PUBLICATIONS2018-11-06T16:56:44+00:00

Publications

  1. Brashear, W.A., Raudsepp, T., and W.J. Murphy. Evolutionary conservation of Y chromosome ampliconic gene families despite extensive structural variation. [Genome Research in press].
  2. Mason, V.C., Helgen, K.M., and W.J. Murphy. 2018. Comparative biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland. Journal of Heredity Sep 21. doi: 10.1093/jhered/esy046.
  3. Janečka, J.E., Davis, B.W., Ghosh, S., Paria, N., Das, P., Orlando, L., Schubert, M., Nielsen, M., Stout, T., Brashear, W.A., Li, G., Johnson, C., Metz, R., A., Al Zadjali, A. M., Love, C., Varner, D., Bellott, D., Murphy, W.J., Chowdhary, B.P., and T. Raudsepp. 2018. Horse Y chromosome assembly displays unique evolutionary features, putative stallion fertility genes. Nature Communications 9: 2945.
  4. Janečka, J.E., Janecka, M.J., Helgen, K.M., and Murphy W.J. The validity of three snow leopard subspecies: response to Senn et al. Heredity 120: 586-590.
  5. Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Dodman, N.H., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Pederson, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., and L.A. Lyons. 2018. Applications and efficiencies of the first cat 63K DNA array. Scientific Reports 8: 7024.
  6. Hughes, G.M., Boston, E.M., Finarelli, J.A., Murphy, W.J., Higgins, D.G., and E.C. Teeling. 2018. The birth and death of olfactory receptor gene families in mammalian niche adaptation. Molecular Biology and Evolution  35: 1390-1406.
  7. Bird, D.J., Murphy, W.J., Fox-Rosales, L., Hamid, I., and B. Van Valkenburg. 2018. Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia. Proc. Royal Soc. B. Mar 14;285(1874). pii: 20180100.
  8. Springer, M.S., Murphy, W.J., and A.L. Roca. 2018. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution 121:158-165.
  9. Brandt, A.L., Grigorev, K., Afanador-Hernandez, Y.M., Paulino, L.A., Murphy, W.J., Nuñez, A., Komissarov, A., Brandt, J.R., Maria, R., O’Brien, S.J., Rodriguez, L.E., Martinez-Cruzado, J.C., Oleksyk, T.K., and A.L. Roca. 2017. Mitogenomic sequences support a north-south subdivision within Solenodon paradoxus. Mitochondrial DNA, A DNA Mapp. Seq Anal. 20: 1-9.
  10. 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.
  11. Gatesy, J., Meredith, R.W., Janečka, J.E., Simmons, M.P., Murphy, W.J., and M.S. Springer. 2017. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia. Cladistics, 33: 295-332.
  12. 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.
  13. A., Pearce, J.W., Gandolfi, B., Creighton, E.K., Suedmeyer, W.K., Selig, M., Bosiack, A.P., Castaner, L.J., Whiting, R.E., Belknap, E.B., and L.A. Lyons. 2017. 99 Lives Consortium. Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes). Scientific Reports  7: 43918.
  14. Mauler, D.A., Gandolfi, B., Reinero, C.R., O’Brien, D.P., Spooner, J.L., Lyons, L.A., 99 Lives Consortium. 2017. Precision medicine in cats: novel Niemann-Pick Type C diagnosed by whole genome sequencing. Journal of Veterinary Internal Medicine 31: 539-544.
  15. 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.
  16. Aberdein, D., Munday, J.S., Gandolfi, B., Dittmer, K.E., Malik, R., Garrick, D.J., Lyons, L.A., 99 Lives Consortium. 2017. A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats. Mammalian Genome, 28: 47-55.
  17. Abascal, F., Alioto, T., Cruz, F., Corvelo, A., Villanueva-Cañas, J.L., Vlasova, A., Marcet-Houben, M., Martínez-Cruz, B., Prieto, P., Yu Cheng, J., Quesada, V., Lorente-Galdos, B., Li, G., García, F., Rodríguez, J.L., Frias, L., Ribeca, P., Câmara, F., Lowy, E., Cozzuto, L., Erb, I., Tress, M.L., Rubio-Camarillo, M., Capella-Gutiérrez, S., Rodriguez-Alés, J.L., Ruiz-Orera, J., Reverter, F., Casas-Marce, M., Soriano, L., Rodríguez-Arango, J., Puente, X.S., Derdak, S., Galán, B., Blanc, J., Gut, M., Quilez, J., Andrés-Nieto, M., Mailund, T., Murphy, W.J., Notredame, C., Roma, G., Gabaldón, T., Mar Albà, M., López-Otín, C., Ruiz-Herrera, A., Marques-Bonet, T., Valencia, A., Gut, I., García, J.L., Guigó, R., and J.A. Godoy. 2016. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology, 17: 251.
  18. 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.
  19. 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 (Bethesda), 6: 1-10.
  20. Lacher, T.E., Murphy, W.J., Rogan, J., Smith, A.T., and N.S. Upham. 2016. “Evolution, phylogeny, ecology, and conservation of the clade Glires: Lagomorpha and Rodentia”. Pp. 15-26 In: Handbook of the Mammals of the World (D.E. Wilson, T.E. Lacher, and R.A. Mittermeier, eds.) Lynx Edicions, Barcelona.
  21. 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 Research 26: 1-11.
  22. Halley, Y.A., Oldeshulte, D.L., Bhattarai, E.K., Hill, J., Metz, R.P., Johnson, C.D., Presley, S.M., Ruzicka, R.E., Rollins, D., Peterson, M.J., Murphy, W.J., and C.M. Seabury. 2015. Northern bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy. PLOS ONE 10: e0144913.
  23. Springer, M.S., Signore, A.V., Paijmans, J.L.A., Vélez-Juarbe, J., Domning, D.P., Bauer, C.E., He, K., Crerar, L., Murphy, W.J., Meredith, R.W., Gatesy, J., Willerslev, E., MacPhee, R.D.E., Hofreiter, M., and K.L. Campbell. Interordinal gene capture, the phylogenetic position of Steller’s Sea Cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. 2015. Molecular Phylogenetics and Evolution 91: 178-193.
  24. 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 Evolution 32: 2534-2546.
  25. 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.
  26. Gershony, L.C., Cortes, A., Penedo, M.C.T., Davis, B.W., Murphy, W.J., Helps, C.R., and L.A. Lyons. 2014. Who’s behind that mask and cape? The Asian Leopard Cat’s Agouti (ASIP) allele affects coat colour phenotype in the Bengal cat breed. Animal Genetics 45: 893-897.
  27. Soh, Y.Q., Alföldi, J., Pyntikova, T., Brown, L.G., Graves, T., Minx, P.J., Fulton, R.S., Kremitzki, C., Koutseva, N., Mueller, J.L., Rozen, S., Hughes, J.F., Owens, E., Womack, J.E., Murphy, W.J., Cao Q., de Jong, P., Warren, W.C., Wilson, R.K., Skaletsky, H., and D.C. Page. 2014. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159: 800-813.
  28. Janečka, J.E., Jackson, R., Munkhtsog, B., and W. J. Murphy. 2014. Characterization of 9 microsatellites and primers in snow leopards, and a species-specific PCR assay for identifying non-invasive samples. Conservation Genetics Resources 6: 369-373.
  29. Hayden, S., Davalos, L.M., Bekaert, M., Goodbla, A., Murphy, W.J., and E.C. Teeling. 2014. A cluster of olfactory receptor genes linked to frugivory in bats. Molecular Biology and Evolution 31: 917-927.
  30. Li, G., Davis, B.W., Raudsepp, T., Pearks Wilkerson, A.J., Mason, V.C., Ferguson-Smith, M.A., O’Brien, P., Waters, P., and W. J. Murphy.  2013. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Research 23: 1486-1495.
  31. Springer M.S., Meredith, R.W., Teeling, E.C., and W. J. Murphy. 2013. Technical comment on “The placental mammal ancestor and the post-KPg radiation of placental mammals“. Science 341: 613.
  32. Hughes, G., Li, G., Murphy, W. J., Higgins, D., and E.C. Teeling. 2013. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Molecular Ecology Resources 13: 510-521.
  33. Springer, M. S., Meredith, R. W., Gatesy, J., Emerling, C.A., Park, J., Rabosky, D.L., Stadler, T., Steiner, C., Ryder, O.A., Janecka, J.E., Fisher, C.A. and W. J. Murphy. 2012. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE 7: e49521.
  34. Janečka, J. E., Chowdhary, B., and W. Murphy. 2012. Exploring the correlations between sequence evolution rate and phenotypic divergence across the mammalian tree provides insight into adaptive evolution. Journal of Biosciences 37: 897-909.
  35. Murphy, W. J., Janečka, J.E., Stadler, T., Eizirik, E., Ryder, O.A., Gatesy, J., Meredith, R.W., and M.S. Springer. 2012. Response to comment on “Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification.” Science 337: 34.
  36. Janečka, J. E., Tewes, M.E., Laack, L.L., Caso, A., Grassman, L.I., Haines, A.M., Shindle, D.B., Davis, B.W., Murphy, W. J., and R.L. Honeycutt. 2011. Reduced genetic diversity and isolation of remnant ocelot populations occupying a severely fragmented landscape in southern Texas. Animal Conservation 14: 608-619.
  37. 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.
  38. Mason, V.C., Li, G., Helgen, K. M., and W. J. Murphy. 2011. Efficient cross-species capture hybridization and next-generation DNA sequencing of mitochondrial genomes from non-invasively sampled museum specimens. Genome Research 21: 1695-1704.
  39. Springer, M. S., Meredith, R., Janecka, J.E., and W. J. Murphy. 2011. The Historical Biogeography of Mammalia.  Philosophical Transactions of the Royal Society, B: Biological Sciences 366: 2478-2502.
  40. Janečka, J.E., Jackson, R.M., Munkhtsog, B., Mallon, D.P., Naranbaatar, G., and W. J. Murphy. 2011. Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards. Journal of Mammalogy 92: 771-783.
  41. Paria, N., Raudsepp, T., Pearks Wilkerson, A.J., O’Brien, P.C., Ferguson-Smith, M.A., Love, C.C., Arnold, C., Rakestraw, P., Murphy, W. J., Chowdhary, B.P. 2011. A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals. PLoS ONE  6: e21374.
  42. Brinkmeyer-Langford, C., Murphy, W. J., Childers, C., and L.C. Skow. 2010. A conserved segmental duplication within ELA. Animal Genetics 41 Suppl. 2: 186-95.
  43. Li, G., Janečka, J.E., and W. J. Murphy. 2011. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family. Molecular Biology and Evolution 28: 911-920.
  44. Davis, B.W., Li, G., and W. J. Murphy. 2010. Supermatrix and supertree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivore, Felidae). Molecular Phylogenetics and Evolution 56: 64-76.
  45. Eizirik, E., Murphy, W. J., Koepfli, K.-P., Johnson, W.E., Dragoo, J., Wayne, R.K., and S.J. O’Brien. 2010. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution 56: 49-63.
  46. Hayden, S., Bekaert, M., Crider, T., Mariani, S., Murphy, W. J., and E.C. Teeling. 2010. Ecological adaptation determines functional mammalian olfactory subgenomes.  Genome Research 20: 1-9.
  47. Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., and M. S. Springer. 2009. Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamelin in the fossil record of placental mammals. PLoS Genetics 5: e1000634.
  48. 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.
  49. Murphy, W. J. and E. Eizirik. 2009. “Placental Mammals (Eutheria)”. Pp. 471-474 In: The Timetree of Life, (S.B. Hedges and S. Kumar, eds.) Oxford University Press, Oxford.
  50. Eizirik, E., and Murphy, W. J. 2009. “Carnivores (Carnivora)”. Pp. 504-507 In: The Timetree of Life (S.B. Hedges and S. Kumar, eds.) Oxford University Press, Oxford.
  51. Miller, W., Drautz, D. I., Janečka, J. E., Lesk, A.M., Ratan, A., Tomsho, L.P., Packard, M., Zhang, Y., McClellan, L., Qi, J., Zhao, F., Gilbert, M.T.P., Dalén, L., Arsuaga, J.L., Ericson, P.G.P., Huson, D. H., Helgen, K. M., Murphy, W.J., Götherström, A., and S.C. Schuster. 2009. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19: 213-220.
  52. Collier, G.E., Murphy, W.J., and M. Espinoza. 2009. Phylogeography of the genus Epiplatys (Aplocheiloidea: Cyprinodontiformes). Molecular Phylogenetics Evolution 50: 190-6.
  53. Haussler, S. J. O’Brien, O.A. Ryder, F. K. Barker, M. Clamp, A. J. Crawford, R. Hanner, O. Hanotte, W. E. Johnson, J. A. McGuire, W. Miller, W. J. Murphy, F. H. Sheldon, B. Sinervo, B. Venkatesh, E. O. Wiley, F. W. Allendorf, C. S. Baker, A. Bauer, A. Beja-Pereira, E. Bermingham, G. Bernardi, C. R. Bonvicino, S. Brenner, T. Burke, J. Cracraft, M. Diekhans, S. Edwards, P. Ericson, J. Estes, J. Fjelsa, N. Flesness, T. Gamble, P. Gaubert, A. S. Graphodatsky, J. A. Marshall Graves, E. D. Green, R. E. Green, S. Hackett, P. Hebert, K. M. Helgen, L. Joseph, B. Kessing, D. M. Kingsley, H. A. Lewin, G. Luikart, P. Martelli, M. A.M. Moreira, N. Nguyen, G. Ortí, B. L. Pike, D. M. Rawson, S. C. Schuster, H. N. Seuánez, H. B. Shaffer, M. S. Springer, J. M. Stuart, J. Sumner, E. C. Teeling, R. C. Vrijenhoek, R. D. Ward, W. C. Warren, R. K. Wayne, T. M. Williams, N. D. Wolfe, Y.-P. Zhang. 2009. Genome 10K: A proposal to obtain whole genome sequence for 10,000 vertebrate species. Journal of Heredity 100: 659-674.
  54. Pearks Wilkerson, A. J., Raudsepp, T., Graves, T., Warren, W., Chowdhary, B. P., Skow, L. C., and W. J. Murphy. 2008. Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics 92: 329-338.
  55. Janečka, J. E., Helgen, K. M., Lim, N., Baba, M., Izawa, M., Boeadi, and W. J. Murphy. 2008. Evidence for multiple species of Sunda colugo. Current Biology 18: pR1001-1003.
  56. Janečka, J. E., Jackson, R., Li, D.-Q., Zhang, Y.-Q., F., Munkhtsog, B., Buckley-Beason, V., and W. J. Murphy. 2008. Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. Animal Conservation 11: 401-411.
  57. Springer, M. S., Meredith, R.W., Eizirik, E., Teeling, E., and W. J. Murphy. 2008. Morphology and placental mammal phylogeny. Systematic Biology 57: 499-503.
  58. Graphodatsky, A. S., Yang, F., Dobigny, G., Biltueva, L., Romanenko, S., Perelman, P., Serdukova, N., Alkalaeva, E., Ferguson-Smith, M. A., Murphy, W. J., and T. J. Robinson. 2008. Tracking genome evolution in rodents by Zoo-FISH. Chromosome Research 16: 261-274.
  59. Page, J.C. and W.J. Murphy. 2008. “Construction of radiation hybrid panels”. Pp. 51-64 In: Methods in Molecular Biology, Vol. 422: Phylogenomics (W. J. Murphy, ed.) Humana Press, Totowa, New Jersey.
  60. Holmes, R. S., Chan, J., Cox, L.A., Murphy, W. J., and J. VandeBerg. 2008. Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor. BMC Evolutionary Biology 8:54.
  61. Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., and W. J. Kent. 2007. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research 17: 1797-1808.
  62. 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.
  63. Springer, M. S., Murphy, W. J., Eizirik, E., Madsen, O., Scally, M. S., Douady, C., Teeling, E., Stanhope, M. J., de Jong, W. W., and S. J. O’Brien. 2007. “A molecular classification for the living orders of placental mammals and the phylogenetic placement of primates.” Pp 1-28 In: Primate Origins: Adaptations & Evolution (M. Ravosa and M. Dagosta, eds.) Plenum Press, New York.
  64. Murphy, W. J., and S. J. O’Brien. 2007. Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference in mammals. Nature Protocols 2: 3022-3030.
  65. Pontius, J. U., Mullikin, J.C., Smith, D., Lindblad-Toh, K., Gnerre, S., Clamp, M., Stephens, R., Neelam, B., Volfovsky, N., Schäffer, A.A., Agarwala, R., Narfstrom, K., Murphy, W. J., Giger, U., Roca, A.L., O’hUigin, C., Antunes, A., Menotti-Raymond, M., Yuhki N., Pecon Slattery J., Johnson, W.E., Bourqe, G, Tesler, G. and S. J. O’Brien. 2007. Initial sequence and comparative analysis of the cat genome. Genome Research 17: 1675-1689.
  66. Vasquez-Salat, N., Beck, T. W., Yuhki, N., O’Brien, S. J., and W. J. Murphy. 2007. Gene conversion within the mammalian CC chemokine receptor cluster promotes receptor dimerization. Genomics 90: 213-224.
  67. Springer, M. S., Burk, A., Meredith, R., Eizirik, E., Teeling, E. C., O’Brien, S. J., and W. J. Murphy. 2007. The adequacy of morphology for reconstructing the early phylogenetic history of placental mammals. Systematic Biology 56: 673-684.
  68. Springer, M. S., and W. J. Murphy. 2007. Mammalian evolution and biomedicine: new views from phylogeny. Biological Reviews 82: 375-392.
  69. Miller-Butterworth, C. M., Murphy, W. J., O’Brien, S. J., Jacobs, D. S., Springer, M. S., and E. C. Teeling. 2007. A family matter: conclusive resolution of the taxonomic position of the long-fingered bats, Miniopterus. Molecular Biology and Evolution 24: 1553-1561.
  70. Murphy, W. J., Pringle, T., Crider, T., Springer, M. S., and W. Miller. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Research 17: 413-421.
  71. Murphy, W. J., Davis, B., David, V. A., Agarwala, R., Schäffer, A. A., Pearks-Wilkerson, A. J., Neelam, B., O’Brien, S. J. and M. Menotti-Raymond. 2007. A 1.5-megabase-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 89: 189-196.
  72. Kohn, M. H., Murphy, W. J., Ostrander, E. A., and R. K. Wayne. 2006. Genomics and conservation genetics. Trends in Ecology and Evolution 21: 629-637.
  73. Fyfe, J. C., M. Menotti-Raymond David, V., Schäffer, A. A., Brichta, L., Drummond, M. C., Buzzell, B. G., Gregory, B. L., Agarwala, R., Murphy, W. J., Wirth, B., and S. J. O’Brien. 2006. An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Research 16: 1084-1090.
  74. Murphy, W. J. 2006. “The feline genome”. Pp. 60-68 in Genome Dynamics: Structure and Evolution of Vertebrate Genomes (Volff, J. N., ed.) Karger Press, Basel, Switzerland.
  75. Murphy, W. J., Pearks Wilkerson, A. J., Raudsepp, T., Agarwala, R., Schäffer, A. A., Stanyon, R., and B. P. Chowdhary. 2006. Novel gene acquisition on carnivore Y chromosomes. PLoS Genetics 2: e43.
  76. Johnson, W. E., Eizirik, E., Pecon-Slattery, J., Murphy, W. J., Antunes, A., Teeling, E. C., and S. J. O’Brien. 2006. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311: 73-77.
  77. Murphy, W. J., Stephens, R., Agarwala, R., Schaafer, A., Smith, C. J., Crumpler, N., David, V. A. and S. J. O’Brien. 2005. A rhesus macaque radiation hybrid map and comparative analysis with the human genome.  Genomics 86: 383-395.
  78. 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.
  79. Springer, M. S., Murphy, W. J., Eizirik, E., and S. J. O’Brien. 2005. “Evidence for major placental clades. Pp. 37-49 In The Rise of Placental Mammals (K.D. Rose & J.D. Archibald, eds.) The Johns Hopkins University Press, Baltimore, MD.
  80. Roca, A. L., Nash, W. G., Menninger, J., Murphy, W. J., and S. J. O’Brien. 2005. Insertional polymorphisms of endogenous feline leukemia viruses.  Journal of Virology 79: 3979-3986.
  81. He, Q., Lowrie, C., Shelton, G. D., Menotti-Raymond, M., Murphy, W. J., Swanson, W. F. and J. C. Fyfe. 2005. Inherited motor neuron disease in domestic cats: A model of spinal muscular atrophy. Pediatric Research 57: 324-330.
  82. 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.
  83. Beck, T. W., Menninger, J. Murphy, W. J., Nash, W. G., O’Brien, S. J. and N. Yuhki. 2005. The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 56: 702-709.
  84. Murphy, W. J., Pevzner, P. and S. J. O’Brien.  2004. Mammalian phylogenomics comes of age. Trends in Genetics 20: 631-639. (Review).
  85. Eizirik, E., Murphy, W. J., Springer, M. S., and S. J. O’Brien. 2004. “Molecular phylogeny and dating of early primate divergences.”  Pp. 45-64 in Anthropoid Origins, New Visions (R. Kay & C. Ross, eds.). Kluwer/Plenum.
  86. Pecon-Slattery, J., Pearks Wilkerson, A. J., Murphy, W. J., and S. J. O’Brien.  2004. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree. Molecular Biology and Evolution 21: 2299-2309.
  87. Roca, A. L.*, Kahila Bar-Gal, G.*, Eizirik, E., Helgen, K.M., Maria, R., Springer, M.S., O’Brien, S. J., and W. J. Murphy. 2004. Mesozoic origin for West Indian insectivores. Nature 429: 649-651.
  88. Menotti-Raymond, M., David, V. A., Stephens, R., Agarwala, R., Schaffer, A., O’Brien, S. J., and W. J. Murphy. 2003. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenetics and Genome Research 102: 272-276.
  89. Murphy, W. J., Bourque, G., Telser, G., Pevzner, P., and S. J. O’Brien.  2003. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Human Genomics 1: 30-40.
  90. O’Brien, S. J. and W. J. Murphy. 2003.  Genomics. A dog’s breakfast?  Science 301: 1854-1855. (Review).
  91. Kuznetsov, S. B., Matveeva, M. M., Murphy, W. J., O’Brien S. J. and O. L. Serov.  2003.  Mapping of 53 loci in American mink (Mustela vison). Journal of Heredity 94: 386-391.
  92. Teeling, E. C., Madsen, O., Murphy, W. J., Springer, M. S., and S. J. O’Brien. 2003. Nuclear gene sequences confirm an ancient link between New Zealand’s short-tailed bat and South American noctilionoid bats. Molecular Phylogenetics and Evolution 28: 308-319.
  93. Murphy, W. J., Fröenicke, L., O’Brien, S. J., and R. Stanyon. 2003. The origin of human chromosome 1 and its homologues in placental mammals. Genome Research 13: 1880-1888.
  94. Springer, M. S., Murphy, W. J., Eizirik, E., and S. J. O’Brien. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proceedings of the National Academy of Sciences USA 100: 1056-1061.
  95. Menotti-Raymond, M., David, V. A., Roelke-Parker, M., Sun, S., Schäffer, A., Agarwala, R., Tomlin, J.F., O’Brien, S. J. and W. J. Murphy.  2003.  Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenetics and Genome Research 102: 272-276.
  96. Menotti-Raymond, M., David, V. A., Roelke-Parker, M., Sun, S., Schäffer, A., Agarwala, R., Tomlin, J.F., O’Brien, S. J. and W. J. Murphy.  2003.  Second generation integrated linkage and radiation hybrid maps of the domestic cat.  Journal of Heredity 94: 95-106.
  97. 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.
  98. Murphy, W. J.*, Eizirik, E.*, O’Brien, S. J., Madsen, O., Scally, M., Douady, C., Teeling, E. C., Ryder, O. A., Stanhope, M., De Jong, W. W. and M. S. Springer.  2001.  Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
  99. Murphy, W. J., Page, J., Smith, C. J., Desrosiers, R. C. and S. J. O’Brien.  2001. A radiation hybrid mapping panel for the rhesus macaque.  Journal of Heredity 92: 516-519.
  100. O’Brien, S. J., Eizirik, E., and W. J. Murphy.  2001.  Genomics. On choosing mammalian genomes for sequencing.  Science 292: 2264-2266.
  101. Sun, S., Murphy, W. J., Menotti-Raymond, M., and S. J. O’Brien.  2001. Integration of the feline radiation hybrid and linkage maps.  Mammalian Genome 12: 436-441.
  102. Murphy, W. J., Stanyon, R., and S. J. O’Brien. 2001.  Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biology 2: 0005.1-0005.8. (Review).
  103. Parker, J. S. L., Murphy, W. J., Wang, D., O’Brien, S. J., and C. R. Parrish.  2001.  Canine and feline parvoviruses can use human or feline transferrin receptors to bind, enter, and infect cells.  Journal of Virology 75: 3896-3902.
  104. Eizirik, E., Murphy, W. J., and S. J. O’Brien.  2001.  Molecular dating and biogeography of the early placental mammal radiation.  Journal of Heredity 92: 212-219.
  105. 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.
  106. Pecon-Slattery, J., Murphy, W. J., and S. J. O’Brien.  2000.  Patterns of diversity among SINE elements isolated from three Y-chromosome genes in carnivores.  Molecular Biology and Evolution 17: 825-829.
  107. Murphy, W. J., Shan, 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.
  108. Murphy, W. J., Shan, 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.
  109. Murphy, W.J., Thomerson, J.E., and G.E. Collier. 1999. Phylogeny of the Neotropical fish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences.  Molecular Phylogenetics and Evolution 13: 289-301.
  110. O’Brien, S. J., Eisenberg, J. F., Miyamoto, M., Hedges, S. B., Kumar, S., Wilson, D. E., Menotti-Raymond, M., Murphy, W. J., Nash, W. G., Lyons, L. A., Menninger, J. C., Stanyon, R., Wienberg, J., Copeland, N. G., Jenkins, N. A., Gellin, J., Yerle, M., Andersson, L., Womack, J., Broad, T., Postlewait, J., Serov, O., Bailey, E., James, M. R., Marshall Graves, J. A. 1999.  Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart.  Science 286: 463-478.
  111. O’Brien, S. J., Menotti-Raymond, M., Murphy, W. J., Nash, W. G., Wienberg, J., Stanyon, R., Copeland, N. G., Jenkins, N. A., Womack, J. E., and J. A. Marshall-Graves.  1999.  The promise of comparative genomics in mammals.  Science 286: 458-481.
  112. Murphy, W.J., Nguyen, T., Taylor, E.B., and G.E. Collier. 1999. Mitochondrial DNA phylogeny of West African killifishes. Molecular Phylogenetics and Evolution 11: 343-350.
  113. Murphy, W.J. and G.E. Collier. 1999. Phylogenetic relationships within the African killifish genera Aphyosemion and FundulopanchaxMolecular Phylogenetics and Evolution 11: 351-360.
  114. Murphy, W. J., Menotti-Raymond, M., Lyons, L. A., Thompson, M. A., and S. J. O’Brien. 1999. Development of a feline whole genome radiation hybrid panel and comparative mapping of human chromosome 12 and 22 loci.  Genomics 57: 1-8.
  115. Collier, G.E., Espinoza, M., and W.J. Murphy. 1998. Forensic phylogenetics of killifish. Journal of the American Killifish Association 31: 35-41.
  116. Murphy, W.J. and G.E. Collier. 1997.  A molecular phylogeny for aplocheiloid killifishes (Atherinomorpha, Cyprinodontiformes):  the role of vicariance and the origins of annualism.  Molecular Biology and Evolution 14:  790-799.
  117. Murphy, W. J. and G.E. Collier. 1996. Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae):  implications for Caribbean and Central American biogeography. Molecular Biology and Evolution 13:  642-649.