Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Molecular Biology and Evolution

Volumn 19, Issue 10, 2002, Pages 1656-1671

  Delsuc, Frédéric ^a   Scally, Mark ^g   Madsen, Ole ^d   Stanhope, Michael J ^b,c,e   De Jong, Wilfried W ^d,f   Catzeflis, François M ^a   Springer, Mark S ^b,c   Douzery, Emmanuel J P ^a  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e GLAXOSMITHKLINE   (United States)

^f UNIVERSITY OF AMSTERDAM   (Netherlands)

^g NONE

Author keywords

Evolutionary dynamics; Maximum likelihood and Bayesian phylogenetics; Nuclear markers; Placentals; Taxon and character sampling; Xenarthran phylogeny

Indexed keywords

ALPHA 2 ADRENERGIC RECEPTOR; BRCA1 PROTEIN; VON WILLEBRAND FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; EDENTATA; EXON; GENETIC VARIABILITY; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; TAXONOMIC IDENTIFICATION;

DASYPODIDAE; EDENTATA; EUTHERIA; MAMMALIA; METATHERIA; MYRMECOPHAGIDAE;

EID: 0036792101     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a003989     Document Type: Article

References (87)

1. Adkins, R. M., E. L. Gelke, D. Rowe, and R. L. Honeycutt. 2001. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18:777-791.
2. Arnason, U., A. Gullberg, and A. Janke. 1997. Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and Ferungulates. Mol. Biol. Evol. 14:762-768.
3. Bernardi, G. 2001. Misunderstandings about isochores. Part 1. Gene 276:3-13.
4. Cao, Y., M. Fujiwara, M. Nikaido, N. Okada, and M. Hasegawa. 2000. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene 259:149-158.
5. Catzeflis, F. 1991. Animal tissue collections for molecular genetics and systematics. Trends Ecol. Evol. 6:168.
6. Cetica, P. D., A. J. Solari, M. S. Merani, J. C. De Rosas, and M. H. Burgos. 1998. Evolutionary sperm morphology and morphometry in armadillos. J. Submicroscop. Cytol. Pathol. 30:309-314.
7. de Jong, W. W., J. A. M. Leunissen, and G. J. Wistow. 1993. Eye lens crystallins and the phylogeny of placental orders: evidence for a Macroscelid-Paenungulate clade? Pp. 5-12 in M. J. N. a. M. C. M. E. F. S. Sazlay, ed. Mammal phylogeny (placentals). Springer-Verlag, New York.
8. de Jong, W. W., A. Zweers, K. A. Joysey, J. T. Gleaves, and D. Boulter. 1985. Protein sequence analysis applied to Xenarthran and Pholidote phylogeny. Pp. 65-76 in G. G. Montgomery, ed. The evolution and ecology of armadillos, sloths and vermilinguas. Smithsonian Institution, Washington, DC.
9. Delsuc, F., F. M. Catzeflis, M. J. Stanhope, and E. J. Douzery. 2001. The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua. Proc. R. Soc. Lond. B Biol. Sci. 268:1605-1615.
10. Deng, C.-X., and S. G. Brodie. 2000. Roles of BRCA1 and its interacting proteins. Bioessays 22:728-737.
11. Douzery, E., and F. M. Catzeflis. 1995. Molecular evolution of the mitochondrial 12S rRNA in Ungulata (Mammalia). J. Mol. Evol. 41:622-636.
12. Eizirik, E., W. J. Murphy, and S. J. O'Brien. 2001. Molecular dating and biogeography of the early placental mammal radiation. J. Hered. 92:212-219.
13. Engelmann, G. F. 1985. The phylogeny of the Xenarthra. Pp. 51-63 in G. G. Montgomery, ed. The evolution and ecology of armadillos, sloths and vermilinguas. Smithsonian Institution, Washington, DC.
14. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
15. Gatesy, J., M. C. Milinkovitch, V. G. Waddell, and M. S. Stanhope. 1999. Stability of cladistic relationships between Cetacea and higher-level Artiodactyl taxa. Syst. Biol. 48:6-20.
16. Gaudin, T. J. 1999. The morphology of xenarthrous vertebrae (Mammalia: Xenarthra). Fieldiana: Geology, New Ser. 41:1-38.
17. Gaudin, T. J., and D. G. Branham. 1998. The phylogeny of the Myrmecophagidae (Mammalia, Xenarthra, Vermilingua) and the relationship of Eurotamandua to the Vermilingua. J. Mamm. Evol. 5:237-265.
18. Gaudin, T. J., J. R. Wible, J. A. Hopson, and W. D. Turnbull. 1996. Reexamination of the morphological evidence for the Cohort Epitheria (Mammalia, Eutheria). J. Mamm. Evol. 3:31-78.
19. Gingerich, P. D., M. Haq, I. S. Zalmout, I. H. Khan, and M. S. Malkani. 2001. Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from Pakistan. Science 293:2239-2242.
20. Greenwood, A. D., J. Castresana, G. Feldmaeir-Fuchs, and S. Pääbo. 2001. A molecular phylogeny of two extinct sloths. Mol. Phylogenet. Evol. 18:94-103.
21. Gregory, W. K. 1910. The orders of mammals. Bull. Am. Mus. Nat. Hist. 27:1-524.
22. Guth, C. 1961. La région temporale des Edentés. Doctoral dissertation, University of Paris, Paris, France.
23. Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
24. Huchon, D., O. Madsen, M. J. J. B. Sibbald, K. Ament, M. J. Stanhope, F. Catzeflis, W. W. de Jong, and E. J. P. Douzery. 2002. Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol. Biol. Evol. 19:1053-1065.
25. Huelsenbeck, J. P., and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-32.
26. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
27. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
28. Hutcheon, J. M., J. A. Kirsch, and J. D. Pettigrew. 1998. Base-compositional biases and the bat problem. III. The questions of microchiropteran monophyly. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353:607-617.
29. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
30. Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
31. Lavergne, A., E. Douzery, T. Stichler, F. M. Catzeflis, and M. S. Springer. 1996. Interordinal mammalian relationships: evidence for Paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences. Mol. Phylogenet. Evol. 6:245-258.
32. Lecointre, G., H. Philippe, H. L. vân Lê, and H. Le Guyader. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2:205-224.
33. Loughry, W. J., P. A. Prodöhl, C. M. McDonough, and J. C. Avise. 1998. Polyembryony in armadillos. Am. Sci. 86:274-279.
34. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. DeBry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Parallel adaptative radiations in two major clades of placental mammals. Nature 409:610-614.
35. McKenna, M. C. 1975. Toward a phylogenetic classification of the Mammalia. Pp. 21-46 in W. P. Luckett and F. S. Szalay, eds. Phylogeny of the primates. Plenum Press, New York.
36. McKenna, M. C., and S. K. Bell. 1997. Classification of mammals above the species level. Columbia University Press, New York.
37. Montgelard, C., F. M. Catzeflis, and E. Douzery. 1997. Phylogenetic relationships of artiodactyls and Ceteacans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences. Mol. Biol. Evol. 14:550-559.
38. Mouchaty, S. K., A. Gullberg, A. Janke, and U. Arnason. 2000a. Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi. Zool. Scr. 29:307-317.
39. -. 2000b. The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences. Mol. Biol. Evol. 17:60-67.
40. Murphy, W. J., E. Eizirik, W. E. Jonhson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
41. Murphy, W. J., E. Eizirik, S. J. O'Brien et al. (11 co-authors). 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
42. Nikaido, M., K. Kawai, Y. Cao, M. Harada, S. Tomita, N. Okada, and M. Hasegawa. 2001. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores. J. Mol. Evol. 53:508-516.
43. Nikaido, M., A. P. Rooney, and N. Okada. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96:10261-10266.
44. Novacek, M. J. 1992. Mammalian phylogeny: shaking the tree. Nature 356:121-125.
45. -. 2001. Mammalian phylogeny: genes and supertrees. Curr. Biol. 11:R573-R575.
46. Patterson, B., and R. Pascual. 1972. The fossil mammal fauna of South-America. Pp. 247-309 in A. Keast, F. C. Erk, and B. P. Glass, eds. Evolution, mammals and southern continents. State University of New-York Press, Albany, NY.
47. Patterson, B., W. Segall, and W. D. Turnbull. 1989. The ear region in xenarthrans (= Edentata, Mammalia). Part I. Cingulates. Fieldiana: Geology, New Ser. 18:1-46.
48. Patterson, B., W. Segall, W. D. Turnbull, and T. J. Gaudin. 1992. The ear region in xenarthrans (= Edentata, Mammalia). Part II. Sloths, Anteaters, Palaeanodonts, and a Miscellany. Fieldiana: Geology, New Ser. 24:1-79.
49. Philippe, H. 1993. MUST: a computer package of management utilities for sequences and trees. Nucleic Acids Res. 21:5264-5272.
50. Philippe, H., and P. Forterre. 1999. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49:509-523.
51. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
52. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 19:817-818.
53. Rannala, B., J. P. Huelsenbeck, Z. H. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
54. Rose, K. D., and R. J. Emry. 1993. Relationships of Xenarthra, Pholidota, and Fossil "Edentates": the morphological evidence. Pp. 81-102 in F. S. Sazlay, M. J. Novacek, and M. C. McKenna, eds. Mammal phylogeny (placentals). Springer-Verlag, New York.
55. Rosenberg, M. S., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98:10751-6.
56. Scally, M., O. Madsen, C. J. Douady, W. W. de Jong, M. J. Stanhope, and M. S. Springer. 2001. Molecular evidence for the major clades of placental mammals. J. Mamm. Evol. 8:239-277.
57. Shimamura, M., H. Yasue, K. Ohshima, H. Abe, H. Kato, T. Kishiro, M. Goto, I. Munechika, and N. Okada. 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666-670.
58. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
59. Shoshani, J. 1986. Mammalian phylogeny: comparison of morphological and molecular results. Mol. Biol. Evol. 3:222-242.
60. Shoshani, J., and M. C. McKenna. 1998. Higher taxonomic relationships among extant Mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9:572-584.
61. Simpson, G. G. 1945. The principles of classification and a classification of mammals. Bull. Am. Mus. Nat. Hist. 85:1-350.
62. Springer, M. S., H. M. Amrine, A. Burk, and M. J. Stanhope. 1999. Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogenous base composition. Syst. Biol. 48:65-75.
63. Springer, M. S., G. C. Cleven, O. Madsen, W. W. de Jong, V. G. Waddell, H. M. Amrine, and M. J. Stanhope. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61-64.
64. Springer, M. S., R. W. Debry, C. Douady, H. M. Amrine, O. Madsen, W. W. de Jong, and M. J. Stanhope. 2001. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol. Biol. Evol. 18:132-143.
65. Springer, M. S., and W. W. de Jong. 2001. Which mammalian supertree to bark up? Science 291:1709-1711.
66. Springer, M. S., E. C. Teeling, O. Madsen, M. J. Stanhope, and W. W. de Jong. 2001. Integrated fossil and molecular data reconstruct bat echolocation. Proc. Natl. Acad. Sci. USA 98:6241-6246.
67. Stanhope, M. J., O. Madsen, V. G. Waddell, G. C. Cleven, W. W. de Jong, and M. S. Springer. 1998b. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9:501-508.
68. Stanhope, M. J., V. G. Waddell, O. Madsen, W. W. de Jong, S. Blair Hedges, G. C. Cleven, D. Kao, and M. S. Springer. 1998a. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci. USA 95:9967-9972.
69. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
70. Swofford, D. L. 1998. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4.0b8. Sinauer Associates, Sunderland, Mass.
71. Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
72. Teeling, E. C., O. Madsen, R. A. Van Den Bussche, W. W. de Jong, M. J. Stanhope, and M. S. Springer. 2002. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc. Natl. Acad. Sci. USA 99:1431-1436.
73. Teeling, E. C., M. Scally, D. J. Kao, M. L. Romagnoli, M. S. Springer, and M. J. Stanhope. 2000. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 403:188-192.
74. Thewissen, J. G., E. M. Williams, L. J. Roe, and S. T. Hussain. 2001. Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature 413:277-281.
75. Ursing, B. M., and U. Arnason. 1998. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc. R. Soc. Lond. B 265:2251-2255.
76. van Dijk, M. A., O. Madsen, F. Catzeflis, M. J. Stanhope, W. W. de Jong, and M. Pagel. 2001. Protein sequence signatures support the African clade of mammals. Proc. Natl. Acad. Sci. USA 98:188-193.
77. van Dijk, M. A. M., E. Paradis, F. Catzeflis, and W. W. de Jong. 1999. The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in alphaA-crystallin. Syst. Biol. 48:94-106.
78. Vizcaíno, S. F. 1995. Identificación específica de las "mulitas", género Dasypus L. (Mammalia, Dasypodidae), del noroeste argentino. Descripción de una nueva espécie. Mastozool. Neotrop. 2:5-13.
79. Waddell, P. J., Y. Cao, J. Hauf, and M. Hasegawa. 1999. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-logDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Syst. Biol. 48:31-53.
80. Waddell, P. J., N. Okada, and M. Hasegawa. 1999. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48:1-5.
81. Wetzel, R. M. 1985. The identification and distribution of recent Xenarthra (= Edentata). Pp. 5-21 in G. G. Montgomery, ed. The evolution and ecology of armadillos, sloths and vermilinguas. Smithsonian Institution, Washington, DC.
82. Whelan, S., P. Lio, and N. Goldman. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17:262-272.
83. Yang, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
84. -. 1996a. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-372.
85. -. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
86. -. 1997. PAML: phylogenetic analysis by maximum likelihood. University College London, London.
87. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.