Using genomic data to unravel the root of the placental mammal phylogeny

Genome Research

Volumn 17, Issue 4, 2007, Pages 413-421

  Murphy, William J ^a   Pringle, Thomas H ^b   Crider, Tess A ^a   Springer, Mark S ^c   Miller, Webb ^d  

^a TEXAS A AND M UNIVERSITY   (United States)

^b Sperling Foundation   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE SEQUENCE; GENETIC ANALYSIS; GENOME ANALYSIS; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLACENTAL MAMMALS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RETROPOSON; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AFROTHERIA; ARMADILLO; DIDELPHIDAE; EUTHERIA; MAMMALIA; XENARTHRA;

EID: 34147184456     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5918807     Document Type: Article

References (52)

1. Amrine-Madsen, H., Koepfli, K.P., Wayne, R.K., and Springer, M.S. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28: 225-240.
2. Bashir, A., Ye, C., Price, A.L., and Bafna, V. 2005. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 15: 998-1006.
3. Blanchette, M., Green, E.D., Miller, W., and Haussler, D. 2004. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 14: 2412-2423.
4. Cantrell, M.A., Filanoski, B.J., Ingermann, A.R., Olsson, K., DiLuglio, N., Lister, Z., and Wichman, H.A. 2001. An ancient retrovirus-like element contains hotspots for SINE insertion. Genetics 158: 769-777.
5. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., and Thompson, J.D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500.
6. de Jong, W.W., van Dijk, M.A.M., Poux, C., Kappe, G., van Rheede, T., and Madsen, O. 2003. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol. Phylogenet. Evol. 28: 328-340.
7. Delsuc, F., Scally, M., Madsen, O., Stanhope, M.J., de Jong, W.W., Catzeflis, F.M., Springer, M.S., and Douzery, E.J. 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol. Biol. Evol. 19: 1656-1671.
8. Douady, C.J. and Douzery, E.J.P. 2003. Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora." Mol. Phylogenet. Evol. 28: 285-296.
9. Eizirik, E., Murphy, W.J., and O'Brien, S.J. 2001. Molecular dating and biogeography of the early placental mammal radiation. J. Hered. 92: 212-219.
10. Graham, T. and Boissinot, S. 2006. The genomic distribution of L1 elements: The role of insertion bias and natural selection. J. Biomed. Biotechnol. 1: 75327.
11. Hay, W.W., DeConto, R.M., Wold, C.N., Wilson, K.M., Voigt, S., Schulz, M., Wold-Rossby, A., Dullo, W.-C., Ronov, A.B., Balukhovsky, A.N., et al. 1999. Alternative global Cretaceous paleogeography. In Evolution of the Cretaceous ocean/climate system (eds. E. Barrera and C. Johnson), pp. 1-48. The Geological Society of America, Boulder, CO.
12. Hunter, J.P. and Janis, C.M. 2006. "Garden of Eden" or "Fool's Paradise"? Phylogeny, dispersal, and the southern continent hypothesis of placental mammal origins. Paleobiology 32: 339-344.
13. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006.
14. Kishino, H., Thorne, J.L., and Bruno, W.J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate estimation. Mol. Biol. Evol. 18: 352-361.
15. Kjer, K.M. and Honeycutt, R.L. 2007. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evol. Biol 7: 8.
16. Kriegs, J.O., Churakov, G., Kiefmann, M., Jordan, U., Brosius, J., and Schmitz, J. 2006. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4: e91.
17. Kumar, S. and Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
18. Ludwig, A., Rozhdestvensky, T.S., Kuryshev, V.Y., Schmitz, J., and Brosius, J. 2005. An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J. Mol. Biol. 350: 200-214.
19. Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, W.J., Blanchette, M., Haussler, D., and Miller, W. 2006. Reconstructing contiguous regions of an ancestral genome. Genome Res. 16: 1557-1565.
20. Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong, W.W., and Springer, M.S. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409: 610-614.
21. Margulies, E.H., Vinson, J.P., NISC Comparative Sequencing Program, Miller, W., Jaffe, D.B., Lindblad-Toh, K., Chang, J.L., Green, E.D., Lander, E.S., Mullikin, J.C., et al. 2005. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc. Natl. Acad. Sci. 102: 4795-4800.
22. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., and O'Brien, S.J. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.
23. Murphy, W.J., Eizirik, E., O'Brien, S.J., Madsen, O., Scally, M., Douady, C.J., Teeling, E., Ryder, O.A., Stanhope, M.J., de Jong, W.W., et al. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
24. Murphy, W.J., Pevzner, P., and O'Brien, S.J. 2004. Mammalian phylogenomics comes of age. Trends Genet. 20: 631-639.
25. Nikaido, M., Nishihara, H., Hukumoto, Y., and Okada, N. 2003. Ancient SINEs from African endemic mammals. Mol. Biol. Evol. 20: 522-527.
26. Nishihara, H., Satta, Y., Nikaido, M., Thewissen, J.G.M., Stanhope, M.J., and Okada, N. 2005. A retroposon analysis of Afrotherian phylogeny. Mol. Biol. Evol. 22: 1823-1833.
27. Nishihara, H., Hasegawa, M., and Okada, N. 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. 103: 9929-9934.
28. Notredame, C., Higgins, D., and Heringa, J. 2000. T-Coffee: A novel method for multiple sequence alignments. J. Mol. Biol. 302: 205-217.
29. Pecon-Slattery, J., Pearks-Wilkerson, A.J., Murphy, W.J., and O'Brien, S.J. 2004. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree. Mol. Biol. Evol. 21: 2299-2309.
30. Poux, C., van Rheede, T., Madsen, O., and de Jong, W.W. 2002. Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol. Biol. Evol. 19: 2035-2037.
31. Roca, A., Bar-Gal, G.-K., Eizirik, E., Helgen, K.M., Maria, R., Springer, M.S., O'Brien, S.J., and Murphy, W.J. 2004. Mesozoic origin for West Indian insectivores. Nature 429: 649-651.
32. Rokas, A. and Carroll, S.B. 2006. Bushes in the tree of life. PLoS Biol. 4: e352.
33. Rokas, A. and Holland, P.W.H. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15: 454-459.
34. Rosenbloom, K., Taylor, J., Schaeffer, S., Kent, J., Haussler, D., and Miller, W. Phylogenomic resources at the UCSC Genome Browser. In Methods in molecular biology: Phylogenomics (ed. W.J. Murphy). Humana Press, Totowa, NJ. (in press).
35. Schwartz, M., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
36. Shedlock, A.M. and Okada, N. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 28: 148-160.
37. Shedlock, A.M., Takahashi, K., and Okada, N. 2004. SINEs of speciation: Tracking lineages with retroposons. Trends Ecol. Evol. 19: 545-553.
38. Shoshani, J. and McKenna, M.C. 1998. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9: 572-584.
39. Smith, A.G., Smith, D.G., and Funnell, B.M. 1994. Atlas of Cenozoic and Mesozoic coastlines. Cambridge University Press, Cambridge, UK.
40. Springer, M.S., Murphy, W.J., Eizirik, E., and O'Brien, S.J. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. 100: 1056-1061.
41. Springer, M.S., Stanhope, M.J., Madsen, O., and de Jong, W.W. 2004. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 19: 430-438.
42. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
43. Thorne, J.L., Kishino, H., and Painter, L.S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15: 1647-1657.
44. van de Lagemaat, L.N., Gagnier, L., Medstrand, P., and Mager, D.L. 2005. Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res. 15: 1243-1249.
45. van Rheede, T., Bastiaans, T., Boone, D.N., Hedges, S.B., de Jong, W.W., and Madsen, O. 2006. The platypus is in its place: Nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23: 587-597.
46. Waddell, P.J. and Shelley, S. 2003. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28: 197-224.
47. Waddell, P., Okada, N., and Hasegawa, M. 1999. Toward resolving the inter-ordinal relationships of placental mammals. Syst. Biol. 48: 1-5.
48. Waddell, P.J., Kishino, H., and Ota, R. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. Ser. Workshop Genome Inform. 12: 141-154.
49. Wheeler, W.A. 2003. Implied alignment: A synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19: 261-268.
50. Wilson, M.D., Riemer, C., Martindale, D., Schnupf, P., Boright, A., Cheung, T., Hardy, D., Schwartz, S., Scherer, S., Tsui, L.C., et al. 2001. Comparative analysis of the gene dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res. 29: 1352-1365.
51. Woodburne, M.O., Rich, T.H., and Springer, M.S. 2003. The evolution of tribospheny and the antiquity of mammalian clades. Mol. Phylogenet. Evol. 28: 360-385.
52. Yu, L. and Zhang, Y.P. 2005. Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals. Mamm. Genome 16: 651-660.