On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence

Biology Direct

Volumn 6, Issue , 2011, Pages

  Theobald, Douglas L ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BAYES THEOREM; BIOGENESIS; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BAYES THEOREM; BIOGENESIS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; PHYLOGENY;

EID: 82055175876     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-60     Document Type: Article

References (132)

1. Theobald DL. A formal test of the theory of universal common ancestry. Nature 2010, 465(7295):219-22. 10.1038/nature09014, 20463738.
2. Koonin EV, Wolf YI. The common ancestry of life. Biol Direct 2010, 5:64. 10.1186/1745-6150-5-64, 2993666, 21087490.
3. Darwin C. On the origin of the species by means of natural selection, or, The preservation of favoured races in the struggle for life. 1859, London: J. Murray.
4. Dobzhansky T. Nothing in biology makes sense except in the light of evolution. Am Biol Teach 1973, 35(3):125-129.
5. Freeman S, Herron JC. Evolutionary analysis. 2007, Upper Saddle River, NJ: Pearson Prentice Hall.
6. Futuyma DJ. Evolutionary biology. 1998, Sunderland, Mass: Sinauer Associates.
7. Penny D, Foulds LR, Hendy MD. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 1982, 297(5863):197-200. 10.1038/297197a0, 7078635.
8. Penny D, Hendy MD, Steel MA. Testing the theory of descent. Phylogenetic analysis of DNA sequences 1991, 155-183. New York: Oxford University Press, Miyamoto MM, Cracraft J.
9. Penny D, Hendy MD, Poole AM. Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 2003, 223(3):377-385. 10.1016/S0022-5193(03)00099-7, 12850457.
10. Ridley M. Evolution. 2003, Wiley-Blackwell.
11. Sober E, Steel M. Testing the hypothesis of common ancestry. Journal of Theoretical Biology 2002, 218(4):395-408.
12. Sober E. Evidence and Evolution. 2008, Cambridge University Press.
13. Theobald DL. 29+ Evidences for Macroevolution: The Scientific Case for Common Descent. The Talk Origins Archive 2009,
14. Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. Evolving genes and proteins 1965, 97-166. New York: Academic Press, Bryson V, Vogel HJ.
15. Doolittle WF. The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them. Philos Trans R Soc Lond B Biol Sci 2009, 364(1527):2221-8. 10.1098/rstb.2009.0032, 2873000, 19571242.
16. Syvanen M. On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes. J Mol Evol 2002, 54(2):258-266. 10.1007/s0023901-0007-z, 11821918.
17. Venter C. Chapter 3: J. CRAIG VENTER. Life: What a Concept! 2008, New York, NY: Edge Foundation, Brockman J, Edge.
18. Woese CR. On the evolution of cells. 2002, 99(13):8742-8747. Proceedings of the National Academy of Sciences of the United States of America.
19. Doolittle WF, Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 2007, 104(7):2043-9. 10.1073/pnas.0610699104, 1892968, 17261804.
20. Crick F. The recent excitement in the coding problem. Progress in Nucleic Acids Research 1963, 1:163-217.
21. Hinegardner R, Engelberg J. Rationale for a universal genetic code. Science 1963, 142:1083-1085. 10.1126/science.142.3595.1083, 14068231.
22. Hinegardner R, Engelberg J. Universality in the genetic code. Science 1964, 144:1030-1031. 10.1126/science.144.3621.1030, 14137944.
23. Woese CR. Universality in the genetic code. Science 1964, 144:1030-1. 10.1126/science.144.3621.1030, 14137944.
24. Crick F. The origin of the genetic code. Journal of Molecular Biology 1968, 38:367-379. 10.1016/0022-2836(68)90392-6, 4887876.
25. Koonin EV, Novozhilov AS. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 2009, 61(2):99-111. 10.1002/iub.146, 3293468, 19117371.
26. Woese CR. The genetic code: the molecular basis for genetic expression. 1967, New York: Harper and Row.
27. Knight RD, Freeland SJ, Landweber LF. Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2001, 2:49-58. 10.1038/35047500, 11253070.
28. Yarus M, Caporaso JG, Knight R. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 2005, 74:179-98. 10.1146/annurev.biochem.74.082803.133119, 15952885.
29. Yarus M, Widmann JJ, Knight R. RNA-amino acid binding: a stereochemical era for the genetic code. J Mol Evol 2009, 69(5):406-29. 10.1007/s00239-009-9270-1, 19795157.
30. Syvanen M. Recent emergence of the modern genetic code: A proposal. Trends in Genetics 2002, 18(5):245-248. 10.1016/S0168-9525(02)02647-1, 12047948.
31. Felsenstein J. Inferring phylogenies. 2004, Sunderland, Mass: Sinauer Associates.
32. Doolittle RF. Similar amino acid sequences: Chance or common ancestry?. Science 1981, 214(4517):149-59. 10.1126/science.7280687, 7280687.
33. Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99-113. 10.2307/2412448, 5449325.
34. Ghiselin M. The distinction between similarity and homology. Systematic Biology 1969, 18:148.
35. Hillis DM. Homology in Molecular Biology. Homology: The hierarchical basis of comparative biology 1994, San Diego: Academic Press, Hall BK.
36. Lewin R. When does homology mean something else?. Science 1987, 237(4822):1570. 10.1126/science.3629257, 3629257.
37. Mindell D, Meyer A. Homology evolving. Trends in Ecology & Evolution 2001, 16(8):434-440. 10.1016/S0169-5347(01)02206-6, 22220863.
38. Molecular Biology and Evolution Instructions to Authors. 2011, Molecular Biology and Evolution., http://www.oxfordjournals.org/our journals/molbev/for authors/msprep submission.html
39. Patterson C. Homology in classical and molecular biology. Mol Biol Evol 1988, 5(6):603-25.
40. Reeck GR, de Haen C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE, Chambon P, McLachlan AD, Margoliash E, Jukes TH. "Homology" in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 1987, 50(5):667. 10.1016/0092-8674(87)90322-9, 3621342.
41. Altschul S, Gish W. Local alignment statistics. Methods Enzymol 1996, 266:460-80.
42. Karlin S, Altschul S. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 1990, 87(6):2264-8. 10.1073/pnas.87.6.2264, 53667, 2315319.
43. Karlin S, Dembo A, Kawabata T. Statistical composition of high-scoring segments from molecular sequences. The Annals of Statistics 1990, 18(2):571-581.
44. Bakan D. The test of significance in psychological research. Psychol Bull 1966, 66(6):423-37.
45. Berger J, Sellke T. Testing a point null hypothesis: The irreconcilability of P-values and evidence. Journal Of The American Statistical Association 1987, 82(397):112-122.
46. Berkson J. Tests of significance considered as evidence. Journal of the American Statistical Association 1942, 37:325-335.
47. Burnham KP, Anderson DR. Model selection and inference: A practical information-theoretic approach. 1998, New York: Springer.
48. Carver RP. Case against statistical significance testing. Harvard Educational Review 1978, 48(3):378-399.
49. Chow S, Blaich C, Boklage C, Bookstein F, Dar R, Erwin E, Frick R, Gigerenzer G, Gluck J, Vitouch O, . Others Precis of statistical significance: Rationale, validity, and utility. Commentaries. Behavioral and brain sciences 1998, 21(2):169-239. Author's reply, Others.
50. Cohen J. The earth is round (P <:05). American Psychologist 1994, 49(12):997-1003.
51. Gelman A. Bayesian data analysis. 2004, Boca Raton, Fla: Chapman and Hall/CRC, 2.
52. Gigerenzer G. Mindless statistics. Journal of Socio-Economics 2004, 33(5):587-606.
53. Gill J. The insignificance of null hypothesis significance testing. Political Research Quarterly 1999, 52(3):647-674.
54. Gill J. Grappling with Fisher's legacy in social science hypothesis testing: Some comments on Denis. Journal de la Societe Francaise de Statistique 2004, 145(4):1-9.
55. Goodman SN. Toward evidence-based medical statistics. 1: The P value fallacy. Ann Intern Med 1999, 130(12):995-1004.
56. Greenwald A. Consequences of prejudice against the null hypothesis. Psychological Bulletin 1975, 82:1-20.
57. Harlow LL, Mulaik SA, Steiger JH. What If There Were No Significance Tests?. Lawrence Erlbaum 1997,
58. Howson C, Urbach P. Scientific reasoning: The Bayesian approach. 2005, Chicago: Open Court, 3.
59. Hunter J. Needed: A ban on the significance test. Psychological Science 1997, 8(1):3-7.
60. Jaynes ET, Bretthorst GL. Probability theory: The logic of science. 2003, Cambridge, UK: Cambridge UniversityPress.
61. Jeffreys H. Theory of probability. 1961, The International series of monographs on physics, Oxford: Clarendon Press, 3.
62. Loftus G. On the tyranny of hypothesis testing in the social sciences. Contemporary Psychology 1991, 36:102-105.
63. Meehl P. Theoretical risks and tabular asterisks: Sir Karl, Sir Ronald, and the slow progress of soft psychology. Journal of Consulting and Clinical Psychology 1978, 46:806-834.
64. Morrison DE, Henkel RE, . Eds The Significance Test Controversy: A Reader. 1970, Methodological perspectives, London: Butterworths, Eds.
65. Royall R. Statistical evidence: A Likelihood Paradigm. of Monographs on Statistics and Applied Probability 1997, 71. Chapman and Hall, London New York.
66. Rozeboom WW. The fallacy of the null-hypothesis significance test. Psychol Bull 1960, 57:416-28.
67. Schmidt F. Statistical significance testing and cumulative knowledge in psychology: Implications for training of researchers. Psychological methods 1996, 1(2):115.
68. Serlin R, Lapsley D. Rational appraisal of psychological research and the good-enough principle. A handbook for data analysis in the behavioral sciences: Methodological issues 1993, 199-228.
69. Wacholder S, Chanock S, Garcia-Closas M, El Ghormli L, Rothman N. Assessing the probability that a positive report is false: An approach for molecular epidemiology studies. J Natl Cancer Inst 2004, 96(6):434-42. 10.1093/jnci/djh075, 15026468.
70. Wagenmakers EJ. A practical solution to the pervasive problems of p values. Psychon Bull Rev 2007, 14(5):779-804. 10.3758/BF03194105, 18087943.
71. Ziliak ST, McCloskey DN. The cult of statistical significance: How the standard error costs us jobs, justice, and lives. 2008, Ann Arbor: University of Michigan Press.
72. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-10.
73. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89(22):10915-9. 10.1073/pnas.89.22.10915, 50453, 1438297.
74. Fisher RA. Statistical methods for research workers. 1925, Edinburgh: Oliver and Boyd.
75. Henkel RE. Tests of significance. A Sage university paper: Quantitative applications in the social sciences; ser. no. 07-004 1976, Beverly Hills, Calif: Sage Publications.
76. Lehmann EL, Romano JP. Testing statistical hypotheses. 2005, New York: Springer, 3.
77. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-402. 10.1093/nar/25.17.3389, 146917, 9254694.
78. Gilkey L. Creationism on trial: Evolution and God at Little Rock. 1998, Studies in religion and culture, Charlottesville, Va: University Press of Virginia, 1.
79. Fisher RA. The design of experiments. 1937, Edinburgh: Oliver and Boyd, 2.
80. Fisher RA. The design of experiments. 1966, Edinburgh: London Oliver & Boyd, 8.
81. Keren G, Lewis C. A Handbook for data analysis in the behavioral sciences: Methodological issues. 1993, Hillsdale, N.J: L. Erlbaum Associates.
82. Leung W. The prosecutor's fallacy: A pitfall in interpreting probabilities in forensic evidence. Medicine, science, and the law 2002, 42:44.
83. Thompson W, Schumann E. Interpretation of statistical evidence in criminal trials. Law and Human Behavior 1987, 11(3):167-187.
84. Bureau of Health Information, Statistics, Research, and Evaluation Division of Research and Epidemiology Massachusetts Births. 2008, Tech. rep., Commonwealth of Massachusetts Department of Public Health, Bureau of Health Information, Statistics, Research, and Evaluation Division of Research and Epidemiology., http://www.mass.gov/eohhs/docs/dph/research-epi/birth-report-2009.pdf
85. Abascal F, Zardoya R, Posada D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 2005, 21(9):2104-2105. 10.1093/bioinformatics/bti263, 15647292.
86. Beaumont MA, Rannala B. The Bayesian revolution in genetics. Nat Rev Genet 2004, 5(4):251-61.
87. Bollback JP. Bayesian model adequacy and choice in phylogenetics. Mol Biol Evol 2002, 19(7):1171-80. 10.1093/oxfordjournals.molbev.a004175, 12082136.
88. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001, 294(5550):2310-4. 10.1126/science.1065889, 11743192.
89. Johnson JB, Omland KS. Model selection in ecology and evolution. Trends Ecol Evol 2004, 19(2):101-8. 10.1016/j.tree.2003.10.013, 16701236.
90. Posada D, Crandall KA. MODELTEST: Testing the model of DNA substitution. Bioinformatics 1998, 14(9):817-8. 10.1093/bioinformatics/14.9.817, 9918953.
91. Posada D, Buckley TR. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 2004, 53(5):793-808. 10.1080/10635150490522304, 15545256.
92. Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 2001, 18(6):1001-13. 10.1093/oxfordjournals.molbev.a003872, 11371589.
93. Sullivan J, Joyce P. Model selection in phylogenetics. Annual Review of Ecology, Evolution, and Systematics 2005, 36:445.
94. Vuong QH. Likelihood ratio tests for model selection and non-nested hypotheses. Econometrica 1989, 57(2):307-333.
95. Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24(8):1586-91. 10.1093/molbev/msm088, 17483113.
96. Bishop CM. Pattern recognition and machine learning. 2006, Springer, New York.
97. Johnson NL, Kotz S, Balakrishnan N. Discrete multivariate distributions. 1997, Wiley, New York.
98. Bruno WJ. Modeling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evol 1996, 13(10):1368-74.
99. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: Detection of distantly related proteins. Proc Natl Acad Sci USA 1987, 84(13):4355-8. 10.1073/pnas.84.13.4355, 305087, 3474607.
100. Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004, 21(6):1095-109. 10.1093/molbev/msh112, 15014145.
101. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981, 17(6):368-76. 10.1007/BF01734359, 7288891.
102. Li WH. Molecular evolution. 1997, Sunderland, Mass: Sinauer Associates.
103. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. Universal trees based on large combined protein sequence data sets. Nature Genetics 2001, 28(3):281-285. 10.1038/90129, 11431701.
104. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311(5765):1283-7. 10.1126/science.1123061, 16513982.
105. Hurvich CM, Tsai CL. Model selection for extended quasi-likelihood models in small samples. Biometrics 1995, 51(3):1077-84. 10.2307/2533006, 7548692.
106. Kass RE, Raftery AE. Bayes factors. Journal of the American Statistical Association 1995, 90(430):773-795.
107. Halpern AL, Bruno WJ. Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies. Mol Biol Evol 1998, 15(7):910-7.
108. Quang LS, Gascuel O, Lartillot N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 2008, 24(20):2317-23. 10.1093/bioinformatics/btn445, 18718941.
109. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18(5):691-9. 10.1093/oxfordjournals.molbev.a003851, 11319253.
110. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25(7):1307-20. 10.1093/molbev/msn067, 18367465.
111. Atchley WR, Zhao J, Fernandes AD, Druke T. Solving the protein sequence metric problem. Proc Natl Acad Sci USA 2005, 102(18):6395-400. 10.1073/pnas.0408677102, 1088356, 15851683.
112. Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249(4968):505-10. 10.1126/science.2200121, 2200121.
113. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 2003, 20(9):1377-419. 10.1093/molbev/msg140, 12777501.
114. Cheng H, Kim BH, Grishin NV. MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res 2008, (36 Database):D211-7.
115. Krishna SS, Grishin NV. Structurally analogous proteins do exist!. Structure 2004, 12(7):1125-7. 10.1016/j.str.2004.06.004, 15242587.
116. Yonezawa T, Hasegawa M. Was the universal common ancestry proved?. Nature 2010, 468(7326):E19.
117. Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 2006, 22(16):2047-8. 10.1093/bioinformatics/btl175, 16679334.
118. Ronquist F. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574. 10.1093/bioinformatics/btg180, 12912839.
119. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
120. Theobald DL. Was the universal common ancestry proved? Reply. Nature 2010, 468(7326):E10.
121. Altekar G. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 2004, 20(3):407-415. 10.1093/bioinformatics/btg427, 14960467.
122. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.69. , http://evolution.genetics.washington.edu/phylip.html
123. Armitage P, Berry G, Matthews JNS. Statistical methods in medical research. 2001, Malden, MA: Blackwell Science, 4.
124. Kalbeisch J, Sprott D. On Tests of Significance. Foundations of Probability Theory, Statistical Inference, and Statistical Theories of Science 1976, 2. Harper W, Hooker C, Reidel D.
125. Box GEP, Draper NR. Empirical model-building and response surfaces. 1987, New York: Wiley.
126. Galperin MY, Walker DR, Koonin EV. Analogous enzymes: independent inventions in enzyme evolution. Genome Res 1998, 8(8):779-90.
127. Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJE. Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol 2007, 372(3):817-45. 10.1016/j.jmb.2007.06.017, 17681532.
128. Omelchenko MV, Galperin MY, Wolf YI, Koonin EV. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct 2010, 5:31. 10.1186/1745-6150-5-31, 2876114, 20433725.
129. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008, (36 Database):D419-25.
130. Cheng H, Kim BH, Grishin NV. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol 2008, 377(4):1265-78. 10.1016/j.jmb.2007.12.076, 18313074.
131. Cheng H, Kim BH, Grishin NV. MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs. Proteins 2008, 70(4):1162-6.
132. Doolittle RF. Convergent evolution: the need to be explicit. Trends Biochem Sci 1994, 19:15-8. 10.1016/0968-0004(94)90167-8, 8140615.