Aaron is a Research Fish Biologist at the Eastern Ecological Science Center in Kearneysville, WV.
Aaron Aunins obtained his Ph.D. in Integrative Life Sciences from Virginia Commonwealth University in 2011, where he studied the population genetics of American shad in Chesapeake Bay. He began working at the USGS Leetown Science Center in 2012. Aaron’s research interests are very broad – he has worked on conservation genetic studies of many diverse taxa including brook trout, shortnose sturgeon, Atlantic sturgeon, and Northeastern Beach tiger beetles among others. More recently, he has been focused on environmental DNA (eDNA) studies and has worked on eDNA metabarcoding of stream communities in National Capital Region Parks, using eDNA metabarcoding to characterize deep sea communities along the mid-Atlantic U.S. coast, and optimizing methods for detection of pollinators from eDNA left on flowers.
Professional Experience
2019 to present – Research Fish Biologist, U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia
2016 to 2019 – Scientist II (Contractor), Natural Systems Analysts, Winter Park Florida, work location at U.S. Geological Survey, Kearneysville, West Virginia
2014-2016 – Genetics Biologist (Contractor), Cherokee Nation Technology Solutions, Tulsa OK, work location at U.S. Geological Survey, Kearneysville, West Virginia
Education and Certifications
2011. PhD. in Integrative Life Sciences, Virginia Commonwealth University.
2006. M.S. in Marine Science, Virginia Institute of Marine Science of the College of William and Mary
2001. B.A. in Biology, University of Richmond
Science and Products
Advancing the Environmental DNA Toolkit for Ecosystem Monitoring and Management
Using Pollinator Environmental DNA to Assess the Ecological Resilience of America’s Grasslands
Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly Euchloe ausonides insulanus
Bioinformatics
Droplet digital PCR data for the detection of Smoky Mountain Madtoms in Great Smoky Mountains National Park
Population genetic data for three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana
SARS-CoV-2 Data from National Wastewater Surveillance System Surge Capacity Sampling, September 2021
Novel genetic resources for Clubshell freshwater mussels (Pleurobema clava, P. oviforme) for enhanced conservation
Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling
Development of a ddPCR assay for the detection of the Smoky Madtom (Noturus baileyi) from eDNA in stream water samples
Population genetics of three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana
Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning
Red Knot (Calidris canutus) research—Preliminary results and future opportunities
Development of microsatellite markers for three at risk tiger beetles Cicindela dorsalis dorsalis, C. d. media, and C. puritana
Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon
The complete maternal mitochondrial genome sequences of two imperiled North American freshwater mussels: Alasmidonta heterodon and Alasmidonta varicosa (Bivalvia: Unionoida: Unionidae)
The complete mitochondrial genome of the stalk-forming diatom Didymosphenia geminata
Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus)
Draft genome sequence of a picorna-like virus associated with gill tissue in clinically normal brook trout, Salvelinus fontinalis
Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda)
Science and Products
- Science
Advancing the Environmental DNA Toolkit for Ecosystem Monitoring and Management
The emerging field of Environmental DNA (eDNA) analysis allows characterization of species presence and community biodiversity by identifying trace amounts of genetic material left behind as organisms move through their environments. EESC scientists have been using eDNA technologies to detect native and rare species and as community biomonitoring tools.Using Pollinator Environmental DNA to Assess the Ecological Resilience of America’s Grasslands
Scientists from six USGS science centers are collaborating with USDA, university, and Tribal partners, and Department of the Interior land managers, to assess the status of pollinator communities and the distribution of species of conservation concern using environmental DNA. These methods will be used to improve assessments of habitat quality and pollinator responses to restoration, including...BySpecies Management Research Program, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Great Lakes Science Center, Northern Prairie Wildlife Research Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Pacific Northwest Environmental DNA LaboratoryConservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly Euchloe ausonides insulanus
The island marble butterfly (Euchloe ausonides insulanus) was first discovered on Vancouver Island, Canada in 1861. Based on morphological characteristics, it has been described as a subspecies of Euchloe ausonides. After a collection was made in 1908 on Gabriola Island, Canada, the island marble was not seen again until 1998 on San Juan Island, Washington, USA. Recent surveys have determined that...Bioinformatics
Bioinformatics is a relatively new field of science that incorporates elements of biology and computer science together for the purpose of developing efficient and robust methods for the analyses and interpretation of large amounts of biological data, typically DNA or RNA sequence data. - Data
Droplet digital PCR data for the detection of Smoky Mountain Madtoms in Great Smoky Mountains National Park
Environmental DNA water samples were collected at multiple sites in Great Smoky Mountains National Park in 2016 and 2017 and analyzed with a droplet digital PCR assay to screen for the presence of smoky mountain madtoms. Smoky Mountain madtoms were detected within a section of Abrams Creek, known as the only stream in Great Smoky Mountains National Park that supports this species.Population genetic data for three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana
This dataset includes microsatellite genotypes for 16 collections of tiger beetles (Ellipsoptera puritana) distributed in Connecticut and Maryland, United States and 44 collections of Habroscelimorpha dorsalis dorsalis and 14 collections of H. d. media distributed from Massachusetts to Florida, United States.SARS-CoV-2 Data from National Wastewater Surveillance System Surge Capacity Sampling, September 2021
Wastewater-based epidemiology (WBE) is used to determine the consumption of, or exposure to, chemicals or pathogens in human populations, and is conducted by collecting representative samples of untreated wastewater (influent) to quantify pathogens shed in the population served by the sampled wastewater system. The Centers for Disease Control and Prevention (CDC) and the US Department of Health anNovel genetic resources for Clubshell freshwater mussels (Pleurobema clava, P. oviforme) for enhanced conservation
Here we provide public access to two mitochondrial DNA sequence alignments, multi-locus microsatellite DNA genotypes, morphometric measurements and details on all specimens utilized in Morrison et al., 2021 (In press). - Publications
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Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling
BackgroundBenthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods.MethodsWe evaluated eDNA analogs of BI metrics in tAuthorsAaron Aunins, Sara J. Mueller, Jennifer A. Fike, Robert S. CornmanDevelopment of a ddPCR assay for the detection of the Smoky Madtom (Noturus baileyi) from eDNA in stream water samples
The Smoky Madtom Noturus baileyi is a federally endangered species, whose native distribution includes lower Abrams Creek in Great Smoky Mountains National Park (GRSM) and Citico Creek in nearby Cherokee National Forest. Due to challenges for bio-monitoring posed by its nocturnality and cryptic life history, an environmental DNA (eDNA)-based approach for detection would be useful to complement exiAuthorsAaron Aunins, Michael S. Eackles, Paul E Super, Matt A. Kulp, Becky J Nichols, Barbara A. Lubinski, Cheryl L. Morrison, Timothy L. KingPopulation genetics of three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana
Many tiger beetles (Family Cicindelidae) are critically imperiled due to their dependence on small patches of suitable habitat that are frequently threatened by natural and anthropogenic disturbances. In the eastern United States, conservation of three tiger beetles - Habroscelimorpha dorsalis dorsalis, H. dorsalis media, and Ellipsoptera puritana - has been inhibited by the absence of populationAuthorsDavid C. Kazyak, Aaron Aunins, Shannon L. White, Michael S. Eackles, C. Barry KnisleyGenetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning
The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined toAuthorsCheryl Morrison, Nathan A. Johnson, Jess W Jones, Michael S. Eackles, Aaron Aunins, Daniel Bruce Fitzgerald, Eric M. Hallerman, Timothy L. KingRed Knot (Calidris canutus) research—Preliminary results and future opportunities
The Red Knot, Calidris canutus, is a highly migratory shorebird with a cosmopolitan distribution. Six subspecies have been identified, two of which occur regularly in North America (C.c. rufa and C.c. roselaari). Given their long-distance migrations through many jurisdictions and conservation status, tools are needed to reliably distinguish the subspecies when captured away from their breeding areAuthorsDavid C. Kazyak, Aaron Aunins, Robin L. JohnsonDevelopment of microsatellite markers for three at risk tiger beetles Cicindela dorsalis dorsalis, C. d. media, and C. puritana
ObjectiveTiger beetles inhabiting sandy beaches and cliffs along the east coast of the United States are facing increasing habitat loss due to erosion, urbanization, and sea level rise. The northeastern beach tiger beetle Cicindela dorsalis dorsalis and Puritan tiger beetle Cicindela puritana are both listed as threatened under the Endangered Species Act of 1973, while the white beach tiger beetleAuthorsAaron Aunins, Michael S. Eackles, David C. Kazyak, Michael Drummond, Tim L. KingUsing advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon
Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). TAuthorsDavid C. Kazyak, Aaron Aunins, Robin L. Johnson, Barbara A. Lubinski, Michael S. Eackles, Tim L. KingThe complete maternal mitochondrial genome sequences of two imperiled North American freshwater mussels: Alasmidonta heterodon and Alasmidonta varicosa (Bivalvia: Unionoida: Unionidae)
The freshwater mussels Alasmidonta heterodon and A. varicosa historically inhabited rivers along the North American Atlantic coast from the Carolinas, U.S.A., to New Brunswick, CA. However, many populations have been extirpated, and A. heterodon is now federally listed in the U.S.A. as endangered, and both A. heterodon and A. varicosa are listed as vulnerable on the IUCN Red List. To facilitate geAuthorsAaron Aunins, Cheryl L. Morrison, Heather Galbraith, Michael S. Eackles, W. Bane Schill, Tim L. KingThe complete mitochondrial genome of the stalk-forming diatom Didymosphenia geminata
The complete mitogenome of the stalk-forming diatom Didymosphenia geminata collected from Mineral County, WV, USA was sequenced on the Ion Torrent PGM and Proton sequencers. The D. geminata mitogenome is 37,765 bp and encodes 35 protein coding genes, 25 tRNAs, and both large and small subunit ribosomal RNA genes. The nad11 gene is split into two domains as observed in Phaeodactylum tricornutum, anAuthorsAaron Aunins, Donald Hamilton, Tim L. KingMicrosatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus)
ObjectiveThe New England cottontail (Sylvilagus transitionalis) is a species of high conservation priority in the Northeastern United States, and was a candidate for federal listing under the Endangered Species Act until a recent decision determined that conservation actions were sufficient to preclude listing. The aim of this study was to develop a suite of microsatellite loci to guide future resAuthorsTim L. King, Michael S. Eackles, Aaron Aunins, Thomas J. Jr. McGreevy, Thomas P. Husband, Anthony Tur, Adrienne I. KovachDraft genome sequence of a picorna-like virus associated with gill tissue in clinically normal brook trout, Salvelinus fontinalis
Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.AuthorsLuke R. Iwanowicz, Deborah D. Iwanowicz, Cynthia R. Adams, Heather S. Galbraith, Aaron Aunins, Robert S. CornmanComparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda)
The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus, S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S.AuthorsAaron Aunins, David L. Nelms, Christopher S. Hobson, Tim L. King - Multimedia