Lily Hughes

Research Curator, Ichthyology

11 West Jones Street, Raleigh, NC 27601


  • Ph.D. in Biological Sciences, George Washington University, 2018
  • M.A. in Biology, Clark University, 2012
  • B.A. in Biology, Clark University, 2013


  • Postdoc, University of Chicago, 2020-2021
  • Postdoc, George Washington University, 2018-2019
  • Research Associate, National Museum of Natural History, Smithsonian Institution, 2018-2020

Research Interests

Lily’s research combines data from natural history collections and modern genomic techniques to better understand the diversity of fishes. With more than 35,000 living species inhabiting aquatic habitats around the globe, ray-finned fishes are a wonderful study system to ask questions about the patterns and processes that generate biodiversity. Her interests include systematics, phylogenomics, biogeography, phylogeography, and adaptation genomics. A newcomer to North Carolina, Lily is looking forward to establishing projects focused on local fish biodiversity.

Selected Publications

  • Arcila, D., Hughes, L.C., Melendez, F., Baldwin, C.C., White, W.T., Carpenter, K., Williams, J.T., Santos, M.D., Pogonoski, J., Graham, A., Miya, M., Ortí, G., Betancur-R., R. 2021. Testing the utility of alternative metrics of branch support to resolve the rapid evolutionary radiation of tunas, stromateiods, and allies (Teleostei: Pelagiaria). Systematic Biology, 70(6): 1123-1144.
  • Hughes, L.C., Ortí, G., Saad, H., Li, C., White, W.T., Baldwin, C.C., Crandall, K.A., Arcila, D., Betancur-R., R. 2021. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Molecular Ecology Resources, 21(3): 816-833.
  • Kolmann, M.A., Hughes, L.C., Hernandez, L.P., Arcila, D., Betancur-R., R., Sabaj, M.H., López-Fernández, H., Ortí, G. 2021. Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy. Systematic Biology, 70(3): 576-592.
  • Hughes, L.C., Cardoso, Y.P., Sommer, J., Cifuentes, R., Cuello, M., Somoza, G.M., González-Castro, M., Malabarba, L.R., Cussac, V., Habit, E.M., Betancur-R., R., and Ortí, G. 2020. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. Molecular Ecology, 29(4): 738-751.
  • Hughes, L.C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C.C., Thompson, A.W., Arcila, D.K., Betancur-R., R., Li, C., Becker, L., Bellora, N., Zhao, Z., Li, X., Wang, M., Fang, C., Xie, B., Zhou, Z., Huang, H., Chen, S., Venkatesh, B., and Shi, Q. 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences, 115(24): 6249-6254.
  • Hughes, L.C., Somoza, G.M., Nguyen, B., Bernot, J.P., González-Castro, M., Diaz de Astarloa, J.M., and Ortí, G. 2017. Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes). Ecology and Evolution, 7(14): 5258-5268.


Fields of Research