National Genomics Center for Wildlife and Fish Conservation

National Genomics Center for Wildlife and Fish Conservation

The National Genomics Center for Wildlife and Fish Conservation is a state-of-the art facility for advanced research providing expertise in DNA sequencing and environmental and forensic DNA sampling. The Center is designed for cross-agency partnerships to provide cost-effective and reliable genetic and genomic data for species monitoring. Click here to meet our team.

The Genomics Center has its roots in the genetics laboratory managed by the USDA Forest Service’s Rocky Mountain Research Station and is located on the University of Montana campus in Missoula. Scientists conduct research at the genetics laboratory with a focus on delivering science that addresses the needs of land managers. Founded in 1998, the laboratory has grown into a national resource for states, tribes, universities, and private groups that need answers to pressing wildlife management questions for more than 60 species, including wolverines, lynx, and sage grouse.

Overview
eDNA
Genetic Sampling
Genomics
Species Profiles
People
Resources

The Genomics Center provides advanced methods for species monitoring in the following main categories:

eDNA: Environmental DNA can be collected from bodies of water and offers great potential for monitoring and detecting species of interest.
Non-Invasive Genetic Sampling: This sampling technique uses forensic-style DNA samples, such as hair and feathers, for a more efficient method to monitor rare and sensitive species.
Genomics: Genomics allows the biology of wildlife populations to be explored in great detail, through cutting-edge DNA sequencing technologies.

Forest Service partners from other agencies, industry, nongovernmental organizations, tribes, and states need timely and usable information on wildlife and fish populations to make informed decisions on natural resource policy and management.

The Genomics Center was developed with the recognition that synergy could be gained by multiple agencies working together to tackle natural resource problems with genomic information. While each agency has different mandates, there are times when similar information can be collected jointly and expertise can be shared, leading to better management decisions.

Agencies interested in becoming partners with the center can refer to the contact list linked above. For general inquiries, email NGC@usda.gov.

Sample collection protocols and forms are also available in the Resources tab.

Keeping tabs on the whereabouts of invasive or endangered species is an important job for managers, but it can be a nearly impossible task to accomplish across a vast landscape. Traditionally, species monitoring has relied on physical observations of organisms in the field. These surveys can be labor-intensive, particularly when surveying in remote areas or for organisms that are rare or difficult to find. Today, there is a powerful new approach that can determine the presence of a species simply by sampling a cup of water: environmental DNA (eDNA).

Organisms continually shed cells containing their DNA into their surroundings. For example, DNA in skin cells sloughed from a fish can be found in water, or DNA in plant pollen can be found in the air. That DNA persists in the environment, where it can be collected in an air, soil, or water sample and analyzed for species of interest.

Katie Zarn collects an eDNA sample from Fossil Creek in Arizona. Photo by Matthew R. Jones.

Environmental DNA is major breakthrough in wildlife and fish monitoring. It ties traditional field-based ecology to advanced computational tools and exacting molecular methods, such as quantitative polymerase chain reaction (qPCR), which is able to detect DNA from just a couple cells in an environmental sample. It can reveal important information about species presence or absence more quickly and cost-effectively than traditional sampling techniques. It is particularly useful for detecting organisms in low abundance, like threatened and endangered species or individuals at the leading edge of an invasion. For example, scientists used filtered water samples to detect the spread of invasive feral pigs in the Southwestern United States and Burmese python in Florida. Scientists are using similar techniques in the Rocky Mountains to determine the distribution of endangered bull trout, invasive brook trout, Canada lynx, and wolverine.

This technology has been used primarily to survey for fishes and amphibians. However, samples collected from water, air, and soil all contain DNA of many species, and applications are expanding to other aquatic taxa, such as mollusks and insects, as well as semi-aquatic mammals like river otter and beaver. Environmental DNA is also found in snow tracks allowing reliable species identification of carnivores such as wolverine, fisher, and Canada lynx.

Lab techniques for eDNA analysis vary depending on the specific research question. For example, targeted analysis designed to detect a particular species may be used to detect the presence or absence of a rare species. Nontargeted approaches are less sensitive for individual species, but can be used to answer questions about community diversity or reveal previously unknown members of ecological communities. The National Genomics center is also pioneering a third option, high-throughput qPCR, which completes multiple targeted analyses simultaneously. For example, identifying which species is responsible for a track in snow is one of the many potential application for high-throughput qPCR.

Non-Invasive Genetic Sampling

Non-invasive genetic sampling uses forensic-style DNA samples, such as hair, scats and feathers collected without ever seeing an animal, to monitor rare and sensitive species. This non-invasive approach offers a number of advantages over conventional methods, including increased probability of "capturing" an individual, reduced loss of tags, and minimizing the effects of capture and tagging on animals. The NGC has over 20 years' experience processing non-invasive samples.

A Montane Red Fox jumping off a tree trunk at a DNA collection site

Population Genetics

Non-invasive samples, as well as traditional blood and tissue samples, are useful for population genetics, the study of the genetic composition and connectivity of populations. The formal linking of these samples to specific landscapes is called landscape genetics. These samples can also be used in a genetic mark-recapture framework in order to monitor populations and track movement of individuals through time and space and for the analysis of hybridization. Samples can be combined with our existing genetic databases in order to ask broader landscape questions and provide greater understandings of species' distribution and population dynamics.

Forensic Samples

The USFS NGC is a member lab of the Society for Wildlife Forensic Sciences and has protocols in place to process forensic samples. We analyze samples related to law enforcement cases for State and Federal agencies when our databases can provide valuable information. If you are a land manager with a forensic/law enforcement case that we may assist you with, please contact lab supervisor Kristy Pilgrim.

Historical/Ancient Samples

The NGC has a dedicated Ancient DNA laboratory and extensive expertise in working with historic/ancient DNA, primarily from museum specimens. Such samples are incredibly valuable for providing genetic context and a historical picture for comparison to modern samples.

Cryptic Species

The NGC can help with species identification and phylogenetic context for species that are difficult to identify without morphological expertise, such as many invertebrates. We have several ongoing projects identifying stoneflies, butterflies, springsnails, and other gastropods.

Featured Species and Genetic Databases

The NGC has extensive genetic databases on a variety of carnivores and other species. The list below features several of the species for which we have databases available:

Fisher
Wolverine
Lynx
Sage Grouse
Marten
Cougar
Bobcat
Woodpecker
Wolves
Moose
Deer
Bighorn Sheep
Salmonids

Services

Species Identification
Individual Identification
Sex Identification
Re-capture Analysis
Population Assignment
Population Genetic Analysis
Landscape Genetic Analysis
Forensic/Law Enforcement Samples
Ancient/Historic DNA

Software

Genotyping error, often associated with low-quantity/quality DNA samples, is an important issue when using genetic tags to estimate abundance using capture-mark-recapture (CMR). DROPOUT, a MS-Windows program, identifies both loci and samples that likely contain errors affecting CMR estimates. DROPOUT uses a 'bimodal test' that enumerates the number of loci different between each pair of samples and a 'difference in capture history test' (DCH) to determine those loci producing the most errors. Importantly, the DCH test allows one to determine that a data set is error-free.

DROPOUT is free software for the MS-Windows operating system. The software was developed by Kevin McKelvey. The download file is in ZIP format and includes documentation.

Big Data has transformed medicine, transport, finance, and countless other facets of our lives. Conservation science is no different. Rapid technology advancement has made genomics – the analysis of thousands to millions of genetic data points at a time – a cost-effective and powerful tool for describing communities, distinguishing distinct population segments, and understanding the interplay between genetics and ecology. The National Genomics Center uses genomics to better understand where species live, what they eat, and how they might respond to a rapidly changing world. This science helps inform effective management of species ranging from stoneflies to wolves.

A person wearing gloves using a PCR setup in a lab

Ongoing Work

Ongoing work at the NGC using genomics tools includes:

Using genome-wide to assess genetic connectivity and identify functional genetic variation in Greater Sage Grouse
Assessing potential genetic inbreeding in southeast Alaska wolf populations
Understanding how the diets of fishers may respond to ecological changes
Characterizing springsnail species and their distributions across the western U.S.

Future Directions

Genomics is one of the most rapidly evolving fields in conservation research. Our team of scientists is working towards implementing rapid bioassessment tools for cost-effective monitoring, understanding how genetic traits may impact population resiliency to ecological change, and illuminating unseen diversity at landscape scales. These efforts build on a long history of partnership with the National Forest System and other stakeholders to bring high-quality genetic inferences to bear on today’s most pressing management questions.

Services

There are many tools in the genomics toolbox and our team of scientists wants to help you find the one that best fits your question. We want to partner with you from project conception through study design, analysis, and final interpretation in order to maximize the impact of your best work. Some of the services that we can provide include:

Population genomics analysis, including from non-invasive (e.g., hair, scat) samples
Community assessment from environmental samples
Diet reconstruction from fecal samples

Working With Us

If you are interested in working with us on a genomics project, please contact NGC@usda.gov.

The Genomics Center works on more than 75 species. Below is a sampling.

Greater Sage-Grouse

The greater sage-grouse (Centrocercus urophasianus) is an iconic species of the American West, representative of the sagebrush ecosystem. Although sagebrush is resistant to environmental extremes, such as drought, it can take many years to reestablish following disturbance such as fire or land use conversion. As a result, the "sagebrush sea", found throughout the intermountain lowlands, is one of the most threatened ecosystems in North America.

Sage grouse. Photo by Tom Koerner, US Fish & Wildlife Service.

Greater sage-grouse management is a major conservation priority for stakeholders across the West. The U.S. Fish and Wildlife Service will be making a final listing determination for the species in 2015, after previously finding it "warranted for listing but precluded." The greater sage-grouse once occupied 1.2 million square kilometers (nearly 300 million acres) across western North America. Now, the species occupies less than 700,000 acres across 11 Western states and two Canadian provinces. Nearly 75 percent of greater sage-grouse habitat is located on federally owned lands.

To help these efforts, the Genomics Center is investigating greater sage-grouse genetic variation, population structure, and population connectivity. This research is providing scientific support for prioritizing conservation actions on the ground for the greater sage-grouse, such as identifying critical habitat and breeding grounds, or leks. Most importantly, the research from the Genomics Center will allow managers to evaluate how disturbances at individual leks influence the overall connectivity of the breeding network. The Genomics Center is analyzing genetic data from several thousand samples, collected from over 800 leks across Idaho, Montana, North Dakota, and South Dakota. This research is done in collaboration with other federal agencies, non-profit organizations, and eleven state fish and wildlife agencies.

Cougar

The cougar (Puma concolor), also known as the mountain lion, puma, and panther, was once lost, or extirpated, from the eastern portion of the United States, with the exception of the Florida Panther population in the Everglades. However, over the past 30 years, the species has been expanding and establishing new populations in the eastern portion of its range. The Genomics Center has been studying cougars for nearly a decade, done in partnership with 15 state, federal, and Tribal partners. This work focuses on understanding cougar population sizes, movement patterns, and recolonization of former habitat and ranges to inform conservation and management decisions. The Genomics Center currently houses the largest, most geographically extensive genetic database on cougars.

Trout

The Genomics Center is working with over a dozen federal, state, and Tribal partners on monitoring and assessment efforts, with an emphasis on genetic approaches, of native and non-native trout species. These include the threatened native bull trout and a number of cutthroat trout subspecies, nearly all of which have been petitioned for listing under the U.S. Endangered Species Act. Bull trout and cutthroat trout are important game species, prized by fisherman, but have experienced significant declines due to habitat loss and fragmentation and the introduction of non-native trout species.