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At least 55 records · Page 3Linked to original sources
USGS2014

Development and characterization of microsatellite markers for the Hawaiian coot, Fulica alai , and Hawaiian gallinule, Gallinula galeata sandvicensis , through next-generation sequencing

We used next generation shotgun sequencing to develop novel microsatellite markers for two endangered waterbirds; the Hawaiian coot ( Fulica alai ) and Hawaiian gallinule ( Gallinula galeata sandvicensis ). The 20 loci polymorphic in the Hawaiian coot displayed moderate allelic diversity (average 3.8 alleles/locus) and heterozygosity (average 59.5 %). The 12 loci variable for the Hawaiian gallinule exhibited lower levels of allelic diversity (average 2.4 alleles/locus) and heterozygosity (average 47.5 %). Loci were in linkage equilibrium and only one locus deviated from Hardy–Weinberg equilibrium. These loci are sufficiently variable to assess levels of genetic diversity and will be useful for conservation genetic studies to aid in the management of these endangered waterbirds.

Conservation Genetics Resources↗
USGS2021

Understanding genetics for successful conservation and restoration of resilient Chesapeake Bay brook trout populations

Traditionally, fisheries management has focused on the abundance, distribution, and size structure of populations. Although these factors remain key aspects of management, a large and growing body of evidence highlights the importance of genetics in conserving wild populations, especially when populations are small and isolated (Frankham et al. 2017). Local adaptations are very common among fishes and help populations cope with specific conditions in their local environment (Fraser et al. 2011). The field of conservation genetics and genomics is highly technical and has advanced rapidly in recent years, offering a wealth of information to support brook trout conservation and restoration. A major impediment to successfully incorporating these advances into conservation outcomes is that most fisheries managers have only a basic understanding of fish genetics and its relevance to their management decisions.

Maryland, Virginia↗
USGS2025

Development of species-specific primers for the identification of Atlantic and shortnose sturgeons

Atlantic ( Acipenser oxyrinchus oxyrinchus ) and shortnose sturgeon ( Acipenser brevirostrum ) are broadly distributed along the Atlantic Coast of North America, where they use rivers, estuaries, and coastal habitats. In order to support management under the U.S. Endangered Species Act, it is important to understand when and where these fish occur. However, this presents a challenge as the two taxa are sometimes misidentified and some life stages (e.g., eggs) are challenging to identify with confidence. In this study, we used cytochrome b sequences to develop molecular primers to confirm the identity of shortnose and Atlantic sturgeon samples. We tested these primers using reference DNA samples for these two species. The results suggested that the primers were able to positively identify and distinguish Atlantic and shortnose sturgeon. The accuracy of the Atlantic sturgeon primers was 95.34%, whereas the accuracy of the shortnose sturgeon primers was 90.7%. Even though there were some individuals that were not positively identified as their corresponding species (false negatives), we did not observe any false positives. Our paper does not aim to develop eDNA markers; rather, the objective of our study was to create species-specific, unlabeled, and cost-effective primers which can be amplified using conventional PCR. The amplification product can be observed in a 2% agarose gel run through electrophoresis. This entire procedure is relatively inexpensive and involves basic instruments found in most conservation genetics laboratories.

Conservation Genetics Resources↗
USGS2017

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

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

Conservation Genetics↗
USGS2013

Genetic population structure of muskellunge in the Great Lakes

We quantified genetic relationships among Muskellunge Esox masquinongy from 15 locations in the Great Lakes to determine the extent and distribution of measurable population structure and to identify appropriate spatial scales for fishery management and genetic conservation. We hypothesized that Muskellunge from each area represented genetically distinct populations, which would be evident from analyses of genotype data. A total of 691 Muskellunge were sampled ( n = 10–127/site) and genetic data were collected at 13 microsatellite loci. Results from a suite of analyses (including pairwise genetic differentiation, Bayesian admixture prediction, analysis of molecular variance, and tests of isolation by distance) indicated the presence of nine distinct genetic groups, including two that were approximately 50 km apart. Geographic proximity and low habitat complexity seemed to facilitate genetic similarity among areas, whereas Muskellunge from areas of greater habitat heterogeneity exhibited high differentiation. Muskellunge from most areas contained private alleles, and mean within-area genetic variation was similar to that reported for other freshwater fishes. Management programs aimed at conserving the broader diversity and long-term sustainability of Muskellunge could benefit by considering the genetically distinct groups as independent fisheries, and individual spawning and nursery habitats could subsequently be protected to conserve the evolutionary potential of Muskellunge.

Great Lakes↗
USGS2024

DNA-based studies and genetic diversity indicator assessments are complementary approaches to conserving evolutionary potential

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic studies, when available, provide detailed information that is important for management, such as estimates of gene flow, inbreeding, genetic erosion and adaptation. In this article, we argue that the development and advancement of genetic diversity indicators is a complementary approach to genetic studies in conservation biology, but not a substitute. Genetic diversity indicators and empirical genetic data can provide different information for conserving genetic diversity. Genetic diversity indicators enable affordable tracking, reporting, prioritization and communication, although, being proxies, do not provide comprehensive evaluation of the genetic status of a species. Conversely, genetic methods offer detailed analysis of the genetic status of a given species or population, although they remain challenging to implement for most species globally, given current capacity and resourcing. We conclude that indicators and genetic studies are both important for genetic conservation actions and recommend they be used in combination for conserving and monitoring genetic diversity.

Conservation Genetics↗
USGS2021

Global commitments to conserving and monitoring genetic diversity are now necessary and feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

BioScience↗
USGS2022

Genetic diversity and mate selection in a reintroduced population of gray wolves

The genetic composition of an individual can markedly affect its survival, reproduction, and ultimately fitness. As some wildlife populations become smaller, conserving genetic diversity will be a conservation challenge. Many imperiled species are already supported through population augmentation efforts and we often do not know if or how genetic diversity is maintained in translocated species. As a case study for understanding the maintenance of genetic diversity in augmented populations, I wanted to know if genetic diversity (i.e., observed heterozygosity) remained high in a population of gray wolves in the Rocky Mountains of the U.S. > 20 years after reintroduction. Additionally, I wanted to know if a potential mechanism for such diversity was individuals with below average genetic diversity choosing mates with above average diversity. I also asked whether there was a preference for mating with unrelated individuals. Finally, I hypothesized that mated pairs with above average heterozygosity would have increased survival of young. Ultimately, I found that females with below average heterozygosity did not choose mates with above average heterozygosity and wolves chose mates randomly with respect to genetic relatedness. Pup survival was not higher for mated pairs with above average heterozygosity in my models. The dominant variables predicting pup survival were harvest rate during their first year of life and years pairs were mated. Ultimately, genetic diversity was relatively unchanged > 20 years after reintroduction. The mechanism for maintaining such diversity does not appear related to individuals preferentially choosing more genetically diverse mates. Inbreeding avoidance, however, appears to be at least one mechanism maintaining genetic diversity in this population.

Idaho↗
USGS2020

Development of microsatellite markers for three at risk tiger beetles Cicindela dorsalis dorsalis, C. d. media, and C. puritana

Objective Tiger beetles inhabiting sandy beaches and cliffs along the east coast of the United States are facing increasing habitat loss due to erosion, urbanization, and sea level rise. The northeastern beach tiger beetle Cicindela dorsalis dorsalis and Puritan tiger beetle Cicindela puritana are both listed as threatened under the Endangered Species Act of 1973, while the white beach tiger beetle Cicindela dorsalis media is not listed but has been declining. Extirpation of these beetles, in some cases from entire states, has isolated many populations reducing gene flow and elevating the risk for the loss of genetic variation. To facilitate investigations of population genetic structure, we developed suites of microsatellite loci for conservation genetic studies. Results Shotgun genomic sequencing of all species identified thousands of candidate microsatellite loci, among which 17 loci were optimized and verified to cross-amplify within C. d. media and C. d. dorsalis , and eight separate loci were optimized for C. puritana . Most loci conformed to Hardy–Weinberg equilibrium, showed no evidence of linkage disequilibrium or null alleles, and revealed population genetic characteristics informative for natural resource managers among the populations tested.

BMC Research Notes↗
USGS2018

Hybridization and genetic structure of Neosho Smallmouth Bass in the Ozark Highlands

The Neosho Smallmouth Bass Micropterus dolomieu velox is endemic to Arkansas River tributaries originating in the Ozark Highlands and Boston Mountains. Although morphologically and genetically distinct from other populations of Smallmouth Bass M. dolomieu , the conservation‐genetic status of Neosho Smallmouth Bass is largely unknown. To assist in filling this data gap, we quantified introgressive hybridization, genetic diversity, and population structure of Neosho Smallmouth Bass in two major river basins (Grand River and Illinois River) using seven polymorphic microsatellite markers. Introgressive hybridization with stocked Tennessee lake‐strain Smallmouth Bass was most prevalent in the Illinois River, wherein the overall genomic proportion of Neosho Smallmouth Bass alleles was only 0.422. After accounting for hybrid individuals, genetic diversity of Neosho Smallmouth Bass was generally higher in larger rivers and lower in smaller, isolated streams. Three distinct population clusters were identified at the uppermost level of genetic structure—one from the Illinois River basin and two from the Grand River basin. These three population boundaries accounted for approximately 7% of the hierarchical genetic variation within our data set, and substructure below the uppermost level accounted for an additional 2% of genetic variation. The population structure we discovered can provide a blueprint for management that conserves diversity within and among populations; for example, population boundaries can be used to determine brood source locations for supplemental stocking efforts to counter nonnative introgression. Introgressive hybridization with nonnative Smallmouth Bass appears to be the most pertinent threat to the Neosho Smallmouth Bass subspecies, which is of conservation value to the overall adaptability of Smallmouth Bass as a species.

Missouri, Oklahoma↗
USGS2018

Genetic population structure of Shoal Bass within their native range

Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites ( N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is conserved and overall adaptability of the species is maintained.

Apalachicola–Chattahoochee–Flint River Basin↗
USGS2011

Investigating and managing the rapid emergence of white-nose syndrome, a novel, fatal, infectious disease of hibernating bats

White-nose syndrome (WNS) is a fatal disease of bats that hibernate. The etiologic agent of WNS is the fungus Geomyces destructans , which infects the skin and wing membranes. Over 1 million bats in six species in eastern North America have died from WNS since 2006, and as a result several species of bats may become endangered or extinct. Information is lacking on the pathogenesis of G. destructans and WNS, WNS transmission and maintenance, individual and site factors that contribute to the probability of an outbreak of WNS, and spatial dynamics of WNS spread in North America. We considered how descriptive and analytical epidemiology could be used to fill these information gaps, including a four-step (modified) outbreak investigation, application of a set of criteria (Hill's) for assessing causation, compartment models of disease dynamics, and spatial modeling. We cataloged and critiqued adaptive-management options that have been either previously proposed for WNS or were helpful in addressing other emerging diseases of wild animals. These include an ongoing program of prospective surveillance of bats and hibernacula for WNS, treatment of individual bats, increasing population resistance to WNS (through vaccines, immunomodulators, or other methods), improving probability of survival from starvation and dehydration associated with WNS, modifying hibernacula environments to eliminate G. destructans , culling individuals or populations, controlling anthropogenic spread of WNS, conserving genetic diversity of bats, and educating the public about bats and bat conservation issues associated with WNS.

Conservation Biology↗
USGS1986

Changing landscapes and the cosmopolitism of the eastern Colorado avifauna

The avifauna of continental North America has changed dramatically since colonial times. Excessive hunting contributed, at least in part, to the extinction of birds such as the great auk ( Pinguinus impennis ) and passenger pigeon ( Ectopistes migratorius ), while more recently organochlorine insecticide residues have resulted in drastic reductions in numbers of brown pelicans ( Pelecanus occidentalis ) (Anderson et al. 1975) and other species. Generally, however, vertebrate populations change in direct response to changes in their habitats. For example, herring gulls ( Larus argentatus ) have increased in numners (Kadlec and Drury 1968) with urbanization of the New England coastline, in the same locations formerly occupied by the extinct heath hen ( Tympanuchus cupido cupido ). Also, passerine birds of forest interiors have declined in numbers with fragmentation of the eastern deciduous forest into small stands; this fragmentation has led to increases in numbers of edge species (Robbins 1979, Ambuel and Temple 1983). Even subtle community shifts can introduce new competitive processes that can augment population changes among species (Brittingham and Temple 1983). Such studies of broad-scale changes in vegetative communities and their influence on native wildlife species have fostered the recent topical emphasis on "conservation biology" (Soule and Wilcox 1980, Soule 1985) and "landscape ecology" (Burgess and Sharpe 1981, Harris 1984:25-43). As changes in landscapes are causing subtle (but potentially dramatic) changes in the distribution of native species, conservation biologists are finding that mere presence-absence data on populations, or even accurate information on reproductive success, is inadequate to evaluate management activities or environmental perturbations. The principles of "conservation genetics" are attracting interest in the management of natural preserves especially (Schonewald-Cox et al. 1983). Changing patterns in landscape complexion or genetic makeup of a population are difficult to detect locally. Contemporary issues in the conservation of native species demand regional and continental perspectives (Samson and Knopf 1982). Thus, management activities at specific sites are often viewed as short-sighted by planners and conservation critics. This paper illustrates how these contemporary theories can influence a local conservation perspective. That perspective is developed around historical processes that have led to cosmopolitism of the local avifauna on the Colorado Division of Wildlife's South Platte Wildlife Management Area (SPWMA) near Crook, Colorado.

Colorado↗
USGS2025

Genetic analysis of Missouri’s Topeka Shiners with implications for the propagation of understudied small-bodied freshwater fishes

Objective Best practices for conservation hatcheries to conserve genetic diversity and minimize adaptation to captivity have been established for decades, but how to apply them is not clear in every circumstance. As a growing number of aquatic species are propagated in captive settings, addressing the fit of these practices to each system will help managers operate optimally while conserving hatchery resources. Small-bodied freshwater fish present a unique set of traits compared with species that are typically considered for propagation (i.e., salmonids), including a patchy distribution within a watercourse. We examine the propagation and reintroduction program that supports the Topeka Shiner Miniellus topeka , an endangered minnow in the Midwestern USA. Methods We genotyped shiners from groups with different histories (two reintroduced, three captive, and two remnant populations) at 11 microsatellite loci and compared genetic diversity, genetic structure, effective population size, and evidence of population bottlenecks. We also looked at the breeding structure by genetically assigning hatchery-reared young ( n = 148) to candidate parents. Results We documented high levels of genetic structure among the two natural populations in our study. We also noted lower diversity and evidence of bottlenecks in hatchery-reared groups. However, hatcheries may support sufficient (>50) effective population sizes with minimal space. Conclusions Hatcheries may avoid bottlenecks in other small-bodied freshwater fish by collecting wild fish from a broad area and frequently incorporating them into the captive population. Within the hatchery, we emphasize the need to reduce generational overlap by stocking all production fish and/or subdividing the captive populations.

Missouri↗
USGS2018

Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for non-invasive sampling

Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA.

Colorado↗
USGS2012

Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

The Condor↗
USGS2013

The silent threat of low genetic diversity

Across the Caribbean, protected coastal waters have served as primary feeding and breeding grounds for the endangered Antillean manatee. Unfortunately, these same coastal waters are also a popular “habitat” for humans. In the past, the overlap between human and manatee habitat allowed for manatee hunting and threatened the survival of these gentle marine mammals. Today, however, threats are much more inadvertent and are often related to coastal development, degraded habitats and boat strikes. In the state of Florida, decades of research on the species’ biological needs have helped conservationists address threats to its survival. For example, low wake zones and boater education have protected manatees from boat strikes, and many of their critical winter refuges are now protected. The Florida population has grown steadily, thus increasing from approximately 1,200 in 1991 to more than 5,000 in 2010. It is conceivable that in Florida manatees may one day be reclassified as “threatened” rather than “endangered.” Yet, in other parts of the Caribbean, threats still loom. This includes small, isolated manatee populations found on islands that can be more susceptible to extinction and lack of genetic diversity. To ensure the species’ long-term viability, scientists have turned their sights to the overall population dynamics of manatees throughout the Caribbean. Molecular genetics has provided new insights into long-term threats the species faces. Fortunately, the emerging field of conservation genetics provides managers with tools and strategies for protecting the species’ long-term viability.

livebetter Magazine↗