We use comparative genomic approaches to describe and understand the processes of adaptation, speciation, and diversification in mammals to connect genotype to phenotype. Current research includes the generation and application of T2T genome assemblies to improve genetic mapping resolution and to study the role of structural variation in speciation and diversification in cats and other mammal clades.

1. Yuan, J., Wang, G., Zhao, L., Sun, T., Kitchener, A.C., Chen, W., Huang, C., Wang, C., Xu, X., Wang, J., Lu, H., Xu, L., Jiangzuo, Q., Murphy, W.J., Wu, D., and Li. 2023. How genomic insights into the evolutionary history of clouded leopards inform their conservation. Science Advances In press
2. Bredemeyer, K.R., Hillier, L., Harris, A.J., Hughes, G.M., Foley, N.M., Lawless, C., Carroll, R.A., Storer, J.M., Batzer, M.A., Rice, E.S., Davis, B.W., Raudsepp, T., O’Brien, S.J., Lyons, L.A., Warren, W.C., and W.J. Murphy. 2023. Single-haplotype comparative genomics reveals the role of structural innovations during cat evolution. Nature Genetics In press
3. Foley, N.M., Mason, V.C., Harris, A.J., Bredemeyer, K.R., Damas, J., Lewin, H.A., Eizirik, E., Gatesy, J., Karlsson E., Lindblad-Toh, K., Zoonomia Consortium, Springer, M.S., and W.J. Murphy. 2023. A genomic timescale for placental mammal evolution. Science 380: eabl8189.
4. Christmas, M.J., Kaplow, I.M., Genereux, D.P., Dong, M.X., Hughes, G.M., Li, X., Sullivan, P.F., Hindle, A.G., Andrews, G., Armstrong, J.C., Bianchi, M., Breit, A.M., Diekhans, M., Fanter, F., Foley, N.M., Goodman, L., Keoug, K.C., Kirilenko, B., Kowalczyk, A., Lawless, C., Lind, A., Meadows, J.R.S., Moreira, L., Ryan, L., Swofford, R., Valenzuela, A., Wagner, F., Wallerman, O., Damas, J., Fan, K., Grimshaw, J., Johnson, J., Kozyrev, S.V., Lawler, A.J., Marinescu, V.D., Osmanski, A., Paulat, N.S., Phan, B.A., Reilly, S.K., Schäffer, D.E., Steiner, C., Supple, M.A., Wilder, A.P., Wirthlin, M.E., Xue, J.R., Zoonomia Consortium, Birren, B.W., Gazal, S., Hubley, R.M., Koepfli, K.P., Marques-Bonet, T., Meyer, W., Nweeia, M., Shapiro, B., Smit, A.F., Springer, M., Teeling, E.C., Weng, Z., Hiller, M., Levesque, D.L., Lewin, H.A., Murphy, W.J., Navarro, A., Paten, B., Pollard, K.S., Ray, D.R., Ruf, R., Ryder, O.A., Pfenning, A.R., Lindblad-Toh, K., and E.K. Karlsson. 2023. Evolutionary constraint and innovation across hundreds of placental mammals. Science 380: eabl3943.
5. Dindot, S.V., Christian, S., Murphy W.J., Berent, A., Panagoulias, J., Shlafer, A., Ballard, J., Radeva, K., Robinson, R., Myers, L., Jepp, T., Shaheen, H., Hillman, P., Kongati, K., Hillhouse, A., Bredemeyer, K.R., Black, L., Douville, J., and the FIRE Consortium. 2023. An ASO therapy for Angelman syndrome that targets an evolutionarily conserved region at the start of the UBE3A-AS transcript. Science Translational Medicine 2023 Mar 22;15(688): eabf4077.
6. vonHoldt, B.M., Brzeski, K., Aardema, M., Schell, C., Rutledge, L.Y., Fain, S., Shutt, A., Linderholm, A., and W.J. Murphy. 2022. Persistence and expansion of cryptic red wolf genomic ancestry along the American Gulf coast. Molecular Ecology 31: 5440-5454.
7. Wang, R.J., Raveendram, M., Harris, R.A., Murphy, W.J., Lyons, L.A., Rogers, J., and M.W. Hahn. 2022. De novo mutations in domestic cat are consistent with an effect of reproductive longevity on both the rate and spectrum of mutations. Molecular Biology and Evolution Jul 2; 39(7). doi: 10.1093/molbev/msac147.
8. Harris, A.J., Foley, N.M., Williams, T., and W.J. Murphy. 2022. TreeHouseExplorer (THEx): A novel genome browser for phylogenomics. Molecular Biology and Evolution doi: 10.1093/molbev/msac130.
9. Myers, A.N., Lawhon, S.D., Diesel, A.B., Liu, W., Rodrigues Hoffmann, A., 99Lives Genome Consortium, and W.J. Murphy. 2022. An ancient haplotype containing antimicrobial peptide genes is associated with severe fungal skin disease in Persian cats. PLoS Genetics 18(2): e1010062.
10. Bredemeyer, K.R., Seabury, C.M., Stickney, M.J., McCarrey, J.R., vonHoldt, B.M., and W.J. Murphy. 2021. Rapid macrosatellite evolution promotes X-linked hybrid male sterility in a feline interspecies cross. Molecular Biology and Evolution 38: 5588-5609.