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A very shallow river with large rocks and stones banked by green forests
Information icon Cahaba River above Shades Creek. Photo by Nathan Whelan, USFWS.

Research Projects

Research in the lab addresses conservation issues pertaining to brood stock management, systematics of imperiled aquatic organisms, and population genetics for species of concern or management interest in the southeast. We also study the evolution of aquatic animals using genomic tools. The lab provides technical coordination for numerous southeastern aquatic species, focusing on fishes and mollusks.

Broodstock Evaluation and Monitoring Programs

Genetic assessment of American shad in the Edisto River

An aquarium with dozens of narrow silver fishes
American shad juveniles at the Bears Bluff National Fish Hatchery. Photo by USFWS.

In an effort to rebuild American shad populations, Bears Bluff National Fish Hatchery propagates and releases American shad into the Edisto River each year. Genetic data are essential for evaluating program success. The Southeast Conservation Genetics Lab (SECGL) is using microsatellites to generate estimates of genetic diversity for American shad in the Edisto. With genetic parentage analyses, we are also evaluating the success of the program by determining the contribution of hatchery-produced fish to the wild population.

Genetic Monitoring of lake sturgeon in the Tennessee River

A female biologist working on samples in a lab
Ashantye Williams performing DNA extractions of Lake sturgeon. Photo by USFWS.

The Tennessee River Lake Sturgeon Reintroduction Working Group was created in 1998 to start a reintroduction program for lake sturgeon in Tennessee. The group includes state, federal, and university scientists working towards the goal of establishing a naturally reproducing population of Lake sturgeon in the Tennessee River. To ensure long-term success, the group developed a management plan that addresses genetic guidelines for stocking and genetic monitoring. Our lake sturgeon genetics work focuses on evaluating program success by examining genetic diversity of broodstock and captively reared individuals being reintroduced into the Tennessee River system. Data generated allows us to provide expertise and guidance to the working group.

Genetic assessment of striped bass broodstock repository lakes in the Apalachicola-Chattahoochee-Flint river systems

Seven silver fish with several dark stripes down it's side
Gulf Coast striped bass in the Gulf of Mexico. Photo by USFWS.

The Striped Bass Technical Task Force was created (ACF) to increase the dwindling population sizes of striped bass in the Apalachicola-Chattahoochee-Flint river systems of Alabama, Georgia, and FloridaA series of reservoirs that would serve as striped bass broodstock repositories (Lewis Smith Lake, Alabama, Lake Talquin, Florida, Lake Seminole and West Point Lake, Georgia) were designated to aid in maximizing and maintaining genetic integrity in the ACF. We annually monitor levels of genetic variation of striped bass broodstock repositories and compare the diversity estimates to wild populations in the ACF.

Molecular confirmation of gopher frog species identification

A yellow and brown marbled snail with two yellow antennae and a yellow shell with spotty green algae
Pleurocera alveare from the Elk River in Tennessee. Photo by Thomas Tarpley, ADCNR.

Morphology-based identification of many larvae and eggs is not possible as there are no distinct characters for identification. This is particularly true for gopher frog eggs brought into national fish hatcheries in the southeastern United States. We use DNA barcoding to provide rapid-response molecular-based identification of frog eggs so USFWS hatcheries know the precise species they are raising.

Phylogenetics, taxonomy, and population genetics

Recent advances in genetic sequencing technologies allow us to generate massive genomic datasets in a small amount of time. We use genome-scale datasets to understand species relationships, gene flow among populations, and taxonomic boundaries. These data inform management decisions and result in better conservation outcomes.

Freshwater snail phylogenomics

Freshwater snails are important components of nearly all freshwater ecosystems in the eastern United States. Unfortunately, many are at-risk or listed as threatened or endangered under the Endangered Species Act. We use phylogenomic approaches, mostly anchored hybrid enrichment, to understand freshwater snail evolution. This allows us to place research and conservation efforts in an evolutionary context. Much of the lab’s work focuses on snails in the family pleuroceridae, an ecologically important group that suffers from a 79% imperilment rate.

Population genomics of mollusks and fish

We use molecular data to understand genetic diversity of natural populations and measure gene flow. Genetic diversity measures can indicate whether a species or population has undergone recent declines, which is important for conservation efforts. Gene flow among populations can be used to understand natural migration patterns and aid in assessing taxonomic boundaries. Genomics data are also used to assess the impact of man-made barriers to natural movement of aquatic organisms. We also use population genomic data to test broad hypotheses on how genetic diversity varies across landscapes.

Current population genomics projects in the lab use a variety of methods to generate datasets of thousands of nuclear loci for genetic analyses. Many of our projects currently focus on freshwater mollusks, particular pleurocerid snails and freshwater mussels. We are also working on sicklefin redhorse, a fish found in the upper Tennessee River system.

A scaly brown and green fish with a bright red fin on its tail
Sicklefin redhorse. Photo by Steve Fraley, North Carolina Wildlife Resources Commision.

Evolution and taxonomy of disease-causing fish parasites

Whirling disease causes gross skeletal deformities in trout and is spreading throughout the United States. The cause of whirling disease, Myxobolus cerebralis, is a cnidarian parasite, making it more closely related to corals and jellyfish than many other freshwater fish parasites. In collaboration with the Service’s labs and the Southeastern Cooperative Fish Parasite & Disease Lab at Auburn University, we are studying the genomics and evolutionary relationships of Myxobolus. Genomic analyses will aid in tracking disease spread. Overall, the lab’s fish parasite work will result in better disease management at hatcheries and enhance recreational opportunities for anglers.

Development of Genetic Management Plans

Conservation planning is a collaborative endeavor with multiple stakeholders – government agencies, landowners, businesses, and scientists must all work together to protect natural resources. Genetic diversity and gene flow (transfer of genetic variation between populations) both support the health and long term sustainability of species in the wild.

Genetic management plans (GMPs) are one tool that our lab uses to help describe the genetic status of declining species and provide guidance on how to best direct recovery efforts from a genetic perspective. Often, species facing extinction in the foreseeable future require intervention beyond monitoring and assessment. Managers sometimes make captive propagation, and ultimately reintroduction, a priority to increase the number of individuals and populations. GMPs are a written summary of genetic research findings such as estimated population size, potential barriers to gene flow, levels of inbreeding, ideal locations to choose when sourcing broodstock for captive propagation, and candidate areas for reintroduction. GMPs also provide broad guidance for recovery efforts.

Below are species that have GMPs in development

Louisiana pearlshell

The Louisiana pearlshell (Margaritifera hembeli) is an endangered species of freshwater mussel native to just a handful of streams in Central Louisiana. Threatened by habitat loss and degradation, understanding the biology of this rare species is more important than ever. Since 2016, our lab has been studying the genetics of the Louisiana pearlshell to help conserve it. To do this, we use genomic sequencing techniques to describe genetic diversity, understand gene flow in wild populations, and enhance ongoing captive propagation efforts.

Dozens of freshwater mussels in a shallow bed
Louisiana pearlshell bed. Photo by Paul Johnson ADCNR.

Cumberlandian combshell

The Cumberlandian combshell (Epioblasma brevidens) is historically native to the Tennessee and Cumberland River systems in parts of Alabama, Tennessee, Kentucky, and Virginia. It inhabits sandy shoals and riffles in larger streams and rivers. Due to the impacts of coal mining, sedimentation, and pollution, the combshell has now disappeared from a large portion of its range and remaining populations appear to be in decline.

Seven brownish yellow mussels with bright blue tags in an aquarium
Cumberlandian combshell in captivity. Photo by Nicole Garrison, Auburn University.

Ouachita rock pocketbook

The backwaters and pools of the Ouachita, Little, and Kiamichi River systems in Oklahoma and Arkansas are home to the last remaining populations of the Ouachita rock pocketbook (Arcidens wheeleri). This mussel was listed as endangered in 1991 and continues to be threatened by channel modifications and sedimentation. Their declining numbers and limited distribution make conservation measures for this species urgent. A. wheeleri is currently being propagated and released in Oklahoma with continued monitoring of experimental populations.


A unique species representing an ancient family of mussels, the Margaritiferidae, the Spectaclecase (Cumberlandia monodonta) is found in patches throughout the Eastern and Midwestern United States. This species has a distinct elongated shell shape and can grow to become quite large, about 9 inches long. They inhabit rivers and can often be found under and around large rock slabs and boulders. Efforts to stop the decline of the Spectaclecase include preventing the spread of the invasive zebra mussel and captive propagation. We are interested in understanding the degree of genetic isolation between populations occurring across this relatively broad distribution and in identifying good sources for broodstock.

A biologist in full wet suit searches elbow deep in a stream for mussels
Sampling spectaclecase in Missouri. Photo by Nicole Garrison, Auburn University.


Nathan Whelan, Director Conservation Genetics Lab, (334) 844-9562

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