Learn more about my lab's research!

About My Lab's Research

I am the Director of United States Fish and Wildlife Service's Southeast Conservation Genetics Lab.
We're located in the School of Fisheries, Aquaculture, and Aquatic Sciences at Auburn University.

My lab is broadly interested in relationships among organisms, the evolutionary processes that generate biodiversity,
and how environmental change influences genetic patterns.
Much of our work empahsizes freshwater conservation with a focus on mollusks.

This is Nathan's personal website. Visit my lab's USFWS website here.

  • Freshwater Mollusks

    Freshwater mollusks are the lab's primary study organisms. One reason we study mollusks is to enhance conservation efforts. The health of many freshwater ecosystems, and therefore much of society, rely on freshwater snails and mussels. Unfortunately, over 75% of freshwater mussels and snails are at risk of extinction, and the greatest barrier to effective conservation is a lack of knowledge. We use phylogenetics and conservation genomics to better understand freshwater mollusks.

    Current Projects
  • Phylogenetics and Comparative Biology

    My lab seeks to understand the patterns and processes that have contributed to animal diversification. Our primary study organisms are invertebrates. We have a number of ongoing projects on phylogenomics of freshwater mollusks and conservation genomics of animals ranging from freshwater snails to sturgeon. We are also interested in evolution of gene families, particulary those involved with invertebrate adaptation to freshwater environments.

    Current Projects
  • Conservation Genetics

    A consequence of species decline is often a decline in population-level genetic diversity. Our research aims to understand how conservation efforts can maintain or increase genetic diversity of managed populations and species. We also seek to better understand the molecular ecology of threatened and endangered species. For this research, our lab collaborates with landowners and hatcheries. We also spend time in the field sampling at-risk, threatened, and endangered species, with a focus on rivers in the southeastern United States.

    Current Projects
  • Bioinformatics and Phylogenetic Inference

    Modern genetics research requires a considerable amount of computational biology. Part of my lab's research includes designing new bioinformatics pipelines for evolutionary biology research. We also study the performance of different phylogenetic methods in an effort to determine which models and methods can provide the most accurate inferences about organismal relationships.


Lab members

Swingle Hall, Auburn University, September 2022

Nathan Whelan

Lab Director and Principal Investigator

CV available here.

Austin Hannah

Lab Manager

Conservation genomics and hatchery program evaluation.

Sam Donohoo

PhD Student

Evolution and Systematics of Molluscs.

Mia Adcock

Masters Student

Population and Conservation Genomics of Brook Floater

Raquel Gonzalez (alum)

Former USFWS Directorate Fellow and undergraduate researcher.

Conservation genomics and genetics management of Alabama Pearlshell

Ashantye' Williams (alum)

Lab Manager

Conservation genomics and genetic management of aquatic organisms.

Nick Gladstone (alum)

Masters Student

Evolution of life history behaviors and shell shape in freshwater gastropods.

Nicole Garrison (alum)


Conservation genomics of freshwater mussels. Visit Nicole's website here.

Aaliyah Wright (alum)

Undergraduate Researcher (2019 REU Student)

Conservation genomics of Leptoxis compacta.


Please email me if you don't have access to one of these papers and you would like a copy.
I'd be happy to send you a copy for free.

Gomes-dos-Santos. A, E. Froufe, J. Pfeiffer, N. Johnson, C. Smith, A.M. Machado, L.F.C. Castro, V. Tu Do, A. Hattori, N. Garrison, N.V. Whelan, I.N. Bolotov, I.V. Vikhrev, A.V. Kondakov, M. Ghamizi, V. Prié, A.E. Bogan, M. Lopes Lima. (2023) A Novel assembly pipeline and functional annotations for targeted sequencing: a case study on the globally threatened Margaritiferidae (Bivalvia: Unionida). Molecular Ecology Resources. 23: 1403-1422.. DOI: 10.1111/1755-0998.13802

Whelan. N.V., E.E. Strong, N.S Gladstone, J.W. Mays. (2023) Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail. ZooKeys. 1158: 91-120.. DOI: 10.3897/zookeys.1158.94152

Whelan. N.V., N.A. Johnson, A.S. Williams, M.A. Perkins, C.E. Beaver, J.W. Mays. (2023) Hidden in the hills: phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species. Zoological Journal of the Linnean Society. 198: 650-676.. DOI: 10.1093/zoolinnean/zlac106

Whelan. N.V., K.M. Halanych. (2023) Available data do not rule out Ctenophora as the sister group to all other Metazoa. Nature Communications. 14: 711.. DOI: 0.1038/s41467-023-36151-6

Strong, E.E., J.T. Garner, P.D. Johnson, N.V. Whelan. (2022) A systematic revision of the genus Juga from the freshwaters of the Pacific Northwest, USA (Cerithioidea, Semisulcospiridae). European Journal of Taxonomy. 848: 1-97.. DOI: 10.5852/ejt.2022.848.1993

Gladstone, N.S., N.L. Garrison, T. Lane, P.D. Johnson, J.T. Garner, N.V. Whelan. (2022) Population genomics reveal low differentiation and complex demographic histories in a highly fragmented and endangered freshwater mussel. Aquatic Conservation: Marine and Freshwater Ecosystems. 32: 1235-1248.. DOI: 10.1002/aqc.3849

Whelan, N.V., P.D. Johnson, J.T. Garner, N.L. Garrison⁑, E.E. Strong. (2022) Prodigious polyphyly in Pleuroceridae (Gastropoda: Cerithioidea). Bulletin of the Society of Systematic Biologists. 1: 8419.. DOI: 10.18061/bssb.v1i2.8419

Gladstone, N.S., M.L. Niemiller, B. Hutchins, B. Schwartz, A. Czaja, M.E. Slay, N.V. Whelan (2022) Subterranean freshwater gastropod biodiversity and conservation in the United States and Canada. Conservation Biology. 36: e13722.. DOI: 10.1111/cobi.13722

Gladstone, N.S., N.V. Whelan (2022) Pushing barcodes to their limits: phylogenetic placement of Fontigens Pilsbry, 1933 (Caenogastropoda: Littorinimorpha: Truncatelloidea) and elevation of Fontigentidae Taylor, 1966. Journal of Molluscan Studies. 88: eyab038.. DOI: 10.1093/mollus/eyab038

Whelan, N.V. (2021) Phenotypic plasticity and the endless forms of freshwater gastropod shells. Freshwater Mollusk Biology and Conservation. IN PRESS.

Garrison, N.L., P.D. Johnson, N.V. Whelan. (2021) Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel, Margaritifera hembeli. Conservation Genetics. 22: 217-231. DOI: 10.1007/s10592-020-01329-8

Dutton, H.R., L.H. Du Preez, O. Verneau, N.V. Whelan, S.A. Bullard. (2021) First record of a polystome from the from the alligator snapping turtle, Macrochelys temminckii (Cryptodira: Chelydridae) or Mississippi; with comments on “Neopolystoma orbiculare (Stunkard, 1916)” and its junior system synonyms. Journal of Parasitology. 107: 74-78. DOI: 10.1645/20-96

Whelan, N.V., E.E. Strong. (2021) Genetic diversity and historical demography in Bellamya gastropods from the Lake Victoria ecoregion reveal early and severe population collapse. Molecular Ecology. 39: 361-363. DOI: 10.1111/mec.15711

Ksepka, S.P., B. Hickson, N.V. Whelan, S.A. Bullard. (2020) A new species of Myxobolus Bütschli, 1882 (Bivalvulida: Myxobolidae) infecting stratum spongiosum of the cryptic Sicklefin Redhorse, Moxostoma sp., (Cypriniformes: Catostomidae) from the Little Tennessee River, North Carolina, USA. Folia Parasitologica. 67: 030. DOI: 10.14411/fp.2020.030

Wright, A.D., N.L. Garrison, A.S. Williams, P.D. Johnson, N.V. Whelan. (2020) Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns. PeerJ. 8: e9789. DOI: 10.7717/peerj.9789 (PDF)

Roop, H.J., N.V. Whelan, A.S. Williams, J. Page. (2020) First record of occurrence and genetic characterization of a population of Northern Snakehead Channa argus (Cantor 1842) in Georgia, USA. BioInvasions Records 842-852. DOI: 10.3391/bir.2020.9.4.18

Townsend, J.P., M.G. Tassia, A. Damian-Serrano, N.V. Whelan, K.M. Halanych, A.M. Sweeny. (2020) A mesopelagic ctenophore representing a new family, with notes on family-level taxonomy in Ctenophora: Vampyroctena delmarvensis gen. nov. sp. nov. (Vampyroctenidae, fam. nov.). Marine Biodiversity. 50: 34. DOI: 10.1007/s12526-020-01049-9 (PDF)

Bogantes, V.E., N.V. Whelan, K. Webster, A.R. Mahon, K.M. Halanych. (2020) Unrecognized diversity of a scale worm, Polyeunoa laevis (Annelida: Polynoidae), that feeds on soft coral. Zoologica Scripta. 49: 236-249.DOI: 10.1111/zsc/12400(pdf)

Kspeka, S.P., N.V. Whelan, C.M. Whipps, S.A. Bullard. (2020) A new species of Thelohanellus Kudo, 1933 (Myxozoa: Bilvalvulida) infecting skeletal muscle of Blacktail Shiner, Cyprinella venusta Girard, 1856 (Cypriniformes: Cyprinidae) in the Chattahoochee River Basin, Georgia. Journal of Parasitology. 106: 350-359. DOI: 10.1645/19-162

Ksepka, S.P., J.M Rash, N.V. Whelan, S.A. Bullard. (2019) A new species of Myxobolus (Myxozoa: Bivalvulida) infecting the medulla oblongata and nerve cord of brook trout Salvelinus fontinalis in southern Appalachia (New River, North Carolina, USA). Parasitology Resarch. 118: 3241-3252.DOI: 10.1007/s00436-019-06472-x (PDF)

Bullard, S.A., J.R. Roberts, M.B. Warren, H.R. Dutton, N.V. Whelan, C.F. Ruiz, T.R. Platt, V.V. Tkach, S.V. Brant, K.M. Halanych. (2019) Neotropical turtle blood flukes: two new genera and species from the Amazon River basin with a kay to genera and comments on a marine-derived parasite lineage in South America. Journal of Parasitology. 105: 497-523.DOI: 10.1645/19-27 (PDF)

Warren, M.B., H.R. Dutton, N.V. Whelan, R.P.E. Yanong, S.A. Bullard. (2019) First record of a species of Mermithidae Braun, 1883 infecting a decapod Palaemon paludosus. Journal of Parasitology. 105: 237-247.DOI: 10.1645/18-168 (PDF)

Strong, E.E. & N.V. Whelan. (2019) Assessing the diversity of Western North American Juga. Molecular Phylogenetics and Evolution. 136: 87-103.DOI: 10.1016/j.ympev.2019.04.009(PDF)

Whelan, N.V., M.P. Galaska, B.N. Sipley, J.M. Weber, P.D. Johnson, K.M. Halanych, B.S. Helms. (2019) Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail Leptoxis ampla. Molecular Ecology. 28: 1593-1610. LINK (PDF)

Warren, M.B., C.F. Ruiz, N.V. Whelan, D.C. Kritsky, S.A. Bullard. (2019) Gymnurahemecus bulbosus gen. et sp. nov. (Digenea: Aporocotylidae) infecting smooth butterfly rays, Gymnura micrura (Myliobatiformes: Gymnuridae) in the northern Gulf of Mexico, with a taxonomic key and further evidence for monophyly of chondrichthyan blood flukes. Parasitology Research. 118: 751-762. DOI: 10.1007/s00436-018-06202-9 (PDF)

Whelan, N.V., K.M. Kocot, T.P. Moroz, K. Mukherjee, P. Williams, G. Paulay, L.L. Moroz, K.M. Halanych. (2017) Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology and Evolution. 1: 1737-1746. PDF

Whelan, N.V., P.D. Johnson, J.T. Garner, E.E. Strong. (2017) On the identity of Leptoxis taeniata – a misapplied name for the federally threatened Painted Rocksnail (Cerithioidea: Pleuroceridae). Zookeys. 697: 21-36. doi: 10.3897/zookeys.697.14060.

Tassia, M.G., N.V. Whelan, K.M. Halanych. (2017) Toll-like receptor pathway evolution in deuterostomes. Proceedings of the National Academy of Sciences. 114: 7055–7060. doi: 10.1073/pnas.1617722114.

Costa-Paiva E.M., N.V. Whelan, D.S. Waits, S. Santos, C.G. Schrago, K.M. Halanych. (2017) Discovery and evolution of novel hemerythrin genes in annelid worms. BMC Evolutionary Biology. 17: 85. doi:10.1186/s12862-017-0933-z.

Whelan, N.V., K.M. Halanych. (2017) Who let the CAT Out of the Bag? Accurately dealing with substitutional heterogeneity in phylogenomics. Systematic Biology. 66: 232-255. doi:10.1093/sysbio/syw084.

Yuanning, Li, K.M. Kocot, N.V. Whelan, S.R. Santos, D.S. Waits, D.J. Thornhill, K.M. Halanych. (2017) Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta. 46: 200-213. doi:10.1111/zsc.12201. (pdf)

Whelan, N.V., K.M. Halanych, K.M. Kocot, A.B. Kohn, L.L. Moroz. (2016) Miscues misplace sponges. Proceedings of the National Academy of Sciences. 113: E946-E947. doi:10.1073/pnas.1525332113. (pdf)

Whelan, N.V., E.E. Strong. (2016) Morphology, molecules and taxonomy: extreme incongruence in pleurocerids (Gastropoda, Cerithioidea, Pleuroceridae). Zoologica Scripta. 45: 62-87.doi:10.1111/zsc.12139. (pdf)

Whelan, N.V. (2016) Radular morphology of extinct pleurocerids (Gastropoda: Cerithioidea: Pleuroceridae). American Malacological Bulletin. 33: 221-226.doi:10.4003/006.033.0202. (pdf)

Whelan, N.V., K.M. Kocot, K.M. Halanych. (2015) Employing phylogenomics to resolve the relationships among cnidarians, ctenophores, sponges, placozoans, and bilaterians. Integrative and Comparative Biology. 55: 1084-1095. doi:10.1093/icb/icv037. (pdf)

Whelan, N.V., K.M. Kocot, L.L. Moroz, K.M. Halanych. (2015) Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences. 112: 5773-5778. doi:10.1073/pnas.1503453112. (pdf)

Whelan, N.V., P.D. Johnson, P.M. Harris. (2015) Life-history traits and shell morphology in the genus Leptoxis Rafinesque, 1819 (Gastropoda: Cerithioidea: Pleuroceridae). Journal of Molluscan Studies. 81: 85-95. doi:10.1093/mollus/EYU058. (pdf)

Whelan, N.V., K.M. Kocot, S.R. Santos, K.M. Halanych. (2014) Transcriptome sequencing of nemerteans reveals a diverse suite of toxin genes. Genome Biology and Evolution. 6: 3314-3325. doi:10.1093/gbe/evu258. (pdf)

Whelan, N.V., E.E. Strong. (2014) Seasonal reproductive anatomy and sperm storage in pleurocerid gastropods (Cerithioidea: Pleuroceridae). Canadian Journal of Zoology. 92: 989-995. doi:10.1139/cjz-2014-0165. (pdf)

Benstead, J.P., J.M. Hood, N.V. Whelan, M.R. Kendrick, D. Nelson, A.F. Hanninen, L.M. Demi. (2014) Dietary P-growth coupling across diverse fish taxa: a meta-analysis of experimental aquaculture studies. Ecology. 95: 2768-2777. doi:10.1890/13-1859.1. (pdf)

Johnson, P.D., A.E. Bogan, K.M. Brown, N.M. Burkhead, J.R. Cordeiro, J.T. Garner, P.D. Hartfield, D.A. Lepitzki, G.L. Mackie, E. Pip, T.A. Tarpley, J.S. Tiemann, N.V. Whelan, E.E. Strong. (2013) Conservation status of freshwater gastropods of Canada and the United States. Fisheries. 38: 247-282. doi:10.1080/03632415.2013.785396. (pdf)

Whelan N.V., P.D. Johnson, P.M. Harris. (2012) Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae). PLoS One. 7:e42499. doi:10.1371/journal.pone.0042499. (pdf)

Whelan, N.V., P.D. Johnson, P.M. Harris. (2012) Presence or absence of carinae between closely related populations of Leptoxis ampla (Anthony, 1854) (Gastropoda: Pleuroceridae) is not the result of ecophenotypic plasticity. Journal of Molluscan Studies. 78: 231-233. doi:10.1093/mollus/eys005. (pdf)

Whelan, N.V. (2011) Species tree inference in the age of genomics. Trends in Evolutionary Biology. 3:e5. doi:10.4081/eb.2011.e5. (pdf)

Whelan, N.V., A. Geneva, D.L. Graf. (2011) Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae. Molecular Phylogenetics and Evolution. 61:504-514. doi:10.1016/j.ympev.2011.07.016. (pdf)

Email me

Please contact me if you are interested in joining my lab as a graduate student or postdoc at Auburn University. Potential lab members are encouraged to read our lab manual to learn more about the lab and expectations of lab members. Lab Manual 2023

I am also always happy to answer questions about my research, freshwater conservation, or snails.