American black bear (Ursus americanus). Photo credit: John J. Mosesso/NBII.Gov

Leetown Science Center geneticists have utilized unique multilocus genotypes in mark-recapture models to estimate black bear population size and density and to assess genetic diversity in bears collected from LA, TN, AL, FL, GA, NC and MD.  Hair tufts, obtained from baited barbed-wire traps, are used as a source of DNA for analysis.  A sufficient number of loci are used to distinguish each individual within a study area.  The unique multilocus genotypes are then used to identify re-sampled bears.  In addition to determining population size, these genotypes provide a value-added component in that they allow estimates of genetic diversity and variation within and among populations.  Moreover, sex-specific primers are used to determine the sex of individual bears in some study areas.

For more information contact Timothy L. King at the Leetown Science Center.

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American black bear (Ursus americanus). Photo credit: John J. Mosesso/NBII.Gov

Understanding the population structure of a species is key to developing effective wildlife management strategies. For example, if wildlife managers apply different management strategies on each of two adjacent game management units, but a single population of black bears is represented across both management units, then it is not possible to evaluate either management strategy because the effects are on the population as a whole and not distinguishable between unit boundaries. However, little genetic information is available to assist managers in defining workable “management units” for black bears in Colorado. This project seeks to ascertain population boundaries (if any exist) for black bear populations across the state. FORT geneticists will determine the efficacy of using mitochondrial DNA and microsatellite markers to delineate black bear subpopulations by genotyping approximately 150 individual black bears across 7–10 nuclear microsatellite loci and sequencing a rapidly evolving portion of the control region for each bear. The data will be analyzed using standard population genetic methods.

For more information contact Sara J. Oyler-McCance, Rocky Mountain Center for Conservation Genetics and Systematics.

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Family of brown bears from Brooks River. Photo credit: Sara L. Graziano, USGS

The Alaska Science Center is collaborating with the National Park Service (NPS) to conduct a genetic study on brown bears (Ursus arctos) that populate Brooks River in Katmai National Park and Preserve (KATM), Alaska.  Patterns of brown bear activity at Brooks River coincide with the availability of sockeye salmon (Oncorhynchus nerka) returning to spawn each summer and fall.  This study will establish individual genotypes for brown bears, determine familial and lineage relationships, and explore sequence variation in circadian rhythm genes among brown bears sampled at Brooks River.

For more information contact Jennifer L. Nielsen, Alaska Science Center, and Troy Hamen, National Park Service.

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A female grizzly with two cubs investigates a hair trap in Glacier National Park, MT. USGS Northern Divide Bear Project remote camera photo 8 Aug 2007 by J. Stetz and E. Penn.

The Northern Continental Divide Ecosystem (NCDE) in northwest Montana is one of the last strongholds of the grizzly bear in the lower 48 states. Of the six established grizzly bear recovery zones, the NCDE is the third largest in area, potentially harboring the greatest number of grizzly bears, and is the only zone contiguous to a strong Canadian population. For these reasons it may have the best prospect of long-term survival for this threatened species. However, little information exists about the bears in this region and as agencies strive to recover the threatened grizzly bear, it is clear that there is a need to assess the grizzly bear population in the NCDE.

Managers and biologists are working to identify population size, trend, survival, and the corridors that link separate populations. Advances in genetic technology allow us to address these parameters through the identification of species, sex, and individuals from DNA extracted from bear hair without ever handling a bear. This project will apply these techniques in conjunction with statistical models to estimate the number of grizzly bears inhabiting the NCDE.  DNA will be analyzed from bear hair collected along survey routes and from systematically positioned hair snag stations. Grizzly bears identified from hair samples will be used in a mark recapture model to estimate the population of bears in the NCDE and will provide an independent calibration of the population index developed from survey routes. This information will be used to address future bear conservation issues.

For more information visit the Northern Divide Grizzly Bear Project Web page and contact Katherine C. Kendall, Northern Rocky Mountain Science Center.

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A 258 kg male grizzly bear recovering from anesthesia in a culvert trap after handling on 8 September 2003, in Antelope Creek, Yellowstone National Park, Wyoming. Photo credit: Chad Dickinson, USGS-Interagency Grizzly Bear Study Team

The Greater Yellowstone Ecosystem (GYE) supports one of the two largest remaining grizzly bear populations in the contiguous United States.  Grizzly bears in the GYE are the most southerly extent population in North American occupying some 37,000 km2 in, and around Yellowstone National Park.  The GYE population is also thought to be isolated from other populations, the closest occurring approximately 160 km to the north in the Northern Continental Divide Ecosystem (NCDE) of northwest Montana.  Listed as Threatened under the Endangered Species Act (ESA) in 1975, the GYE populations was removed from Federal protection as of 30 April, 2007 (see Final Rule [FR] Removing the Yellowstone Distinct Population Segment of Grizzly Bears From the Federal List of Endangered and Threatened Wildlife, Federal Register 72:40, March 29 2007 pages 14866-14938).  A task specified in FR is to document natural connectivity, or lack there of, between the GYE and the NCDE grizzly populations.  Samples for DNA genotyping are being collected by bear researchers and managers from live captures and mortalities throughout the Idaho, Montana, and Wyoming portions of the GYE.  Gene flow between these 2 populations will be detected by using an ‘‘assignment test’’ which identifies the ecosystem from which individuals are most likely to have originated based on their unique genetic signature.  The assignment tests will be completed using genetic results from, and in cooperation with the Northern Continental Divide Grizzly Bear Project (NRMSC-Kendall). This technique also has the ability to identify bears that may be the product of reproduction between GYE and NCDE bears.  If gene flow into the GYE from the NCDE grizzly population is not documented by 2020 then the U.S. Fish and Wildlife Service in conjunction with their partners will be required to translocate grizzly bears from other grizzly populations into the GYE to maintain current levels of genetic diversity.  The Interagency Grizzly Bear Study Team (NRMSC-Schwartz) is responsible for collecting and maintaining samples for analysis and has contracted with Wildlife Genetics International (Dr. David Paetkau, Nelson, BC, Canada) to determine individual identity from GYE sampled bears and to conduct the assignment tests.

For more information visit http://www.nrmsc.usgs.gov/research/igbst-home.htm and contact Charles Shwartz, Northern Rocky Mountain Science Center.

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Indiana bat (Myotis sodalis). Photo credit: U.S. Fish and Wildlife Service

Despite the fact that the Indiana bat (Myotis sodalis) has been more intensively studied throughout its range than most other North American bats, managers continue to lack basic information about population dynamics on the summer range. In particular, accurate demographic and relatedness information is needed for the bat’s management and recovery. Limitations associated with traditional mark-recapture techniques do not provide researchers with the ability to regularly monitor individual bats throughout a breeding season. Recent advances in the application of molecular genetic techniques to wildlife biology have made it possible to uniquely identify animals using DNA as an individual mark, but their use for endangered bats has been limited. Now, preliminary work by USGS scientists has shown that DNA can be successfully extracted from Indiana bat fecal pellets collected from underneath roost trees, and molecular markers have been developed for this species. USGS investigators are using these techniques to uniquely identify individual bats for the purposes of investigating genetic relatedness and conducting a mark-recapture study to estimate population size and survival rates.

For more information contact Sara J. Oyler-McCance, Rocky Mountain Center for Conservation Genetics and Systematics.

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Key Largo woodrat. Photo credit: U.S. Fish and Wildlife Service

Key Largo woodrat. Photo credit: U.S. Fish and Wildlife Service

The Key Largo Woodrat (Neotoma floridana smalli) is a subspecies of the Eastern Woodrat (Neotoma floridana floridana) confined to a single small population in less than 900 ha of tropical hardwood forest. Listed under the ESA as endangered since 1984, the continued existence of the Key Largo woodrat is threatened by development and predation by feral cats and other predators. A suite of genetic markers was identified and screened in over 140 wild woodrats allowing LSC geneticist to integrate landscape ecology, spatial statistics and population genetics. This landscape genetics research has determined the presence of five previously unrecognized subpopulations within the range of the Key Largo woodrat (Figure 1). Understanding landscape effects on genetic connectivity among the woodrat has provided insight into identifying specific anthropogenic barriers that reduce gene flow or genetic diversity. This research has allowed prediction of the effects of proposed management alternatives on genetic variation and population connectivity, and identified potential biological corridors to assist with reestablishing gene flow among small isolated subpopulations. Moreover, the threat of extinction of the Key Largo woodrat is so high that managers and scientists settled on captive breeding of some of the few remaining woodrats as the most likely means of staving off extinction and facilitating successful recovery of the subspecies. Geneticists at the Leetown Science Center in West Virginia, in collaboration with the U.S. Fish and Wildlife Service’s South Florida Ecological Services Field Office and Walt Disney World’s Animal Kingdom, have developed a genetics-based captive breeding program to minimize problems arising from inbreeding by preserving and maximizing genetic diversity through paired-matings that artificially reconnect recently isolated subpopulations.

For more information contact Timothy L. King at the Leetown Science Center.

Figure 1: Maps of Geneland individual assignments to clusters for K = 5. The five plots represent the assignment of pixels to each cluster Pop 1 – Pop 5 arranged from the northeast to southwest of Key Largo, Florida.  The y coordinates are latitude and x coordinates are longitude.  The entire range is less than 10 miles in length.  The highest population membership values are in light yellow and the level curves illustrate the spatial changes in assignment values. The plot is based on the highest-probability run at that value of K.  These results should not be cited without permission of Tim King, Leetown Science Center.

Underwater view of a manatee in Crystal River, Florida. Photo credit: Robert K. Bonde, USGS

Dr. Robert K. Bonde (left) and fellow workers with manatee. Photo credit: USGS

Manatees in Florida are a subspecies of the West Indian manatee that inhabits the tropical waters from Florida in the north throughout the Caribbean down the Atlantic to Brazil in the south. In Florida and Puerto Rico the manatee populations are endangered.

Based on genetic data analyses of manatees collected throughout the state of Florida, there is little evidence of organized genetic population structuring. This finding, using microsatellite DNA analyses, supports earlier published results incorporating allozymes, cytochrome-b, and mitochondrial DNA haplotypes. The data suggest that there is little genetic difference between individual manatees in Florida. The implication of this finding is that there has been little time for isolation of present day populations that would result in specialized genes within subpopulations. Nei’s genetic distance and Wright's Fst, calculates the level of population subdivision based on gene flow between populations. With the preliminary microsatellite dataset, the Fst and Nei’s values suggest that there is minimal subdivision of the Florida population based on genetic profiling. This does not imply that the four established management units recognized for the Florida manatee population are not valid. Management units are based on habitat usage and condition, as well as human density and potential threats. Additionally, there is ample variation using existing microsatellite primers in the dataset to detect individual identity which will allow future research efforts to examine overall health of the population in Florida. This will entail studies on pedigrees and familial subunits. More studies are necessary to (1) examine other manatee populations (such as Puerto Rico and Belize) for comparison of these values obtained from Florida and (2) develop more detailed tools to identify specific aspects of overall population fitness.

For more information visit http://fl.biology.usgs.gov/Manatees/manatees.html and the Bonde Genetics Lab featured article from the Soundwaves monthly electronic newsletter site at USGS, Using Genetic Modeling to Assess the Health and Status of Manatee Populations.  You may also contact Robert K. Bonde, Florida Integrated Science Center.

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Workers carry a manatee to return to the water at Crystal River, Florida. Photo credit: Mary E. Greene, USGS

Workers pull in two manatees for health assessments. Photo credit: Mary E. Greene, USGS

At Crystal River National Wildlife Refuge, Florida, USGS scientists and their partners have conducted manatee radio tagging and capture events for the past three years to assess manatee health and provide baseline biological information. These tagging and capture events involve a range of tests such as weighing, blood sampling, measuring the manatee’s length from snout to tail, and taking small skin samples for genetic analyses. The data gathered from the assessments reveal movement patterns and identification of significant habitats, reproduction, survival, population status and trends, and overall population structure.

For more information visit Florida Integrated Science Center's Healthy Springs, Healthy Manatees highlight, download the center's Manatee Captures and Health Assessment handout (PDF, 1339 KB) , and contact Robert K. Bonde, Florida Integrated Science Center.

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Hoary bat (Lasiurus cinereus). Photo credit: Paul Cryan and Keith Geluso

Bats have been documented to be killed in high numbers by collisions with wind turbines in the United States and Canada. As new wind energy projects are established, bat mortality is likely to increase.  This is particularly problematic in the eastern United States where the highest rates of bat mortality have been recorded and wind farms are being proposed and built at a prodigious rate. Bat mortality at wind farms occurs primarily during the late summer and early fall, the peak migration period for many bat species. Three migratory species of bats account for more than half of the fatalities at wind farms: red bats (Lasiurus borealis), hoary bats (Lasiurus cinereus), and silver haired bats (Lasionycteris noctivagans).  The potential for populations of these species to be severely affected by wind turbine kills is high, particularly due to their low reproductive rates.  Currently there are no reliable estimates of historic or current numbers, or population structure of most migratory bat species within North America.  Because of their high mobility, non-colonial and multiple roost sites, and secretive, nocturnal habits, estimation of population sizes of migratory tree bats using conventional census techniques is extremely difficult, if not impossible.  Application of genetic techniques will provide the needed historical and current population size estimates, as well as population structure for these bats, and allow for documentation in the future of any effects on bat populations resulting from wind power development.  This study will provide specific genetic markers necessary to identify the impacts of wind turbine kills on populations of the hoary bat, red bat and silver-haired bat and will allow documentation through time of effects on their populations that may occur as a national network of wind turbines comes on line.

For more information contact John F. Switzer, Leetown Science Center.

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Close-up of male mountain lion (Puma concolor). Photo credit: U.S. Fish and Wildlife Service

Close-up of female mountain lion (Puma concolor). Photo credit: U.S. Fish and Wildlife Service

Using DNA extracted from fecal matter to uniquely identify individuals for capture-recapture studies is becoming increasingly feasible with the advancement of molecular techniques. USGS conservation geneticists are attempting to determine the relationship between quantity/quality of DNA extracted from mountain lion fecal matter and abiotic factors such as temperature, humidity, and time since deposition. To do this, fecal matter from captive mountain lions is being collected and placed in various environmental conditions that simulate those in the wild. Investigators are using highly variable microsatellite loci to determine the quality of the DNA extracted from feces kept at differing conditions and also quantifying actual amounts of mountain lion DNA using Real-time PCR.  This information will be useful in the design of field studies to estimate population dynamics of mountain lions in the wild.

For more information contact Sara J. Oyler-McCance, Rocky Mountain Center for Conservation Genetics and Systematics.

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Nutria in cage at a trip to put telemetry transmitters and collect DNA from nutria. Photo credit: USGS National Wetlands Research Center

Nutria impact on marsh, with view of normal marsh, denuded marsh, and enclosure. Photo credit: USGS National Wetlands Research Center

Netting nutria at a trip to put telemetry transmitters and collect DNA from nutria. Photo credit: USGS National Wetlands Research Center

The invasive nutria, or coypu, causes problems in coastal marshes and bald cypress swamps, especially in Louisiana. Introduced from South America for their fur, they now number in the millions because of the fur trade collapse. Nutria feed on the tender roots of plants, seedlings, and saplings, completely stripping vegetation in areas where they are concentrated (figure Nutria impact on marsh). The USGS studies worldwide nutria distribution and eradication, maps nutria destruction, and develops computer models to predict damage and simulate management options. We are developing several genomic tools to address the nutria problem. These include: DNA finger printing for mark-recapture population estimation. Every nutria's DNA is unique and can be used to identify it. Nutrias are often difficult to catch in live traps and also have low recapture rates. This makes estimating their population difficult. Instead of catching the animal, we are experimenting with hair traps, devices that catch a portion of their hair as they go by. From the DNA in the hair we can identify individuals and make population estimations. DNA can also be used to identify "effective" population size that is how different and how related different populations are. This is useful in understanding how new nutria populations become established. What are the source populations and what pathways they took. Finally we are using DNA to compare nutria populations across the United States and in comparison with population in Northern Italy. Populations that are very diverse or very similar might have different responses to disease, changes in climate, etc.

For more information visit http://www.nwrc.usgs.gov/special/nutria/index.htm and contact Jacoby Carter, National Wetlands Research Center.

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Preble's meadow jumping mouse (Zapus hudsonius preblei). Photo credit: U.S. Fish and Wildlife Service

Preble’s Meadow Jumping Mouse (Zapus hudsonius preblei), listed as threatened under the U.S. Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America.  Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighboring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA.  Geneticists from the Leetown Science Center conducted additional analyses of the phylogeographic structure within Z. hudsonius that called into question previously published data (and conclusions) and confirmed the original taxonomic designations.  A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial (mt) DNA regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies was genetically distinct.  The magnitude of the observed genetic differences was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration.  Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated.  Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), LSC geneticists concluded that the nominal subspecies surveyed did not warrant a taxonomic revision.  Current research is focusing on delineation of the ranges of Z. hudsonius and Z. princeps. 

For more information contact Timothy L. King at the Leetown Science Center.

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