Reanalysis of Murphy et al.'s Data Gives Various Mammalian Phylogenies and Suggests Overcredibility of Bayesian Trees

Journal of Molecular Evolution

Volumn 57, Issue SUPPL. 1, 2003, Pages

  Misawa, Kazuharu ^a   Nei, Masatoshi ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Bayesian method; Credibility value; Mammalian phylogeny

Indexed keywords

DNA;

BAYES THEOREM; CONFERENCE PAPER; DNA SEQUENCE; HUMAN; MAMMAL; MAXIMUM LIKELIHOOD METHOD; MODEL; NONHUMAN; PHYLOGENY; PROBABILITY;

ANIMALS; BAYES THEOREM; MAMMALS; MARSUPIALIA; MODELS, GENETIC; NUCLEAR PROTEINS; PHYLOGENY;

MAMMALIA; RODENTIA;

EID: 0344243515     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-0039-7     Document Type: Conference Paper

References (21)

1. Adachi J, Hasegawa M (1996) MOLPHY: Programs for molecular phylogenetics, version 23. Institute of Statistical Mathematics, Tokyo
2. Arnason U, Adegoke JA, Bodin K, Born EW, Esa YB, Gullberg A, Nilsson M, Short RV, Xu X, Janke A (2002) Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci USA 99:8151-8156
3. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755
4. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
5. Misawa K, Janke A (2003) Revisiting the Glires concept -phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol 28(2):320-327
6. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351
7. Nei M (1996) Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet 30:371-403
8. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
9. Nei M, Glazko GV (2002) Estimation of divergence times for a few mammalian and several primate species. J Hered 93:157-164
10. Poux C, van Rheede T, Madsen O, de Jong WW (2002) Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol Biol Evol 19:2035-2037
11. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
12. Schable KF, Zachau HG (1993) The variable genes of the human immunoglobulin kappa locus. Biol Chem Hoppe Seyler 374:1001-1022
13. Soodyall H, Vigilant L, Hill AV, Stoneking M, Jenkins T (1996) mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans. Am J Hum Genet 58:595-608
14. Su C, Nguyen VK, Nei M (2002) Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids. Mol Biol Evol 19:205-215
15. Sullivan J, Swofford DL (2001) Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst Biol 50:723-729
16. Suzuki Y, Glazko GV, Nei M (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci USA 99:16138-16143
17. Swofford DL (1998) PAUP*, pylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, MA
18. Takahashi K, Nei M (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
19. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
20. Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11:261-277
21. Yang Z (1997) How often do wrong models produce better phytogenies? Mol Biol Evol 14:105-108