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
N.M. Foley, R. Rasulis, Z. Wani, M.N. Mendoza Cerna, H.V. Figuerio, K. P. Koepfli, T. Raudsepp, and W.J. Murphy. 2025. An ancient recombination desert is a speciation supergene in placental mammals. Nature In press 10.1038/s41586-025-09740-2
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
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.
Classics
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
Harris, A.J., Raudsepp, T., Foley, N.M., Warren, W.C., Lyons, L.A., and W.J. Murphy. 2025. Near-gapless genomes of the domestic cat (Felis catus) and the African serval (Leptailurus serval) derived from trio-binning. Journal of Heredity doi: 10.1093/jhered/esaf047.
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.
Classics
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
Burbrink, F.T., DeBaun, D., Foley, N.M., and W.J. Murphy. 2025. Recombination-aware phylogenomics. Trends in Ecology & Evolution Jul 17: S0169-5347(25)00179-X.
Murphy, W.J. & A.J. Harris. 2024. Towards telomere-to-telomere cat genomes for precision medicine & conservation biology. Genome Research 34: 655-664.
Foley, N.M., Harris, A.J., Bredemeyer, K.R., Ruedi, M., Puechmaille, S.J., Teeling, E.C., Criscitiello, M.F., and Murphy W. J. 2024. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. 2024. Cell Genomics 4(2) https://doi.org/10.1016/j.xgen.2023.100482
Classics
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.