RESEARCH2019-12-12T22:44:20+00:00

Comparative Genomics

Even before the completion of the human genome project, studies in the lab have focused on using comparative genomic data to resolve the evolutionary relationships within and between major mammalian lineages, as an evolutionary framework to understand mechanisms of chromosome evolution.

Recent Publications

  1. 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
  2. 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
  3. 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.
  4. Mason, V.C., Li, G., Minx, P., Schmitz, J., Churakov, G., Doronina, L., Melin, A.D., Dominy, N.J., Lim, N. T-L., Springer, M.S., Wilson, R.K., Warren, W.C., Helgen, K.M., and W. J. Murphy. 2016. Genomic analysis reveals remarkable hidden biodiversity within colugos, the sister group to primates. Science Advances, 2: e1600633.

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 Biomedical and 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

  1. 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.
  2. Genova F, Longeri M, Lyons LA, Bagnato A, 99Lives Consortium*, Strillacci MG. 2018. First genome-wide CNV mapping in Felis catus using next generation sequencing data. BMC Genomics 19(1): 895. *Consortium member
  3. 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.
  4. Li, G., Davis, B.W., Eizirik, E., and W.J. Murphy. 2016. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Research26: 1-11.
  5. Davis, B.W., Seabury, C.S., Brashear, W., Li, G., Roelke Parker, M., and W.J. Murphy. 2015. Mechanisms underlying mammalian hybrid sterility in two feline interspecies models. Molecular Biology and Evolution32: 2534-2546.

Classics

  1. 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.
  2. O’Brien, S. J., Menotti-Raymond, M., Murphy, W. J., and N. Yuhki.  2002.  The feline genome project. Annual Reviews of Genetics 36: 657-686.
  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. Beichman, A.C., Koepfli, K.-P., Li G., Murphy, W., Dobrynin, P., Kilver, S., Tinker, T., Schenck, C., Schenck, E., Johnson, J., Karlsson, E., Estes, J., Lohmueller, K., and R.K. Wayne. 2019. Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter (Enhydra lutris) and giant otter (Pteronura brasiliensis). Molecular Biology and Evolution. doi: 10.1093/molbev/msz101
  2. 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.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.
  3. 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 Heredity 108: 597-607.
  4. 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.