Statistics and truth in phylogenomics

Molecular Biology and Evolution

Volumn 29, Issue 2, 2012, Pages 457-472

  Kumar, Sudhir ^a,b   Filipski, Alan J ^a   Battistuzzi, Fabia U ^a   Kosakovsky Pond, Sergei L ^c   Tamura, Koichiro ^d  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

evolutionary tree; molecular evolution; phylogenetics; statistical bias; statistical inference; variance

Indexed keywords

ARTICLE; CODON; EFFECT SIZE; GENE DUPLICATION; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS;

ANIMALS; BIOMETRY; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; HUMANS; MODELS, GENETIC; MODELS, THEORETICAL; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; STATISTICS AS TOPIC;

EID: 84862928655     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr202     Document Type: Article

References (206)

1. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387:489-493. (Pubitemid 27235464)
2. Alfaro ME, Zoller S, Lutzoni F. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol. 20:255-266. (Pubitemid 36237384)
3. Ané C. 2011. Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biol Evol. 3:246-258.
4. Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60:685-699.
5. Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol. 26:255-271.
6. Anisimova M, Yang Z. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol. 24:1219-1228. (Pubitemid 47343648)
7. Armstrong JS. 2007. Significance tests harm progress in forecasting. Int J Forecast. 23:321-327.
8. Ballard JW, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol Ecol. 13:729-744. (Pubitemid 38390584)
9. Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF. 2005. Do orthologous gene phylogenies really support treethinking? BMC Evol Biol. 5:33.
10. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. 2001. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 125:279-284. (Pubitemid 33000466)
11. Blair C, Murphy RW. 2011. Recent trends in molecular phylogenetic analysis: where to next? J Hered. 102:130-138.
12. Blanchette M, Kent WJ, Riemer C, et al. (12 co-authors). 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14:708-715. (Pubitemid 38500244)
13. Bleidorn C, Podsiadlowski L, Zhong M, Eeckhaut I, Hartmann S, Halanych KM, Tiedemann R. 2009. On the phylogenetic position of Myzostomida: can 77 genes get it wrong? BMC Evol Biol. 9:150.
14. Bofkin L, Goldman N. 2007. Variation in evolutionary processes at different codon positions. Mol Biol Evol. 24:513-521. (Pubitemid 46204383)
15. Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Mol Biol Evol. 19:1171-1180. (Pubitemid 34743241)
16. Box GEP, Draper NR. 1987. Empirical model-building and response surfaces. New York: Wiley.
17. Brandley MC, Schmitz A, Reeder TW. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol. 54:373-390. (Pubitemid 41040438)
18. Brown JM, Lemmon AR. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst Biol. 56:643-655.
19. Brown JR. 2003. Ancient horizontal gene transfer. Nat Rev Genet. 4:121-132. (Pubitemid 36150684)
20. Buckley TR. 2002. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst Biol. 51:509-523. (Pubitemid 35180701)
21. Castresana J. 2007. Topological variation in single-gene phylogenetic trees. Genome Biol. 8:216.
22. Chamary J, Hurst L. 2005. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 6:R75.
23. Charlebois RL, Doolittle WF. 2004. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14:2469-2477. (Pubitemid 40012230)
24. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287. (Pubitemid 43334717)
25. Comas I, Moya A, Gonzalez-Candelas F. 2007. From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst Biol. 56:1-16.
26. Conant GC, Stadler PF. 2009. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol. 26:1155-1161.
27. Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, Winka K. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol. 52:477-487. (Pubitemid 36990376)
28. Dagan T, Martin W. 2006. The tree of one percent. Genome Biol. 7:118.
29. Davalos LM, Perkins SL. 2008. Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics 91:433-442.
30. Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL. 2010. CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol. 6:e1000885.
31. Delport W, Scheffler K, Seoighe C. 2008. Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS Pathog. 4:e1000242.
32. Delport W, Scheffler K, Seoighe C. 2009. Models of coding sequence evolution. Brief Bioinform. 10:97-109.
33. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375. (Pubitemid 40577180)
34. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
35. Doolittle WF, Zhaxybayeva O. 2009. On the origin of prokaryotic species. Genome Res. 19:744-756.
36. Doron-Faigenboim A, Pupko T. 2007. A combined empirical and mechanistic codon model. Mol Biol Evol. 24:388-397. (Pubitemid 46204372)
37. Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol. 20:248-254. (Pubitemid 36237383)
38. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113.
39. Efron B, Halloran E, Holmes S. 1996. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci U S A. 93:13429-13434. (Pubitemid 126585356)
40. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-167. (Pubitemid 28177226)
41. Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nat Med. 3:1076-1078. (Pubitemid 27444441)
42. Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Paabo S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872. (Pubitemid 34966304)
43. Erixon P, Svennblad B, Britton T, Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol. 52:665-673. (Pubitemid 37365047)
44. Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P. 2010. The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data sets. Mol Biol Evol. 27:2733-2746.
45. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783-791.
46. Felsenstein J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 22:521-565. (Pubitemid 19156673)
47. Fidler F, Burgman MA, Cumming G, Buttrose R, Thomason N. 2006. Impact of criticism of null-hypothesis significance testing on statistical reporting practices in conservation biology. Conserv Biol. 20:1539-1544. (Pubitemid 44436030)
48. Filipski A, Prohaska S, Kumar S. 2007. Molecular signatures of adaptive evolution. In: Pagel M, Pomiankowski A, editors. Evolutionary genomics and proteomics. Sunderland (MA): Sinauer Associates. p. 241-254.
49. Fisher RA. 1925. Statistical methods for research workers. Edinburgh, (UK): Oliver and Boyd.
50. Fleissner R, Metzler D, von Haeseler A. 2005. Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst Biol. 54:548-561. (Pubitemid 41356469)
51. Fletcher W, Yang Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol. 27:2257-2267.
52. Gadagkar SR, Kumar S. 2005. Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol. 22:2139-2141. (Pubitemid 41437794)
53. Gadagkar SR, Rosenberg MS, Kumar S. 2005. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol. 304:64-74. (Pubitemid 40346325)
54. Gaffney DJ, Keightley PD. 2008. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evol Biol. 8:265.
55. Galtier N, Gouy M. 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A. 92:11317-11321.
56. Ge F, Wang LS, Kim J. 2005. The cobweb of life revealed by genomescale estimates of horizontal gene transfer. PLoS Biol. 3:e316.
57. Gelman A, Stern H. 2006. The difference between "significant" and "not significant" is not itself statistically significant. Am Stat. 60:328-331. (Pubitemid 44727242)
58. Genome KCoS. 2009. Genome 10K: a proposal to obtain wholegenome sequence for 10 000 vertebrate species. J Hered. 100:659-674.
59. Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11:725-736.
60. Good IJ. 1992. The Bayes/non-Bayes compromise: a brief review. J Am Stat Assoc. 87:597-606.
61. Gribaldo S, Philippe H. 2002. Ancient phylogenetic relationships. Theor Popul Biol. 61:391-408. (Pubitemid 38051044)
62. Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C. 2010. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol. 8:743-752.
63. Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc Natl Acad Sci U S A. 101:12957-12962. (Pubitemid 39167565)
64. Hallström BM, Janke A. 2010. Mammalian evolution may not be strictly bifurcating. Mol Biol Evol. 27:2804-2816.
65. Hartmann S, Vision TJ. 2008. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol. 8:95.
66. Hassanin A. 2006. Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol Phylogenet Evol. 38:100-116. (Pubitemid 41773277)
67. Hillis D, Bull J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 42:182-192.
68. Holton TA, Pisani D. 2010. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single-and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol. 2:310-324.
69. Hubbard R, Armstrong JS. 2006. Why we don't really know what "statistical significance" means: a major educational failure. J Mark Educ. 28:114-120. (Pubitemid 44018570)
70. Huelsenbeck J, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53:904-913. (Pubitemid 40141314)
71. Huelsenbeck JP, Jain S, Frost SW, Kosakovsky Pond SL. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci U S A. 103:6263-6268.
72. Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. 2007. The human phylome. Genome Biol. 8:R109.
73. Hughes AL, da Silva J, Friedman R. 2001. Ancient genome duplications did not structure the human hox-bearing chromosomes. Genome Res. 11:771-780. (Pubitemid 32447862)
74. Hughes AL, Friedman R. 2008. Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60:495-506.
75. Jimenez-Baranda S, Greenbaum B, Manches O, Handler J, Rabadan R, Levine A, Bhardwaj N. 2011. Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells. J Virol. 85:3893-3904.
76. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
77. Jukes T, Cantor C. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. p. 21-132.
78. Ke S, Zhang XHF, Chasin LA. 2008. Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res. 18:533-543. (Pubitemid 351482778)
79. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
80. Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984. (Pubitemid 39434418)
81. Kolaczkowski B, Thornton JW. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol. 25:1054-1066.
82. Kondrashov FA, Ogurtsov AY, Kondrashov AS. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J Theor Biol. 240:616-626. (Pubitemid 43765944)
83. Koonin EV, Puigbò P, Wolf YI. 2011. Comparison of phylogenetic trees and search for a central trend in the "forest of life". J Comput Biol. 18:917-924.
84. Koonin EV, Wolf YI. 2009. The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct. 4:33.
85. Kosakovsky Pond SL, Frost SD. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208-1222. (Pubitemid 40577758)
86. Kosakovsky Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ. 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2:e62.
87. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SDW, Delport W, Scheffler K. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 28:3033-3043.
88. Kosakovsky Pond SL, Muse SV. 2005. Site-to-site variation of synonymous substitution rates. Mol Biol Evol. 22:2375-2385. (Pubitemid 41661376)
89. Kosakovsky Pond SL, Poon AFY, Leigh Brown AJ, Frost SDW. 2008. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol. 25:1809-1824.
90. Kosakovsky Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD. 2010. Evolutionary fingerprinting of genes. Mol Biol Evol. 27:520-536.
91. Krauss V, Thummler C, Georgi F, Lehmann J, Stadler PF, Eisenhardt C. 2008. Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Mol Biol Evol. 25:821-830.
92. Kuhn RM, Karolchik D, Zweig AS, et al. (22 co-authors). 2009. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37:D755-D761.
93. Kumar S, Filipski A. 2007. Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Res. 17:127-135. (Pubitemid 46220757)
94. Kumar S, Nei M, Dudley J, Tamura K. 2008. MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 9:299-306. (Pubitemid 351890826)
95. Läärä E. 2009. Statistics: reasoning on uncertainty, and the insignificance of testing null. Ann Zool Fennici. 46:138-157.
96. Lake JA, Rivera MC. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol Biol Evol. 21:681-690. (Pubitemid 38452101)
97. Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol. 20:86-93. (Pubitemid 14116237)
98. Lemmon AR, Moriarty EC. 2004. The importance of proper model assumption in bayesian phylogenetics. Syst Biol. 53:265-277. (Pubitemid 38611183)
99. Li J, Zhang Z, Vang S, Yu J, Wong GK, Wang J. 2009. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol. 68:414-423.
100. Lind PA, Berg OG, Andersson DI. 2010. Mutational robustness of ribosomal protein genes. Science 330:825-827.
101. Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7. (Pubitemid 34008041)
102. Löytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632-1635. (Pubitemid 351931252)
103. Lunter G, Miklos I, Drummond A, Jensen J, Hein J. 2005. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 6:83.
104. Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J. 2008. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res. 18:298-309. (Pubitemid 351240740)
105. Mar. JC, Harlow TJ, Ragan MA. 2005. Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. BMC Evol Biol. 5:8.
106. Massingham T, Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753-1762. (Pubitemid 40547480)
107. Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007. Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics 23:i319-i327. (Pubitemid 47244416)
108. Miller W, Rosenbloom K, Hardison RC, et al. 2007. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17:1797-1808. (Pubitemid 351360004)
109. Misawa K, Nei M. 2003. Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol. 57 (Suppl 1): S290-S296. (Pubitemid 37544019)
110. Mossel E. 2003. On the impossibility of reconstructing ancestral data and phylogenies. J Comput Biol. 10:669-676. (Pubitemid 37392972)
111. Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11:715-724. (Pubitemid 24274880)
112. Nakagawa S, Cuthill IC. 2007. Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol Rev Camb Philos Soc. 82:591-605. (Pubitemid 47609922)
113. Nam J, dePamphilis CW, Ma H, Nei M. 2003. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol Biol Evol. 20:1435-1447. (Pubitemid 37082579)
114. Naylor GJ, Brown WM. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst Biol. 47:61-76. (Pubitemid 128449786)
115. Negrisolo E, Kuhl H, Forcato C, Vitulo N, Reinhardt R, Patarnello T, Bargelloni L. 2010. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species. Mol Biol Evol. 27:2757-2774.
116. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
117. Nei M, Suzuki Y, Nozawa M. 2010. The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet. 11:265-289.
118. Nielsen R. 2005. Statistical methods in molecular evolution. New York: Springer.
119. Nielsen R, Bustamante C, Clark AG, et al. (13 co-authors). 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3:e170.
120. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. 2007. Recent and ongoing selection in the human genome. Nat Rev Genet. 8:857-868. (Pubitemid 47609088)
121. Nielsen R, Huelsenbeck JP. 2002. Detecting positively selected amino acid sites using posterior predictive P-values. Pac Symp Biocomput. 7:576-588.
122. Nielsen R, Yang ZH. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936. (Pubitemid 28169008)
123. Nishihara H, Okada N, Hasegawa M. 2007. Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol. 8:R199.
124. Notredame C. 2007. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 3:e123.
125. Novák Á, Miklós I, Lyngsø R, Hein J. 2008. StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics. 24:2403-2404.
126. Nozawa M, Suzuki Y, Nei M. 2009a. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A. 106:6700-6705.
127. Nozawa M, Suzuki Y, Nei M. 2009b. Response to Yang et al: problems with Bayesian methods of detecting positive selection at the DNA sequence level. Proc Natl Acad Sci U S A. 106.: E96.
128. Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL. 2004. Bayesian phylogenetic analysis of combined data. Syst Biol. 53:47-67. (Pubitemid 38370420)
129. Penny D, McComish BJ, Charleston MA, Hendy MD. 2001. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J Mol Evol. 53:711-723. (Pubitemid 32989425)
130. Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
131. Philippe H, Douady CJ. 2003. Horizontal gene transfer and phylogenetics. Curr Opin Microbiol. 6:498-505. (Pubitemid 37345416)
132. Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol. 5:50.
133. Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol. 24:1752-1760. (Pubitemid 47236695)
134. Pool JE, Hellmann I, Jensen JD, Nielsen R. 2010. Population genetic inference from genomic sequence variation. Genome Res. 20:291-300.
135. Porter TM. 2008. Signifying little. Science 320:1292.
136. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253-1256. (Pubitemid 351882013)
137. Prasad AB, Allard MW, Green ED. 2008. Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol. 25:1795-1808.
138. Pupko T, Galtier N. 2002. A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc R Soc Lond B Biol Sci. 269:1313-1316. (Pubitemid 34753662)
139. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238. (Pubitemid 27249927)
140. Rannala B, Yang Z. 2008. Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet. 9:217-231.
141. Rao CR. 1989. Statistics and truth: putting chance to work. New Delhi (India): Council of Scientific & Industrial Research.
142. Rasmussen MD, Kellis M. 2010. A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol. 28:273-290.
143. Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT. 2010. Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc B Biol Sci. 365:2571-2580.
144. Redelings BD, Suchard MA. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst Biol. 54:401-418. (Pubitemid 41040440)
145. Resch AM, Carmel L, Marino-Ramirez L, Ogurtsov AY, Shabalina SA, Rogozin IB, Koonin EV. 2007. Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol. 24:1821-1831. (Pubitemid 47236700)
146. Ripplinger J, Sullivan J. 2010. Assessment of substitution model adequacy using frequentist and Bayesian methods. Mol Biol Evol. 27:2790-2803.
147. Rodrigue N, Philippe H, Lartillot N. 2010. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci U S A. 107:4629-4634.
148. Rokas A, Chatzimanolis S. 2008. From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain. Methods Mol Biol. 422:1-12.
149. Rokas A, King N, Finnerty J, Carroll SB. 2003. Conflicting phylogenetic signals at the base of the metazoan tree. Evol Dev. 5:346-359. (Pubitemid 36893144)
150. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804. (Pubitemid 37355944)
151. Ronquist F, Deans AR. 2009. Bayesian phylogenetics and its influence on insect systematics. Annu Rev Entomol. 55:189-206.
152. Rosenberg MS. 2009. Sequence alignment: methods, models, concepts, and strategies. Berkeley (CA): University of California Press.
153. Rzhetsky A, Nei M. 1993. Theoretical foundation of the minimumevolution method of phylogenetic inference. Mol Biol Evol. 10:1073-1095. (Pubitemid 23260614)
154. Saitou N, Nei M. 1987. The neighbor-joining method-a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
155. Sawyer SL, Emerman M, Malik HS. 2004. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2:E275.
156. Seo TK. 2008. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol Biol Evol. 25:960-971.
157. Seoighe C, Ketwaroo F, Pillay V, et al. (11 co-authors). 2007. A model of directional selection applied to the evolution of drug resistance in HIV-1. Mol Biol Evol. 24:1025-1031. (Pubitemid 46536713)
158. Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of proteincoding sequences. Mol Biol Evol. 23:7-9. (Pubitemid 41785947)
159. Shedlock AM, Takahashi K, Okada N. 2004. SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol. 19:545-553. (Pubitemid 39234761)
160. Shoemaker JS, Fitch WM. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol. 6:270-289.
161. Soltis DE, Albert VA, Savolainen V, et al. (11 co-authors). 2004. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 9:477-483. (Pubitemid 39301185)
162. Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF. 2010. When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol. 35:429-448.
163. Springer MS, DeBry RW, Douady C, Amrine HM, Madsen O, de Jong WW, Stanhope MJ. 2001. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol Biol Evol. 18:132-143. (Pubitemid 32118858)
164. Springer MS, Stanhope MJ, Madsen O, de Jong WW. 2004. Molecules consolidate the placental mammal tree. Trends Ecol Evol. 19:430-438. (Pubitemid 38991669)
165. Strimmer K. 2008. A unified approach to false discovery rate estimation. BMC Bioinformatics 9:303.
166. Subramanian S, Kumar S. 2003. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13:838-844. (Pubitemid 36621744)
167. Subramanian S, Kumar S. 2006. Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol. 23:2283-2287. (Pubitemid 44737122)
168. Susko E. 2008. On the distributions of bootstrap support and posterior distributions for a star tree. Syst Biol. 57:602-612.
169. Suzuki Y, Glazko GV, Nei M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A. 99:16138-16143. (Pubitemid 35462762)
170. Suzuki Y, Gojobori T. 1999. A method for detecting positive selection at single amino acid sites. Mol Biol Evol. 16:1315-1328. (Pubitemid 29473226)
171. Suzuki Y, Gojobori T, Kumar S. 2009. Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Mol Biol Evol. 26:2275-2284.
172. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. Sunderland (MA): Sinauer Associates. p. 407-514.
173. Takezaki N, Gojobori T. 1999. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol Biol Evol. 16:590-601. (Pubitemid 29215371)
174. Tamura K, Kumar S. 2002. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol. 19:1727-1736.
175. Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 101:11030-11035. (Pubitemid 38989579)
176. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
177. Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21:36-44. (Pubitemid 38233516)
178. Tavare S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. In: Robert M. Miura, editor. Lectures in mathematics in the life sciences. Providence (RI): American Mathematical Society. p. 57-86.
179. Telford MJ, Bourlat SJ, Economou A, Papillon D, Rota-Stabelli O. 2008. The evolution of the Ecdysozoa. Philos Trans R Soc Lond B Biol Sci. 363:1529-1537. (Pubitemid 351363977)
180. Venkatesh B, Erdmann MV, Brenner S. 2001. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc Natl Acad Sci U S A. 98:11382-11387. (Pubitemid 32928737)
181. Vos M. 2011. A species concept for bacteria based on adaptive divergence. Trends Microbiol. 19:1-7.
182. Waddell PJ, Kishino H, Ota R. 2002. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome Inform. 13:82-92.
183. Wahlberg N, Weingartner E, Warren A, Nylin S. 2009. Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini). BMC Evol Biol. 9:92.
184. White WT, Hills SF, Gaddam R, Holland BR, Penny D. 2007. Treeness triangles: visualizing the loss of phylogenetic signal. Mol Biol Evol. 24:2029-2039.
185. Wiens JJ. 2006. Missing data and the design of phylogenetic analyses. J Biomed Inform. 39:34-42. (Pubitemid 43138915)
186. Wildman DE, Uddin M, Opazo JC, Liu G, Lefort V, Guindon S, Gascuel O, Grossman LI, Romero R, Goodman M. 2007. Genomics, biogeography, and the
187. Wong WSW, Yang Z, Goldman N, Nielsen R. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051. (Pubitemid 39491478)
188. Wrobel B. 2008. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J Appl Genet. 49:49-67. (Pubitemid 351272301)
189. Wyckoff GJ, Malcom CM, Vallender EJ, Lahn BT. 2005. A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet. 21:381-385. (Pubitemid 40835722)
190. Xia X. 2006. Topological bias in distance-based phylogenetic methods: problems with over-and underestimated genetic distances. Evol Bioinform Online. 2:377-389.
191. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 11:367-372. (Pubitemid 126381530)
192. Yang Z. 2005. Bayesian inference in molecular phylogenetics. In: Gascuel O, editor. Mathematics of evolution and phylogeny. Oxford: Oxford University Press. p. 63-90.
193. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
194. Yang Z. 2008. Empirical evaluation of a prior for Bayesian phylogenetic inference. Philos Trans R Soc B Biol Sci. 363:4031-4039.
195. Yang Z, dos Reis M. 2011. Statistical properties of the branch-site test of positive selection. Mol Biol Evol. 28:1217-1228.
196. Yang Z, Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol. 25:568-579. (Pubitemid 351301912)
197. Yang Z, Nielsen R, Goldman N. 2009. In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A. 106:E95; author reply E96.
198. Yang Z, Rannala B. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst Biol. 54:455-470. (Pubitemid 41040444)
199. Yang Z, Wong WSW, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22:1107-1118. (Pubitemid 40471423)
200. Yokoyama S, Tada T, Zhang H, Britt L. 2008. Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A. 105:13480-13485.
201. Zardoya R, Suarez M. 2008. Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals. Methods Mol Biol. 422:185-200.
202. Zhang J, Nei M. 1996. Evolution of Antennapedia-class homeobox genes. Genetics 142:295-303.
203. Zhang J, Rosenberg HF, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A. 95:3708-3713. (Pubitemid 28173193)
204. Zhou T, Gu W, Wilke CO. 2010. Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol. 27:1912-1922.
205. Ziliak ST, McCloskey DN. 2008. The cult of statistical significance: how the standard error costs us jobs, justice, and lives. Ann Arbor (MI): University of Michigan Press.
206. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press. p. 97-166.