RESEARCH2020-12-17T16:08:39+00:00

Comparative Genomics

Genomes spanning the rich living and extinct diversity of species are being sequenced at an unprecedented rate. Analyses of whole genome alignments of hundreds, and eventually thousands, of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation.

Recent Publications

  1. Murphy, William J., Nicole M. Foley, Kevin R. Bredemeyer, John Gatesy, and Mark S. Springer. 2020. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annual Review of Animal Biosciences 9.
  2. Genereux, Diane P., Aitor Serres, Joel Armstrong, Jeremy Johnson, Voichita Marinescu, Eva Murén, David Juan et al. 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, no. 7833: 240-245.
  3. Hughes, Jennifer F., Helen Skaletsky, Tatyana Pyntikova, Natalia Koutseva, Terje Raudsepp, Laura G. Brown, Daniel W. Bellott et al. 2020. Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages. Genome Research 30, no. 12: 1716-1726.
  4. Brashear, W.A., Raudsepp, T., and W.J. Murphy. 2018. Evolutionary conservation of Y chromosome ampliconic gene families despite extensive structural variation. Genome Research 28: 1841-1815
  5. Figueiró, H.X., Li, G., Trindade, F.J., Assis, J., Pais, F., Fernandes, G., Santos, S.H.D., Hughes, G.M., Komissarov, A., Antunes, A., Trinca, C.S., Rodrigues, M.R., Linderoth, T., Bi, K., Silveira, L., Azevedo, F.C.C, Kantek, D., Ramalho, E., Brassaloti, R.A., Villela, P.M.S., Nunes, A.L.V., Teixeira, R.H.F., Morato, R.G., Loska, D., Saraguëta, P., Gabaldón, T., Teeling, E.C., O’Brien, S.J., Nielsen, R., Coutinho, R.L., Oliveira, G., Murphy, W.J., and E. Eizirik. 2017. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances 3: e1700299.

Classics

  1. 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.
  2. 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.
  3. Murphy, W. J., Pevzner, P. and S. J. O’Brien.  2004. Mammalian phylogenomics comes of age. Trends in Genetics 20: 631-639.

Felid Evolution and 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

  1. Bredemeyer, Kevin R., Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody Roelke-Parker, Stephen J. O’Brien, Leslie A. Lyons, Wesley C. Warren, and William J. Murphy. 2020. Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis). Journal of Heredity https://doi.org/10.1093/jhered/esaa057.
  2. Buckley, R.M., Davis, B.W., Brashear, W.A., Farias, F.H.G., Kuroki, K., Graves, T., Hillier, L.W., Kremitzki, M., Li, G., Middleton, R., Minx, P., Tomlison, C., Lyons, L.A., Murphy, W.J., Warren, W.C., 99 Lives Consortium. 2020. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLOS Genetics, doi: 10.1371/journal.pgen.1008926.
  3. Li, G., Figueiró, H.X., Eizirik, E., and W.J. Murphy. 2019. Recombination-aware phylogenomics reveals the structured genomic landscape of hybridizing cat species. Molecular Biology and Evolution. 36: 2111-2126.
  4. Curry, Caitlin J., Brian W. Davis, Laura D. Bertola, Paula A. White, William J. Murphy, and James N. Derr. 2020. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation Across Africa. Molecular Biology and Evolution https://doi.org/10.1371/journal.pone.0143827.
  5. Li, G., Hillier, L.W., Grahn, R.A., Zimin, A., Makunin, A., David, V.A., Menotti-Raymond, M., Hannah, S., Hendrickson, S., O’Brien, S.J., Minx, P., Wilson, R.K., Lyons, L.A., Warren, W.C., and W.J. Murphy. 2016. A high-resolution SNP array-based linkage map anchors a new domestic cat draft genome assembly and provides detailed patterns of recombination. G3: Genes Genomes & Genetics, 6: 1-10.

Classics

  1. 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.
  2. 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.
  3. Murphy, W. J., Sun, S., Pecon-Slattery, J., Chen, Z. Q., and S. J. O’Brien.  1999.  Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping.  Genome Research 9: 1223-1230

Phylogenetics, Phylogeography and 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

  1. Allen, R., Ryan, H., Davis, B.W., King, C., Frantz, L., Barnett, R., Linderholm, A., Loog, L., Haile, J., Lebrasseur, O., White, M., Kitchener, A., Murphy, W.J., and G. Larson. 2020. Using a genetic divergence proxy to predict the reproductive compatibility of mammalian hybrids. Proceedings of the Royal Society B, Biological Sciences, 287: 20200690.
  2. Springer, M.S., Foley, N.M., Brady, P., Gatesy, J., and W.J. Murphy. 2019. Evolutionary models for the diversification of placental mammals across the KPg boundary. Frontiers in Genetics 10: 1241
  3. Mason, V.C., Helgen, K.M., and W.J. Murphy. 2019. Comparative phylogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland. Journal of Heredity 110: 158-172.
  4. Janečka, J.E., Janecka, M.J., Helgen, K.M., and Murphy W.J.  2018. The validity of three snow leopard subspecies: response to Senn et al. Heredity 120: 586-590.
  5. Janečka, J.E., Zhang, Y-Q., Li, D-Q., Munkhtsog, M., Munkhtsog, B., Galsandorj, N., Wangchuk, T.R., Karmacharya, D., McCarthy, T., Gaur, A., Kumar, S., Hussain, S., Muhammad, G., Jevit, M., Hacker, C., Burger, P., Wultsch, C., Janečka, M. J., Helgen, K.M., Murphy, W.J., and R. Jackson. 2017. Range-wide snow leopard phylogeography supports three subspecies. Journal of Heredity108: 597-607.
  6. Springer M.S., Emerling, C.A., Meredith, R.W., Janečka, J.E., Eizirik, E., and W.J. Murphy. 2017. Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Molecular Phylogenetics and Evolution, 106: 86-102.

Classics

  1. 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.
  2. 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.
  3. 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.