Welcome to My Research Website
Evolution and Conservation
About

About My Research

I am the Director of the Southeast Conservation Genetics Lab at U.S. Fish and Wildlife Service

  • Phylogenetics and Comparative Biology

    My lab seeks to understand the patterns and processes that have contributed to animal diversification. We do this with phylogenetics and comparative genomics. My research includes understanding the phylogenetic patterns of animal diversification with an emphasis on ctenophores and mollusks. Recent work has focused on methods to accurately infer deep phylogeny of animals and examining morphological and behavioural evolution in ctenophores. I am also interested in gene evolution. Past work has included studies on taxon-gene evolution in Ribbon Worms and evolution of Toll-like Receptor pathway evolution in Deuterostomes.

  • Gastropods

    Freshwater mollusks are important components of freshwater systems. Snails graze on algae and are a food source to animals such as turtles and fish. Mussels naturally filter water and many species live for over fifty years. Together snails and mussels keeping drinking water sources clean for the benefit of human society. Yet, freshwater mollusks are one of the most imperiled groups of organisms on the planet.

    Our research aims to improve conservation efforts and understand molluscan diversity by examining mollusk phylogeny and evolutionary genomics. We answer questions about molluscan evolution using genomic data. This includes transcriptome sequencing, RAD-seq for population genomics, and target-capture Illumina sequencing for phylogenetics. Current projects include conservation genomics of Round Rocksnail (Leptoxis ampla) and Louisiana Pearlshell (Margaratifera hembeli), phylogenomics of the snail family Pleuroceridae, and genome sequencing of Round Rocksnail and Lacy Elimia (Elimia crenatella).

  • Conservation Genetics

    A consequence of species decline is often a decline in population-level genetic diversity. Effective conservation must include efforts to increase population-level genetic diversity of any given imperiled species. My research aims to understand how conservation efforts can increase genetic diversity of managed populations and species. We also seek to better understand the molecular ecology of threatened and endangered species. This work includes collaborating landowners and hatcheries. We also spend time in the field sampling threatened and endangered species, with a focus on rivers in the southeastern United States.

  • 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 using large molecular datasets for evolutionary research. We also study the performance of different phylogenetic methods in an effort to determine which models and methods can provide the most accurate estimation of organismal relationships.

Publications

Whelan, N.V., K.M. Kocot, T.P. Moroz, G. Paulay, C.E. Mills, L.L. Moroz, K.M. Halanych. (2017) Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology and Evolution. IN PRESS.

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)

E-mail me.

I'm always happy to answer questions about my research, freshwater conservation, or snails.

nathan.whelan[at]gmail.com