Combining multiple data sets in a likelihood analysis: Which models are the best?

Molecular Biology and Evolution

Volumn 19, Issue 12, 2002, Pages 2294-2307

  Pupko, Tal ^a   Huchon, Dorothée ^b   Cao, Ying ^a   Okada, Norihiro ^b   Hasegawa, Masami ^a  

^a INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Combining data sets; Mammalia; Maximum likelihood; Molecular evolution; Phylogeny

Indexed keywords

ARTICLE; DATA ANALYSIS; GENE SEQUENCE; MAMMAL; NONHUMAN; PHYLOGENY; STATISTICAL ANALYSIS; STATISTICAL MODEL; ANIMAL; CHEMISTRY; HUMAN;

MAMMALIA;

PROTEIN;

ANIMALS; HUMANS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PROTEINS;

EID: 0036900111     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004053     Document Type: Article

References (35)

1. Adachi, J., and M. Hasegawa. 1996. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
2. Arnason, U., A. Gullberg, S. Gretarsdottir, B. Ursing, and A. Janke. 2000. The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates. J. Mol. Evol. 50:569-578.
3. Burnham, K. P., and D. R. Anderson. 1998. Model Selection and Inference: A Practical Information-theoretic Approach. Springer-Verlag, New York.
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. Cao, Y., A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Pääbo, and M. Hasegawa. 1998. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47:307-322.
6. Corneli, P. S., and R. H. Ward. 2000. Mitochondrial genes and mammalian phylogenies: Increasing the reliability of branch length estimation. Mol. Biol. Evol. 17:224-234.
7. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
8. Friedman, N., M. Ninio, I. Pe'er, and T. Pupko. 2001. A structural EM algorithm for phylogenetic inference. Pp. 132-140 in T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner, and M. Waterman, eds. Proceedings of the Fifth Annual International Conference on Computational Biology. ACM Press, New York.
9. Graur, D., and W. H. Li. 1999. Fundamentals of Molecular Evolution. 2nd Edition. Sinauer Press, Sunderland, Mass.
10. Huelsenbeck, J. P., and J. J. Bull. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45: 92-98.
11. Huelsenbeck, J. P., J. J. Bull, and C. W. Cunningham. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-157.
12. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
13. 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.
14. 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.
15. Linhart, H. 1988. A test whether two AIC's differ significantly. S. Afr. Stat. J. 22:153-161.
16. 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 adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
17. McKenna, M. C., and S. K. Bell. 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York.
18. Mouchaty, S. K., F. M. Catzeflis, A. Janke, and U. Arnason. 2001. Molecular evidence of an African Phiomorpha-South-American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of cane rat (Thryonomys swinderianus). Mol. Phylogenet. Evol. 18:127-135.
19. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
20. Nei, M., and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
21. 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.
22. Novacek, M. J. 1992. Mammalian phylogeny: Shaking the tree. Nature 356:121-125.
23. Phillips, M. J., Y.-H. Lin, G. Harrison, and D. Penny. 2001. Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials. Proc. R. Soc. Lond. B 268:1533-1538.
24. Reyes, A., G. Pesole, and C. Saccone. 2000. Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny. Gene 259:177-187.
25. Sakamoto, Y., M. Ishiguro, and G. Kitagawa. 1986. Akaike Information Criterion Statistics. Reidel, Dordrecht, The Netherlands.
26. Schmitz, J., M. Ohme, and H. Zischler. 2000. The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other Eutherian orders. Mol. Biol. Evol. 17:1334-1343.
27. 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 heterogeneous base composition. Syst. Biol. 48:65-75.
28. Springer, M. S., A. Burk, J. R. Kavanagh, V. G. Waddell, and M. J. Stanhope. 1997. The interphotoreceptor retinoid binding protein gene in therian mammals: Implications for higher level relationships and evidence for loss of function in the marsupial mole. Proc. Natl. Acad. Sci. USA 94:13754-13759.
29. 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.
30. Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 4:77-86.
31. Takahashi, K., and M. Nei. 2000. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17:1251-1258.
32. Thewissen, J. G. M., E. M. Williams, J. L. Roe, and S. T. Hussain. 2001. Skeletons of terrestrial cetaceans and the relationships of whales to artiodactyls. Nature 413:277-281.
33. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
34. Yang, Z. 1996a. Among-site rate variation and its impact on phylogenetics analysis. Trends Ecol. Evol. 11:367-372.
35. Yang, Z. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.