SEARCH · USGS Science
Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Environmental DNA (eDNA) analysis refers to the collection of bulk environmental samples such as water, sediment, or air, and studying the genetic remnants that organisms have shed into their environment to gain information about species presence.
Wolves are some of the world's most charismatic and controversial animals, capturing the imaginations of their friends and foes alike. Highly intelligent and adaptable, they hunt and play together in close-knit packs, sometimes roaming over hundreds of square miles in search of food. Once teetering on the brink of extinction across much of the United States and Europe, wolves have made a tremendous comeback in recent years, thanks to legal protection, changing human attitudes, and efforts to reintroduce them to suitable habitats in North America. As wolf populations have rebounded, scientific studies of them have also flourished. But there hasn't been a systematic, comprehensive overview of wolf biology since 1970. In Wolves , many of the world's leading wolf experts provide state-of-the-art coverage of just about everything you could want to know about these fascinating creatures. Individual chapters cover wolf social ecology, behavior, communication, feeding habits and hunting techniques, population dynamics, physiology and pathology, molecular genetics, evolution and taxonomy, interactions with nonhuman animals such as bears and coyotes, reintroduction, interactions with humans, and conservation and recovery efforts. The book discusses both gray and red wolves in detail and includes information about wolves around the world, from the United States and Canada to Italy, Romania, Saudi Arabia, Israel, India, and Mongolia. Wolves is also extensively illustrated with black and white photos, line drawings, maps, and fifty color plates.
Conservation translocations, the human-mediated movement and release of a living organism for a conservation benefit, are increasingly recommended in species’ recovery plans as a technique for mitigating population declines or augmenting genetic diversity. However, translocation protocols for species with broad distributions may require regionally specific considerations to increase success, as environmental gradients may pose different constraints on population establishment and persistence in different parts of the range. Here we report on ongoing, genetically informed translocations of a threatened amphibian, California red-legged frog ( Rana draytonii ), from Baja California, México, to extirpated parts of the range in southern California in the United States, where contemporary stressors related to urbanization, invasive species, and aridification add to the natural environmental challenges already present for amphibians at this ‘warm edge’ of the range. We describe the collaborative binational planning required to jumpstart the effort, the fine-tuning of protocols for collection, transport, headstarting, and release of individuals, and results of multiple translocations, where time will tell whether the successes to date have reached their full potential. The steps outlined in this paper can serve as a template to inform future conservation translocations of imperiled amphibians across the U.S./México border, where the phylogenetics, historical biogeography and future habitat availability of a focal species are blind to political boundaries and critical to guiding recovery actions across the range.
Hybridization is common in bird populations but can be challenging for management, especially if one of the two parent species is of greater conservation concern than the other. King rails (Rallus elegans) and clapper rails (R. crepitans) are two marsh bird species with similar morphologies, behaviors, and overlapping distributions. The two species are found along a salinity gradient with the king rail in freshwater marshes and the clapper in estuarine marshes. However, this separation is not absolute; they are occasionally sympatric, and there are reports of interbreeding. In Virginia, USA, both king and clapper rails are identified by the state as Species of Greater Conservation Need, although clappers are thought to be more abundant and king rails have a higher priority ranking. We used a mitochondrial DNA marker and 13 diagnostic nuclear single nucleotide polymorphisms (SNPs) to identify species, classify the degree of introgression, and explore the evolutionary history of introgression in two putative clapper rail focal populations along a salinity gradient in coastal Virginia. Genetic analyses revealed cryptic introgression with site-specific rates of admixture. We identified a pattern of introgression where clapper rail alleles predominate in brackish marshes. These results suggest clapper rails may be displacing king rails in Virginia coastal waterways, most likely as a result of ecological selection. As introgression can result in various outcomes from outbreeding depression to local adaptation, continued monitoring of these populations would allow further exploration of hybrid fitness and inform conservation management.
Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal, and occupancy data, to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog ( Rana luteiventris ). R. luteiventris occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change, and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (1) assessing support for ESUs within Nevada; (2) evaluating and revising, if warranted, the current delineation of MUs; and (3) evaluating genetic diversity, effective population size, adaptive differentiation, and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.
The warming climate will expose alpine species adapted to a highly seasonal, harsh environment to novel environmental conditions. A species can shift their distribution, acclimate, or adapt in response to a new climate. Alpine species have little suitable habitat to shift their distribution, and the limits of acclimation will likely be tested by climate change in the long-term. Adaptive genetic variation may provide the raw material for species to adapt to this changing environment. Here, we use a genomic approach to describe adaptive divergence in an alpine-obligate species, the white-tailed ptarmigan ( Lagopus leucura ), a species distributed from Alaska to New Mexico, across an environmentally variable geographic range. Previous work has identified genetic structure and morphological, behavioral, and physiological differences across the species’ range; however, those studies were unable to determine the degree to which adaptive divergence is correlated with local variation in environmental conditions. We used a genome-wide dataset generated from 95 white-tailed ptarmigan distributed throughout the species’ range and genotype–environment association analyses to identify the genetic signature and environmental drivers of local adaptation. We detected associations between multiple environmental gradients and candidate adaptive loci, suggesting ptarmigan populations may be locally adapted to the plant community composition, elevation, local climate, and to the seasonality of the environment. Overall, our results suggest there may be groups within the species’ range with genetic variation that could be essential for adapting to a changing climate and helpful in guiding conservation action.
Abstract: We assessed parentage within and among maternity colonies of the northern long-eared bat (Myotis septentrionalis Troessart 1897) in north-central Kentucky from 2011–2013 to better understand colony social structure, formation, and membership dynamics. We intensively sampled colonies in close and remote (> 10 km) spatial proximity both before and after targeted day-roost removal. Colonies were not necessarily comprised of closely related individuals, but natal philopatry was common. Adjacent colonies often contained maternally related individuals, indicating that some pups did disperse, albeit not far from their natal home range. Lack of apparent overlap among maternity colonies, along with no observed individual movements between colonies, suggests that colonies may be relatively closed once established in the maternity season. Whereas some young on site had been sired by males collected on site that by chance had dispersed to the same summering grounds, most had not, as would be expected since the species mates in the fall swarms near hibernacula. The number of parentages that we inferred among colonies, however, suggests that outside the maternity season, social groups may be relatively flexible and open, with individuals moving among groups close to their natal area. Analysis of microsatellite DNA data showed a low FST (= 0.011) and best fit to a model of one multilocus genotypic cluster across the study area. We observed high turnover in colony membership between years in all colonies, regardless of roost removal treatment. Our results suggest that female northern long-eared bats exhibit fidelity to a general geographic area rather than individual colonies between years, and indicate presence of a complex and dynamic social-genetic structure. Greater understanding of colony dynamics, including formation, dissolution, and dispersal patterns, may contribute to conservation and management of this threatened species.
Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat ( Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi.
Introgressive hybridization with introduced rainbow trout (RBT) ( Oncorhynchus mykiss ) has led to the loss of native cutthroat trout species ( O. clarkii ) throughout their range, creating conservation concerns. Monitoring temporal hybridization trends provides resource managers with a tool for determining population status and information for establishing conservation goals for native cutthroat trout. In this study, we re-sampled six locations in 2010 within the Stehekin River watershed, North Cascades National Park, which were originally sampled between 1999 and 2003. We used genetic markers to monitor changes in hybridization levels between sampling periods in the native westslope cutthroat trout (WCT) ( O. c. lewisi ) stemming from past RBT introductions. Additionally, two new locations from the lower Stehekin drainage were added to the baseline data. We found that the frequency of WCT, RBT, and their hybrids was not significantly different between monitoring periods, but that RBT allele frequencies decreased in two locations and increased in one location. We also found a consistent, substantial reduction in the frequency of RBT alleles over the monitoring period in the Stehekin River upstream of Bridge Creek (SR3) compared to the Stehekin River downstream of Bridge Creek (SR1 -2) and within lower Bridge Creek (BR1) although these three locations are confined to a small geographic area (approximately 5 km). Ecological and/or evolutionary processes likely restrict the dispersal of RBT alleles in the Stehekin River upstream of Bridge Creek.
Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears ( Ursus americanus ) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (A R = 9.11) and significantly lower in the translocated populations (A R = 7.07-7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (A R = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas.
The bighead carp Hypophthalmichthys nobilis is native to China but has been introduced to over 70 countries and is established in many large river systems. Genetic diversity and variation in introduced bighead carp have not previously been evaluated, and a systematic comparison among fish from different river systems was unavailable. In this study, 190 bighead carp specimens were sampled from five river systems in three countries (Yangtze, Pearl, and Amur rivers, China; Danube River, Hungary; Mississippi River basin, USA) and their mitochondrial 16S ribosomal RNA gene and D-loop region were sequenced (around 1,345 base pairs). Moderate genetic diversity was found in bighead carp, ranging from 0.0014 to 0.0043 for nucleotide diversity and from 0.6879 to 0.9333 for haplotype diversity. Haplotype analysis provided evidence that (1) multiple haplotype groups might be present among bighead carp, (2) bighead carp probably originated from the Yangtze River, and (3) bighead carp in the Mississippi River basin may have some genetic ancestry in the Danube River. The analysis of molecular variance showed significant genetic differentiation among these five populations but also revealed limited differentiation between the Yangtze and Amur River bighead carp. This large-scale study of bighead carp genetic diversity and variation provides the first global perspective of bighead carp in the context of biodiversity conservation as well as invasive species control and management.
With an estimated breeding population in 2010 of 383,000 pairs, the Golden-winged Warbler ( Vermivora chrysoptera ) is among the most vulnerable and steeply declining of North American passerines. This species also has exhibited among the most dynamic breeding distributions, with populations expanding and then contracting over the past 150 years in response to regional habitat changes, interactions with closely related Blue-winged Warblers ( V. cyanoptera ), and possibly climate change. Since 1966, the rangewide population has declined by >70% (-2.3% per year; latest North American Breeding Bird Survey data), with much steeper declines in the Appalachian Mountains bird conservation region (-8.3% per year, 98% overall decline). Despite apparently stable or increasing populations in the northwestern part of the range (Minnesota, Manitoba), population estimates for Golden-winged Warbler have continued to decline by 18% from the decade of the 1990s to the 2000s. Population modeling predicts a further decline to roughly 37,000 individuals by 2100, with the species likely to persist only in Manitoba, Minnesota, and possibly Ontario. To delineate the present-day distribution and to identify population concentrations that could serve as conservation focus areas, we compiled rangewide survey data collected in 2000-2006 in 21 states and 3 Canadian provinces, as part of the Golden-winged Warbler Atlas Project (GOWAP), supplemented by state and provincial Breeding Bird Atlas data and more recent observations in eBird. Based on >8,000 GOWAP surveys for Golden-winged and Blue-winged warblers and their hybrids, we mapped occurrence of phenotypically pure and mixed populations in a roughly 0.5-degree grid across the species’ ranges. Hybrids and mixed Golden-winged-Blue-winged populations occurred in a relatively narrow zone across Minnesota, Wisconsin, Michigan, southern Ontario, and northern New York. Phenotypically pure Golden-winged Warbler populations occurred north of this hybrid zone, but the future of northern populations in the Great Lakes states and Canada (where >80% of the species occurs at present) is highly uncertain because of continued northward expansion of Blue-winged Warblers and hybridization. A second, now-disjunct band of Golden-winged Warbler populations exists in the Appalachian Mountains from southeastern New York to northern Georgia, surrounded at lower elevations by Blue-winged Warblers. Important concentrations of Golden-winged Warblers persist in the Allegheny Mountains region of West Virginia, the Cumberland Mountains in Tennessee, Blue Ridge Mountains of western North Carolina, Allegheny Plateau and Pocono Mountains in Pennsylvania, and in the Hudson Highlands of southern New York. These high-elevation Appalachian populations have escaped contact with Blue-winged Warblers until very recently and represent important refugia for conservation and management; other Appalachian populations are rapidly declining. In addition, based on historical records and standardized surveys across the wintering grounds, we identified three regions of concentration: highlands and Caribbean slopes from Guatemala and Belize to northwestern Nicaragua; middle elevations (both slopes) in Costa Rica and western Panama; and in an arc of the northern Andes from central Colombia to northern Venezuela. It is possible that the winter range has been shifting towards the northwest in recent decades, paralleling shifts in the breeding distribution. Future conservation efforts for Golden-winged Warbler need to include close monitoring of the dynamic phenotypic and genetic distributional shifts, and may need to consider the “winged warbler” complex together as a highly adaptable evolutionary unit.
Fecundity is a vital population characteristic that is directly linked to the productivity of fish populations. Historic data from Yukon River (Alaska) Chinook salmon Oncorhynchus tshawytscha suggest that length‐adjusted fecundity differs among populations within the drainage and either is temporally variable or has declined. Yukon River Chinook salmon have been harvested in large‐mesh gill‐net fisheries for decades, and a decline in fecundity was considered a potential evolutionary response to size‐selective exploitation. The implications for fishery conservation and management led us to further investigate the fecundity of Yukon River Chinook salmon populations. Matched observations of fecundity, length, and genotype were collected from a sample of adult females captured from the multipopulation spawning migration near the mouth of the Yukon River in 2008. These data were modeled by using a new mixture model, which was developed by extending the conditional maximum likelihood mixture model that is commonly used to estimate the composition of multipopulation mixtures based on genetic data. The new model facilitates maximum likelihood estimation of stock‐specific fecundity parameters without first using individual assignment to a putative population of origin, thus avoiding potential biases caused by assignment error. The hypothesis that fecundity of Chinook salmon has declined was not supported; this result implies that fecundity exhibits high interannual variability. However, length‐adjusted fecundity estimates decreased as migratory distance increased, and fecundity was more strongly dependent on fish size for populations spawning in the middle and upper portions of the drainage. These findings provide insights into potential constraints on reproductive investment imposed by long migrations and warrant consideration in fisheries management and conservation. The new mixture model extends the utility of genetic markers to new applications and can be easily adapted to study any observable trait or condition that may vary among populations.
Piute ground squirrels ( Spermophilus mollis ) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size ( N e ) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 813 km. The ratio of effective population size to census number ( N e / N ) was 0.57. Combining N e / N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Q populations 0.070.10) between subpopulations and no inbreeding within subpopulations ( f = 0.0003). These estimates of population subdivision translate into an effective migration rate ( N e m ) of 2.33.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.
Applications of genetic-based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult encounters. Estimates of breeding population size ( N S ) are particularly amenable to genetic-based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of N S , is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY . We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of N S using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating N S . We applied results of the simulation analysis to evaluate Nˆ S for a population of federally endangered Atlantic sturgeon ( Acipenser oxyrinchus oxyrinchus ) in the Delaware River, USA. Our results indicated that N S is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate N S and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.
Iverson et al. (2004) used estimates of the homing rate for molting adult Harlequin Ducks ( Histrionicus histrionicus ) in Alaska to draw inferences about population structure. Homing rates, defined as one minus the ratio of birds recaptured elsewhere to those recaptured at the original banding site, were high (0.95–1.00) for males and females. Iverson et al. (2004) concluded that these high rates of homing are indicative of demographic independence among molting groups separated by small distances (tens to hundreds of kilometers) and that conservation efforts should recognize this fine-scale population structure. We re-examined their use of the homing rate, because their assumption of equal detection probability across a wide sampling area could have led to an upward bias in their estimates of site fidelity. As a result, we are hesitant to agree with their conclusion of high adult homing to molting areas and that molt-site fidelity is evidence for demographic independence. Our hesitancy stems from the fact that little is known about juvenile and adult movements within and among years, breeding area origins, and the variation of demographic parameters (e.g., survival and productivity) among molting groups. Furthermore, population genetic data of these molting groups suggest gene flow at both nuclear and mitochondrial loci. Such mixed messages between demographic (i.e., banding) and genetic data are increasingly common in ornithological studies and offer unique opportunities to reassess predictions and make more robust inferences about population structure across broad temporal and spatial scales. Thus, we stress that it is this broader scale perspective, which combines both demography and genetics, that biologists should seek to quantify and conservation efforts should seek to recognize.
Water and coral mucus samples were collected from throughout the Florida Keys National Marine Sanctuary and the Dry Tortugas for three years and were analyzed for human enteric viruses (enteroviruses, noroviruses, hepatitis A virus and adenoviruses) as conservative markers of human sewage using molecular methods. Of the 100 coral and water samples collected, 40 contained genetic material from one or more human enteric viruses. DNA-based adenoviruses were detected widely, in 37.8% of samples and at 91% of stations, including ‘pristine’ reefs in the Dry Tortugas; however, the detection rate was ⩽12% for the RNA-based enteroviruses and noroviruses (hepatitis A virus was never detected). The disparity between the prevalence of RNA- and DNA-based viruses suggests the need for additional work to determine the utility of adenovirus as marker of human sewage.
Malacologists generally acknowledge that the Alasminota holstonia (Tennessee Heelsplitter) populations in the Caney Fork, Elk, and Duck river drainages in the Barrens Plateau region of middle Tennessee likely represent a closely related, but distinct, species, collectively referred to as Alasminota sp. (Barrens Heelsplitter). Recent surveys indicate that the species persists in at least 5 streams: Collins River, Pocahontas Branch, Witty Creek, and Pepper Hollow Branch in the Caney Fork River drainage and Little Duck River in the Duck River drainage, with evidence of recruitment in 2 of these streams. These findings suggest a restricted distribution and highlight the need for taxonomic assessment through genetic analysis. If elevated to species status, the Barrens Heelsplitter would represent a narrow endemic that may require conservation attention, underscoring the ecological significance of Tennessee's Barrens Plateau Region.