Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data

Molecular Phylogenetics and Evolution

Volumn 52, Issue 3, 2009, Pages 660-664

  Hou, Zhuo cheng ^a,b,c   Romero, Roberto ^a,b   Wildman, Derek E ^a,b  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Carnivora; Cetartiodactyla; Ferungulata; Molecular phylogeny; Perissodactyla

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; CATTLE; CLASSIFICATION; DNA SEQUENCE; DOG; GENETICS; GENOMICS; HORSE; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; CATTLE; DOGS; EVOLUTION, MOLECULAR; GENOMICS; HORSES; LIKELIHOOD FUNCTIONS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CANIS FAMILIARIS; CARNIVORA; CETARTIODACTYLA; EQUIDAE; LAURASIATHERIA; MAMMALIA; PERISSODACTYLA;

EID: 67649658023     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.05.002     Document Type: Article

References (34)

1. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
2. The Bovine Genome Sequencing and Analysis Consortium,. Elsik C.G., Tellam R.L., and Worley K.C. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324 (2009) 522-528
3. Fadem B.H., and Rayve R.S. Characteristics of the oestrous cycle and influence of social factors in grey short-tailed opossums (Monodelphis domestica). J. Reprod. Fertil. 73 (1985) 337-342
4. Felsenstein J. Statistical Properties of Parsimony. Inferring Phylogenies (2004), Sinauer Associates, Inc., Sunderland, Massachusetts
5. Green P. 2× genomes - does depth matter?. Genome Res. 17 (2007) 1547-1549
6. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
7. Hartl D.L., and Clark A.G. Principles of Population Genetics (2007), Sinauer Associates, Inc., Sunderland, Massachusetts
8. Irwin D.M., and Arnason U. Cytochromeb gene of marine mammals:phylogeny and evolution. J. Mamm. Evol. 2 (1994) 37-55
9. Janecka J.E., Miller W., Pringle T.H., Wiens F., Zitzmann A., Helgen K.M., Springer M.S., and Murphy W.J. Molecular and genomic data identify the closest living relative of primates. Science 318 (2007) 792-794
10. Kleineidam R.G., Pesole G., Breukelman H.J., Beintema J.J., and Kastelein R.A. Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes. J. Mol. Evol. 48 (1999) 360-368
11. Kriegs J.O., Churakov G., Kiefmann M., Jordan U., Brosius J., and Schmitz J. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4 (2006) e91
12. Kullberg M., Nilsson M.A., Arnason U., Harley E.H., and Janke A. Housekeeping genes for phylogenetic analysis of eutherian relationships. Mol. Biol. Evol. 23 (2006) 1493-1503
13. Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J., 3rd, Zody, M.C., Mauceli, E., Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., DeJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.W., Cook, A., Cuff, J., Daly, M.J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.P., Parker, H.G., Pollinger, J.P., Searle, S.M., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., DeGray, S., Dhargay, N., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., FitzGerald, M., Foley, K., Foley, C., Franke, A., Friedrich, D., Gage, D., Garber, M., Gearin, G., Giannoukos, G., Goode, T., Goyette, A., Graham, J., Grandbois, E., Gyaltsen, K., Hafez, N., Hagopian, D., Hagos, B., Hall, J., Healy, C., Hegarty, R., Honan, T., Horn, A., Houde, N., Hughes, L., Hunnicutt, L., Husby, M., Jester, B., Jones, C., Kamat, A., Kanga, B., Kells, C., Khazanovich, D., Kieu, A.C., Kisner, P., Kumar, M., Lance, K., Landers, T., Lara, M., Lee, W., Leger, J.P., Lennon, N., Leuper, L., LeVine, S., Liu, J., Liu, X., Lokyitsang, Y., Lokyitsang, T., Lui, A., Macdonald, J., Major, J., Marabella, R., Maru, K., Matthews, C., McDonough, S., Mehta, T., Meldrim, J., Melnikov, A., Meneus, L., Mihalev, A., Mihova, T., Miller, K., Mittelman, R., Mlenga, V., Mulrain, L., Munson, G., Navidi, A., Naylor, J., Nguyen, T., Nguyen, N., Nguyen, C., Nicol, R., Norbu, N., Norbu, C., Novod, N., Nyima, T., Olandt, P., O'Neill, B., O'Neill, K., Osman, S., Oyono, L., Patti, C., Perrin, D., Phunkhang, P., Pierre, F., Priest, M., Rachupka, A., Raghuraman, S., Rameau, R., Ray, V., Raymond, C., Rege, F., Rise, C., Rogers, J., Rogov, P., Sahalie, J., Settipalli, S., Sharpe, T., Shea, T., Sheehan, M., Sherpa, N., Shi, J., Shih, D., Sloan, J., Smith, C., Sparrow, T., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Stone, S., Sykes, S., Tchuinga, P., Tenzing, P., Tesfaye, S., Thoulutsang, D., Thoulutsang, Y., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Venkataraman, V., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Yang, S., Yang, X., Young, G., Yu, Q., Zainoun, J., Zembek, L., Zimmer, A., Lander, E.S., 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819.
14. Liu G., Uddin M., Islam M., Goodman M., Grossman L.I., Romero R., and Wildman D.E. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences. Source Code Biol. Med. 2 (2007) 5
15. Mess A., and Carter A.M. Evolution of the placenta during the early radiation of placental mammals. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 148 (2007) 769-779
16. Montgelard C., Catzeflis F.M., and Douzery E. Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences. Mol. Biol. Evol. 14 (1997) 550-559
17. Mossman H.W. Vertebrate Fetal Membranes (1987), Rutgers University Press, New Brunswick
18. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryder O.A., and O'Brien S.J. Molecular phylogenetics and the origins of placental mammals. Nature 409 (2001) 614-618
19. 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., and Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294 (2001) 2348-2351
20. Murphy W.J., Pringle T.H., Crider T.A., Springer M.S., and Miller W. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17 (2007) 413-421
21. Nei M., and Kumar S. Molecular Evolution and Phylogenetics (2000), Oxford University Press, New York
22. Nishihara H., Hasegawa M., and Okada N. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. USA 103 (2006) 9929-9934
23. Philippe H., Zhou Y., Brinkmann H., Rodrigue N., and Delsuc F. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 5 (2005) 50
24. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
25. Prasad A.B., Allard M.W., and Green E.D. Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Datasets. Mol. Biol. Evol. 25 (2008) 1795-1808
26. Shoshani J., and McKenna M.C. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9 (1998) 572-584
27. Springer M.S., Burk-Herrick A., Meredith R., Eizirik E., Teeling E., O'Brien S.J., and Murphy W.J. The adequacy of morphology for reconstructing the early history of placental mammals. Syst. Biol. 56 (2007) 673-684
28. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (2006) 2688-2690
29. Strimmer K., and Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc. Biol. Sci. 269 (2002) 137-142
30. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
31. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
32. Ursing B.M., and Arnason U. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc. Biol. Sci. 265 (1998) 2251-2255
33. Wildman D.E., Chen C., Erez O., Grossman L.I., Goodman M., and Romero R. Evolution of the mammalian placenta revealed by phylogenetic analysis. Proc. Natl. Acad. Sci. USA 103 (2006) 3203-3208
34. Wilson D.E., and Reeder D.M. Mammal Species of the World: A Taxonomic and Geographic Reference (2005), Jonhs Hopkins University Press, Baltimore