Conservation Genomics for Imperiled Species

We work with many sample types and a wide range of species to achieve diverse project goals. Notably, our lab has worked to help reclassify species, inform manager’s captive breeding programs, repatriate confiscated turtles to the wild, detect threatened populations, determine population health, and detect threatening diseases all using cutting-edge genomics. Read more below about our recent projects to advance conservation using genomics.

Assessing Genomic Diversity to Guide Management

Extracting DNA from scat samples across the North Carolina mountains, we identified threatened Appalachian Cottontails, distinguished hybrids between Appalachian Cottontails and Eastern Cottontails, and assessed the genetic diversity of the two species to help the Wildlife Resources Commission prioritize areas to conserve Appalachian Cottontails and protect them from Rabbit Hemorrhagic Virus Disease. See report here.

We sequenced hundreds of loci from one of the world’s most endangered salamander: the Flatwoods Salamander (Ambystoma cingulatum). We estimated effective population sizes, and calculated levels of migration between existing wetlands in Florida. Our results helped guide ongoing headstarting and translocation efforts in the wild. See report here.

Using 3RAD, we successfully sequenced dozens of loci from an endangered salamander with one of the largest vertebrate genomes, the Black River Water Dog (Necturus alabamensis). For the first time ever, we were able to tell how dams affected gene flow in the species, and how closely related N. alabamensis is to neighboring populations of N. beyeri.

Identifying Populations of Origin for Confiscated Turtles

Whenever a trafficked turtle is confiscated by authorities it cannot be returned to the wild because it is unclear where it originated. Working with partners at USFWS, US Customs and Border Protection, numerous state wildlife agencies, and veterinarians at the University of Illinois, we designed genomic databases to help repatriate four of the US’ most-trafficked turtles: the Eastern Box Turtle (Terrapene carolinensis), the Bog Turtle (Glyptemys muhlenbergii), the Diamondback Terrapin (Malaclemys terrapin), and the Alligator Snapping Turtle (Macrochelys spp.). Using these genomic databases, we can compare the genomic similarity of confiscated turtles to wild turtles with known locations. By determining which population the confiscated turtle is most closely related to, we can determine where it was likely captured. So far we have helped repatriate dozens of confiscated turtles, and helped increase law enforcement operations in areas from where confiscated turtles consistently originate.

Re-Classifying Species Based on Genome-Scale Data

Using our Alligator Snapping Turtle genomic database (see above), we were able to answer a long-standing taxonomic question: how many species of Alligator Snapping Turtle are there? Our data clearly show that there are three species, not two as previously thought. Our work is in review at Southeastern Naturalist. 

Working with partners at Clemson University, we supplied genomic data to US Fish and Wildlife Service’s Species Status Assessment of the Florida Pinesnake (Pituophis melanoleucus mugitis). Using Ultraconserved Elements and RADseq data, we were able to delineate the genomic boundaries of the Florida Pinesnake, and determine how it is related to the other Pinesnake subspecies.

New species of salamanders are often hiding in plain sight in the North Carolina mountains. Based on mitochondrial sequencing, Four-Toed Salamanders from certain parts of the North Carolina Mountains might be distinct species. We sequenced thousands of Ultra Conserved Elements to determine if those populations were distinct, and if so, whether they required conservation protection.

Again hiding in plain sight, we described a new species of Green Salamander from the Hickory Nut Gorge in North Carolina. Using 3RAD and a variety of morphological analyses, we show that the Hickory Nut Gorge Salamander (Aneides caryaenesis) is distinct from its sister species and does not interbreed. The species is currently petitioned for state and federal listing. See the published results here.

Detecting Threatened Organisms and Dangerous Disease

Using metabarcoding on water samples from dozens of water bodies in Southern Alabama, we detected 128 species of fish, mammal, bird, reptile, amphibian and mussels. We identified species endemic to Alabama, and some not previously known from the river drainages.

We have used our qPCR methods to quantify numerous infections in wild animals. We use qPCR to detect chytridiomycosis (Bd) in numerous frog species, salamander chytridiomycosis (Bsal) in salamanders, Ranavirus in amphibians, and whirling disease in salmonids.

Using a bait sequencing approach, we recently sequenced the mitochondrial genome of a number of Redhorse species (Moxostoma sp.), and designed eDNA primers to detect the rare Sicklefin Redhorse. Our dataset will also be used to help clarify taxonomy of the Redhorses.

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