About Our Research

Comparative Genomics

Placental mammals display a staggering breadth of morphological, karyotypic, and genomic diversity, rivaling or surpassing any other living vertebrate clade. This variation represents the culmination of one hundred million years of diversification and parallel adaptation to tumultuous changes in Earth’s environments, including catastrophic events like the Cretaceous-Paleogene (KPg) bolide impact. Comparative genomic approaches can leverage this diversity to understand the genomic basis of extraordinary mammalian adaptations, inform conservation management plans and glean novel insights of benefit to medical research.

Recent Publications

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 379: eabl8189. doi: 10.1126/science.abl8189

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 379: eabl3943.

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.


Janečka, J. E., Miller, W., Pringle, T. H., Wiens, F., Zitzmann, A., Helgen, K. M., Springer, M. S., and W. J. Murphy.  2007. Molecular and genomic data identify the closest living relative of primates. Science 318: 792-794.

Murphy, W. J., Larkin, D., Everts van-der Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J. E., Chowdhary, B. P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S. N., Ostrander, E. A., Pape, G., Parker, H. G., Raudsepp, T., Rogatcheva, M. B., Schook, L. B., Skow, L. C., Welge, M., Womack, J. E., O’Brien, S. J., Pevzner, P. A., H. A. Lewin. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617.

Murphy, W. J., Pevzner, P. and S. J. O’Brien.  2004. Mammalian phylogenomics comes of age. Trends in Genetics 20: 631-639.

Felid Biomedical
& Evolutionary Genomics

A major focus in the lab is developing and applying genomic resources for the cat family to connect genotype to phenotype, and reveal the evolutionary consequences of historical and contemporary hybridization between species.

Recent Publications

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 provides insights into lineage-specific structural variation during cat evolution. Nature Genetics  doi: 10.1038/s41588-023-01548-y.

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.

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.


Montague, M., Li, G., Gandolfi, B., Khan, R., Aken, B.L., Searle, S.M.J., Minx, P., Hillier, L., Kolboldt, D.C., Davis, B.W., Driscoll, C.A., Barr, C., Blackstone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas G.W.C., Hahn, M.W., Menotti-Raymond, M., O’Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., and W. C. Warren. 2014. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences USA 111: 17230-17235.

Davis, B. W., Raudsepp, T., Pearks Wilkerson, A. J., Agarwala, R., Schäffer, A. A., Houck, M., Chowdhary, B. P., and W.J. Murphy. 2009. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics 93: 299-304.

Murphy, W.J., Sun, S., Chen, Z.-Q., Yuhki, N., Hirschmann, D. A., Menotti-Raymond, M., and S. J. O’Brien.  2000.  A radiation hybrid map of the cat genome: implications for comparative mapping. Genome Research 10: 691-702.

Phylogenetics, Phylogeography
& Conservation Genomics

We use phylogenetic approaches to understand when and how mammals diversified, and to aid in the delimitation of species and conservation units for management.

Recent Publications

Yuan, J., Kitchener, A.C., Sun, T., Jiangzuo, Q., Tuohetahong, Y., Zhao, L., Yang, P., Wang, G., Wang, J., Hou, W., Liu, Y., Chen, W., Murphy, W.J., and Li. The genome of the black-footed cat: revealing a rich natural history and urgent conservation priorities for small felids. Proc. Natl Acad. Sci. USA [in press]

Jamieson, A., Carmagnini, A., Howard-McCombe, J., Doherty, S., Hirons, A.,  Dimopolous, E., Lin, A.T., Allen, R., Anderson-Whymark, H., Barnett, R., Batey, C., Beglane, F., Bowden, W., Bratten, J., Drew, E., Foley, M., Fowler, T., Fox, A., Geigl, E., Gotfredsen, A.B., Grange, T.,  Griffiths, D., Gro, D., Haruda, A., Hjermind, J., Knapp, Z., Lebrasseur, O., Librado, P., Mainland, I., McDonnell, C., Munoz-Fuentes, V., Nowak, C., O’Connor, T., Peters, J., Russo, I.M., Ryan, H., Sheridan, A., Sinding, M.H.S., Skoglund, P., Swali, P., Symmons, R., Thomas, G., Trolle Jensen, T.Z., Kitchener, A.C., Senn, H., Lawson, D., Driscoll, C., Murphy, W.J., Beaumont, M., Ottoni, C., Sykes, N., Larson, G., and L. Frantz. 2023. Limited historical admixture between European wildcats and domestic cats. Current Biology 33: 4751-4760.

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 9(40): eadh9143



Meredith, R. W., Janečka, J.E, Gatesy, J., Ryder, O. A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., Rabosky, D. L., Honeycutt, R. L., Flynn, J. J., Ingram, C. M., Steiner, C., Williams, T. L., Robinson, T. J., Burk-Herrick, A., Westerman, M., Ayoub, N. A., Springer, M. S., and W. J. Murphy. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification. Science 334: 521-525.

Teeling, E. C., Springer, M. S., Madsen, O., Bates, P., O’Brien, S. J., and W. J. Murphy. 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307: 580-584.

Murphy, W. J., Eizirik, E., Johnson, W. J., Zhang, Y. P., Ryder, O. A., and S. J. O’Brien.  2001.  Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.