Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Animal Genetics”

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

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

At least 19 recordsLinked to original sources
USGS2005

Rocky Mountain Center for Conservation Genetics and Systematics

The use of molecular genetic tools has become increasingly important in addressing conservation issues pertaining to plants and animals. Genetic information can be used to augment studies of population dynamics and population viability, investigate systematic, refine taxonomic definitions, investigate population structure and gene flow, and document genetic diversity in a variety of plant and animal species. Further, genetic techniques are being used to investigate mating systems through paternity analysis, and analyze ancient DNA samples from museum specimens, and estimate population size and survival rates using DNA as a unique marker. Such information is essential for the sound management of small, isolated populations of concern and is currently being used by universities, zoos, the U.S. Fish and Wildlife Service, and numerous state fish and wildlife agencies.

Fact Sheet↗
USGS2021

Macrogenetic studies must not ignore limitations of genetic markers and scale

Millette et al . (Ecology Letters, 2020, 23:55–67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

Ecology Letters↗
USGS2019

Within-group relatedness and patterns of reproductive sharing and cooperation in the tropical chestnut-crested yuhina

In cooperatively breeding animals, genetic relatedness among group members often determines the extent of reproductive sharing, cooperation and competition within a group. Studies of species for which cooperative behaviour is not entirely based on kinship are key for understanding the benefits favouring the evolution and maintenance of cooperative breeding among nonrelatives. In the cooperatively breeding chestnut-crested yuhina, Yuhina everetti , a songbird endemic to Borneo, we tested whether unrelated helpers are more likely to gain parentage than are related helpers consistent with the hypothesis that inbreeding risk constrains reproduction by related helpers. We also examined whether related or unrelated helpers provision broods more because of differences in their potential indirect or direct fitness benefits of helping. Kin structure of breeding groups (breeding pair and up to eight helpers of both sexes, median = 2 helpers, 96% of 57 pairs had helpers) based on genetic analysis was mixed; 48% of 76 breeder/helper dyads were first-order (26%) or second-order (22%) relatives of one or both members of the breeding pair, and 52% were nonrelatives. Only unrelated male and female helpers gained parentage, and helpers did not differ in their provisioning rate according to their relatedness to the broods. We documented quasi-parasitism or co-breeding by female helpers in 14% of 29 broods and extrapair paternity by male helpers in 21% of 47 broods. This rate of extrapair paternity is relatively high among the few tropical species examined but fit with predictions for mixed-kin groups where inbreeding is avoided. These findings support the emerging pattern for cooperative breeding in birds with mixed-kin groups, wherein unrelated helpers are more likely to gain parentage than are related helpers and helping effort is not necessarily predicted by kinship.

Animal Behaviour↗
USGS2015

Evaluation of fisher (Pekania pennanti) restoration in Olympic National Park and the Olympic Recovery Area: 2014 annual progress report

With the translocation and release of 90 fishers ( Pekania pennanti ) from British Columbia to Olympic National Park during 2008–2010, the National Park Service and Washington Department of Fish and Wildlife accomplished the first phase of fisher restoration in Washington State. Beginning in 2013, we initiated a new research project to determine the current status of fishers on Washington’s Olympic Peninsula 3–5 years after the releases and evaluate the short-term success of the restoration program. Objectives of the study are to determine the current distribution of fishers and proportion of the recovery area that is currently occupied by fishers, determine several genetic characteristics of the reintroduced population, and determine reproductive success of the founding animals through genetic studies. During 2014, we continued working with a broad coalition of cooperating agencies, tribes, and nongovernmental organizations (NGO) to collect data on fisher distribution and genetics using noninvasive sampling methods. The primary sampling frame consisted of 157 24-square-kilometer hexagons (hexes) distributed across all major land ownerships within the Olympic Peninsula target survey area. In 2014 we expanded the study by adding 58 more hexes to an expanded study area in response to incidental fisher observations outside of the target area obtained in 2013; 49 hexes were added south and 9 to the east of the target area. During 2014, federal, state, tribal and NGO biologists and volunteers established three baited motion-sensing camera stations, paired with hair snaring devices, in 80 hexes; 69 in the targeted area 11 in the expansion areas. Each paired camera/hair station was left in place for approximately 6 weeks, with three checks on 2-week intervals. We documented fisher presence in 5 of the 80 hexagons, and identified 5 different fishers through a combination of microsatellite DNA analyses and camera detections. All fisher detections were in the target area. These 5 individuals included 2 of the original founding population of 90, 1 of the 2 rescued and rehabilitated kits that were released in 2010, and 1 new recruit to the population (1 individual was not identified). Additionally, we identified more than 40 other species of wildlife at the baited camera stations. We also obtained eight incidental fisher observations through photographs and carcass retrieval. During 2015, we plan to sample 75 hexagons in the target area and 12 in the expansion area. We plan to sample all unsampled accessible hexes in the target area (26 hexes), and re-sample accessible hexes sampled in 2013 (49 hexes).

Washington↗
USGS2003

Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): Characterization of a sex-linked (Z-specific) and 14 autosomal loci

Canada goose ( Branta Canadensis ) and harlequin duck ( Histrionicus histrionicus ) DNAs were digested with Sau 3AI, and size selected (300-700 bp) fragments were ligated into Bam HI-digested pBluscriptII KS + . The enrichment protocol of Ostrander et al . 1 was followed. The resulting libraries were screened using a [ƴ- 32 P]ATP end-labelled (CA) 20 oligonucleotides as a hybridization probe. Positive clones were sequenced using cycle-sequencing protocols (Epicentre Technologies, Madison, WI) and primers flanking the inserts. PCR primers were designed to amplify the repeat and yield amplification products of ≈100-200 bp. DNA samples were screened for variation at these loci using [ƴ- 32 P]ATP end-labelled primers. The products were resolved using 6% denaturing polyacrylamide gels and autoradiography.

Animal Genetics↗
USGS1987

Genetic management of endangered species at the Patuxent Wildlife Research Center

Summary: The Patuxent Wildlife Research Center conducts one of the world's largest and best-known research programs for captive propagation of endangered wildlife. In order to be effective and to ensure the long-term survival of species, researchers at Patuxent attempt to manage captive populations according to the principles of population genetics. This includes the use of estimated inbreeding levels for mate selections in Masked Bobwhites and biochemical analyses to measure extant genetic material and determine relationships among Whooping Cranes. As added insurance against catastrophic losses, or even random losses of key individuals representing unique lineages, cryopreservation of semen has been studied and used for some species. Artificial insemination, using either stored or fresh semen, is used to improve fertility rates, thereby increasing the chances for survival of unique genetic lines. Finally, a periodic influx of unrelated stock occurs, when feasible, in order to enhance the genetic base of captive populations. The application of these techniques will ensure that future releases utilize genetically viable animals, thereby improving the potential for successful reintroductions into the wild.

Book chapter↗
USGS1995

Biodiversity: a new challenge

Resource managers at many state and federal agencies are in the middle of a fundamental change in the practice and objectives of conservation. Traditional management has been directed toward maintaining, usually for harvest purposes, populations of individual species such as ducks, deer, or salmon. Increasingly, however, resource managers are recognizing the critical important of conserving biological diversity, or biodiversity. In its simplest terms, biological diversity is the variety of life at all levels: it includes the array of plants and animals; the genetic differences among individuals; the communities, ecosystems, and landscapes in which they occur; and the variety of processes on which they depend. Conserving biological diversity poses dramatic new problems for comprehensive inventory and monitoring: what should be measured or monitored?

Book chapter↗
USGS2018

Isolation by distance versus landscape resistance: Understanding dominant patterns of genetic structure in Northern Spotted Owls (Strix occidentalis caurina)

Landscape genetics investigations examine how the availability and configuration of habitat influence genetic structure of plants and animals. We used landscape genetics to evaluate the role that forest connectivity plays in determining genetic structure of the federally-threatened Northern Spotted Owl ( Strix occidentalis caurina ) using genotypes of 339 Northern Spotted Owls obtained for 10 microsatellite loci. Spatial clustering analyses identified a distinct genetic cluster at the southern extent of the region examined. This cluster could not be linked to landscape connectivity patterns and suggested that post-Pleistocene processes were involved with its development rather than contemporary landscape configuration. We also compared matrices of pairwise inter-individual genetic distances with resistance distances derived from a circuit-theory based framework. Resistance distances were obtained for an idealized raster map that reflected continuous unimpeded dispersal habitat across the landscape along with five empirically-derived raster maps reflecting the 1870’s, 1940’s, 1986, 1994, and 2012. Resistance distances from the idealized map served as surrogates for linear geographic distances. Relative to idealized conditions, resistance distances were ~250% higher in the 1940’s and ~200% higher from 1986 onward. Resistance distances from the 1870’s were ~40% higher than idealized conditions. Inter-individual genetic distances were most highly correlated with resistance distances from the idealized map rather than any of the empirical maps. Two hypotheses explain our results. First, our results may reflect temporal lags between the onset of large-scale habitat alterations and their novel effects on genetic structure in long-lived species such as Northern Spotted Owls. Second, because Northern Spotted Owls disperse over long distances, our results may indicate that forest habitat has never been sufficiently fragmented to the point where connectivity was disrupted. The second hypothesis could indicate that forest management practices mandated by the Northwest Forest Plan succeeded with one of its primary goals. However, our results do not represent a complete portrayal of the status of Northern Spotted Owls given detection of significant population declines and bottlenecks in other studies. Future investigations based on computer simulations may help distinguish between hypotheses.

California, Oregon, Washington↗
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↗
USGS2005

Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout

Because human land use activities often result in increased fragmentation of aquatic and terrestrial habitats, a better understanding of the effects of fragmentation on the genetic heterogeneity of animal populations may be useful for effective management. We used eight microsatellites to examine the genetic structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Camp Creek, an isolated headwater stream in western Oregon. Our objectives were to determine if coastal cutthroat trout were genetically structured within streams and to assess the effects of natural and anthropogenic barriers on coastal cutthroat trout genetic variation. Fish sampling occurred at 10 locations, and allele frequencies differed significantly among all sampling sections. Dispersal barriers strongly influenced coastal cutthroat trout genetic structure and were associated with reduced genetic diversity and increased genetic differentiation. Results indicate that Camp Creek coastal cutthroat trout exist as many small, partially independent populations that are strongly affected by genetic drift. In headwater streams, barriers to movement can result in genetic and demographic isolation leading to reduced coastal cutthroat trout genetic diversity, and potentially compromising long-term population persistence. When habitat fragmentation eliminates gene flow among small populations, similar results may occur in other species.

Oregon↗
USGS2017

Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014

Monitoring the community structure and metabolic activities of cyanobacterial blooms in Upper Klamath Lake, Oregon, is critical to lake management because these blooms degrade water quality and produce toxic microcystins that are harmful to humans, domestic animals, and wildlife. Genetic tools, such as DNA fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analysis, high-throughput DNA sequencing (HTS), and real-time, quantitative polymerase chain reaction (qPCR), provide more sensitive and rapid assessments of bloom ecology than traditional techniques. The objectives of this study were (1) to characterize the microbial community at one site in Upper Klamath Lake and determine changes in the cyanobacterial community through time using T-RFLP and HTS in comparison with traditional light microscopy; (2) to determine relative abundances and changes in abundance over time of toxigenic Microcystis using qPCR; and (3) to determine relative abundances and changes in abundance over time of Aphanizomenon , Microcystis , and total cyanobacteria using qPCR. T-RFLP analysis of total cyanobacteria showed a dominance of only one or two distinct genotypes in samples from 2013, but results of HTS in 2013 and 2014 showed more variations in the bloom cycle that fit with the previous understanding of bloom dynamics in Upper Klamath Lake and indicated that potentially toxigenic Microcystis was more prevalent in 2014 than in years prior. The qPCR-estimated copy numbers of all target genes were higher in 2014 than in 2013, when microcystin concentrations also were higher. Total Microcystis density was shown with qPCR to be a better predictor of late-season increases in microcystin concentrations than the relative proportions of potentially toxigenic cells. In addition, qPCR targeting Aphanizomenon at one site in Upper Klamath Lake indicated a moderate bloom of this species (corresponding to chlorophyll a concentrations between approximately 75 and 200 micrograms per liter) from mid-June to mid-August, 2014. After August 18, the Aphanizomenon bloom was overtaken by Microcystis late in the season as microcystin concentrations peaked. Overall, results of this study showed how DNA-based, genetic methods may provide rapid and sensitive diagnoses for the presence of toxigenic cyanobacteria and that they are useful for general monitoring or ecological studies and identification of cyanobacterial community members in complex aquatic habitats. These same methods can also be used to simultaneously address spatial (horizontal and vertical) and temporal variation and under different conditions. Additionally, with some modifications, the same techniques can be applied to different sample types, including water, sediment, and tissue.

Oregon↗
USGS2022

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition, ecological impacts of removing scat, and zoonotic risks. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii , California, US, and Morafka's desert tortoise, G. morafkai , Arizona, US) and the common chuckwalla (Sauromalus atar ) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, varied between studies, with 15% for Agassiz's desert tortoise and 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study demonstrates that genotypes can successfully be obtained from swabs of herbivorous reptile scat collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for genetic identification of individuals from non-invasive samples.

Arizona, California↗
USGS2006

Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed

The common occurrence of Escherichia coli in temperate soils has previously been reported, however, there are few studies to date to characterize its source, distribution, persistent capability and genetic diversity. In this study, undisturbed, forest soils within six randomly selected 0.5 m2 exclosure plots (covered by netting of 2.3 mm2 mesh size) were monitored from March to October 2003 for E. coli in order to describe its numerical and population characteristics. Culturable E. coli occurred in 88% of the samples collected, with overall mean counts of 16 MPN g-1, ranging from <1 to 1657 (n = 66). Escherichia coli counts did not correlate with substrate moisture content, air, or soil temperatures, suggesting that seasonality were not a strong factor in population density control. Mean E. coli counts in soil samples (n = 60) were significantly higher inside than immediately outside the exclosures; E. coli distribution within the exclosures was patchy. Repetitive extragenic palindromic polymerase chain reaction (Rep-PCR) demonstrated genetic heterogeneity of E. coli within and among exclosure sites, and the soil strains were genetically distinct from animal (E. coli) strains tested (i.e. gulls, terns, deer and most geese). These results suggest that E. coli can occur and persist for extended periods in undisturbed temperate forest soils independent of recent allochthonous input and season, and that the soil E. coli populations formed a cohesive phylogenetic group in comparison to the set of fecal strains with which they were compared. Thus, in assessing E. coli sources within a stream, it is important to differentiate background soil loadings from inputs derived from animal and human fecal contamination. ?? 2005 Society for Applied Microbiology and Blackwell Publishing Ltd.

Environmental Microbiology↗
USGS2009

Landbird migration in the American West: Recent progress and future research directions

Our knowledge of avian behaviors during the nonbreeding period still lags behind that of the breeding season, but the last decade has witnessed a proliferation in research that has yielded significant progress in understanding migration patterns of North American birds. And, although historically the great majority of migration research has been conducted in the eastern half of the continent, there has been much recent progress on aspects of avian migration in the West. In particular, expanded use of techniques such as radar, plasma metabolites, mist-netting, count surveys, stable isotopes, genetic data, and animal tracking, coupled with an increase in multi-investigator collaborations, have all contributed to this growth of knowledge. There is increasing recognition that migration is likely the most limiting time of year for migratory birds, increasing the importance of continuing to decipher patterns of stopover ecology, identifying critical stopover habitats, and documenting migration routes in the diverse and changing landscapes of the American West. Here, we review and briefly synthesize the latest findings and advances in avian migration and consider research needs to guide future research on migration in the West. ?? 2009 by The Cooper Ornithological Society. All rights reserved.

The Condor↗
USGS2013

Evolutionary hotspots in the Mojave Desert

Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

Mojave Desert↗
USGS2005

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using &theta; values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest &theta; (0.13-0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (&theta; = 0.04-0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Nino Southern Oscillation (ENSO) events along the Pacific coast.

Molecular Ecology↗
USGS2011

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): Implications for managing small populations of long-lived animals

In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle ( Glyptemys muhlenbergii ) in North Carolina. Using capture–recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0.893 (SE = 0.018, 95% confidence interval, 0.853–0.924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4.8 ± 0.5) and observed heterozygosity (0.619 ± 0.064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems.

Conservation Genetics↗