151 collections with an estimated N e < 10). Despite decades of intensive stocking across the state, we found little to no evidence of hatchery introgression in most populations. Although genetic variation was significant at a variety of spatial scales (mean pairwise F ’ ST = 0.73), substantial genetic variation occurred between patches within individual watersheds. Analysis of molecular variance (AMOVA) found that a substantial portion (28.5%) of the observed genetic variation was attributed to differences among populations, with additional genetic variation among hydrological units (HUCs; 16.0%, 16.6%, 12.1%, and 9.4% of the overall variation among twelve‐, ten‐, eight‐, and six‐digit HUCs, respectively). We discuss a suite of potential applications for this type of genetic data to enhance management outcomes, such as conservation prioritization and selection of source stocks for reintroductions or genetic rescue.

North Carolina↗
USGS2023

Genetic analysis of federally endangered Cape Sable seaside sparrow subpopulations in the Greater Everglades, USA

The federally endangered Cape Sable seaside sparrow ( Ammospiza maritima mirabilis ) is endemic to the Greater Everglades ecosystem in southern Florida, inhabiting fragmented marl prairies in six individual subpopulations. The subspecies is threatened by loss of breeding habitat from fire and water management. Genetic information is severely limited for the subspecies but could help inform decisions regarding subpopulation protections and potential translocations for genetic rescue. To provide genetic data and inform management efforts, feather samples were collected across five subpopulations (designated A–E) and protocols were tested to optimize DNA extraction yields. We assessed four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) in 108 sparrows. Mitochondrial DNA sequences revealed low haplotype diversity, with NADH dehydrogenase-2 haplotypes matching to most other extant subspecies and to the Atlantic coast subspecies. Nuclear diversity was low compared to other subspecies, but similar across subpopulations. Samples grouped as one population when analyzed by Principal Component Analysis, Bayesian modelling and genetic distance metrics. Limited genetic emigration was detected from one putative migrant. Relatedness was significantly different for sparrows in the most geographically distant subpopulation (A), likely reflecting high self-recruitment and natal site fidelity ( P = 0.003). The low to moderate effective population size (N E = 202.4; N E :N C = 0.06) and generation time estimates indicated that unique genetic variation could be lost quickly during stochastic events. The sample sizes were limited, which reduced the power to comprehensively address recent population size reductions and any subsequent loss of genetic diversity.

Florida↗