What's in a likelihood? simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

Systematic Biology

Volumn 60, Issue 2, 2011, Pages 161-174

  Lakner, Clemens ^a,b   Holder, Mark T ^c   Goldman, Nick ^d   Naylor, Gavin J P ^b  

^a Section of Ecology and Evolution   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF KANSAS   (United States)

^d EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; GENETICS; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY; PROBABILITY; STATISTICAL MODEL;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PROBABILITY; PROTEINS;

EID: 79951566879     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq088     Document Type: Article

References (60)

1. Adachi J., Hasegawa M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Biol. 42(4): 459-468. (Pubitemid 26154323)
2. Bastolla U., Farwer J., Knapp E.W., Vendruscolo M.H. 2001. How to guarantee optimal stability for most representative structures in the protein data bank. Proteins. 44(2):79-96.
3. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. 2000. The protein data bank. Nucleic Acids Res. 28(1):235-242. (Pubitemid 30047768)
4. Bishop M.J., Friday A.E. 1987. Tetrapod relationships: the molecular evidence. In: Patterson C., editor. Molecules and morphology in evolution: confict or compromise? Cambridge, UK: Cambridge University Press. p. 123-140.
5. Bowie J.U., Lüthy R., Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253(5016):164-170. (Pubitemid 21917131)
6. Cao Y., Janke A., Waddell P.J., Westerman M., Takenaka O., Murata S., Okada N., Pääbo S., Hasegawa M. 1998. Confict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47(3):307-322. (Pubitemid 28455148)
7. Chang B.S.W., Jönsson K., Kazmi M.A., Donoghue M.J., Sakmar T.P. 2002. Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19(9):1483-1489. (Pubitemid 36752773)
8. Chiu T.L., Goldstein R.A. 1998. Optimizing potentials for the inverse protein folding problem. Protein Eng. 11(9):749-752. (Pubitemid 28434483)
9. Choi S.C., Redelings B.D., Thorne J.L. 2008. Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. Philos. Trans. R Soc. Lond., B. Biol. Sci. 363(1512):3931-3939.
10. Collins T., Wimberger P., Naylor G.J.P. 1994. Compositional bias, character state bias, and character state reconstruction using parsimony. Syst. Biol. 43(4):482-496. (Pubitemid 24987230)
11. Das R., Baker D. 2008. Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 77:363-382.
12. Dayhoff M.O., Schwartz R.M., Orcutt B.C. 1978. A model for evolutionary change in proteins. In: Dayhoff, M.O., editor. Atlas of protein sequence and structure. Washington (DC): National Biomedical Research Foundation, p. 5:345-352.
13. Henikoff S., Henikoff J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89(22): 10915-10919.
14. Hillis D.M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
15. Hillis D.M., Pollock D., McGuire J., Zwickl D. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126. (Pubitemid 36300065)
16. Huelsenbeck J.P., Joyce P., Lakner C., Ronquist F. 2008. Bayesian analysis of amino acid substitution models. Phil. Trans. R Soc. B. 363:3941-3953.
17. Jensen J.L., Pedersen A.M.K. 2000. Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv. Appl. Prob. 32:499-517.
18. Jones D.T. 1998. THREADER: protein sequence threading by double dynamic programming. In: Salzberg, S., Searls D., Kasif S., editors. Computational methods in molecular biology. Chapter 13. Amsterdam (The Netherlands): Elsevier Science, p. 285-312.
19. Jones D.T. 1999. GenTHREADER: an effcient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287(4):797-815. (Pubitemid 29176514)
20. Jones D.T., Taylor W.R., Thornton J.M. 1992a. A new approach to protein fold recognition. Nature. 358(6381):86-89.
21. Jones D.T., Taylor W.R., Thornton J.M. 1992b. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8(3):275-282.
22. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor. Mammalian protein metabolism. New York: Academic Press. p. 21-123.
23. Kim D.E., Chivian D., Baker D. 2004. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32(Web Server issue):W526-W531. (Pubitemid 38997389)
24. Koehl P., Levitt M. 1999a. De novo protein design. I. In search of stability and specifcity. J. Mol. Biol. 293(5):1161-1181.
25. Koehl P., Levitt M. 1999b. De novo protein design. II. Plasticity in sequence space. J. Mol. Biol. 293(5):1183-1193.
26. Koshi J.M., Goldstein R.A. 1998. Models of natural mutations including site heterogeneity. Proteins. 32(3):289-295. (Pubitemid 28360825)
27. Koshi J.M., Mindell D.P., Goldstein R.A. 1997. Beyond mutation matrices: physical-chemistry based evolutionary models. Genome. Inform. Ser. Workshop Genome. Inform. 8:80-89.
28. Krishnan N.M., Seligmann H., Stewart C.-B., de Koning A.P.J., Pollock D.D. 2004. Ancestral sequence reconstruction in primate mitochon-drial DNA: compositional bias and effect on functional inference. Mol. Biol. Evol. 21(10):1871-1883. (Pubitemid 39331634)
29. Le S.Q., Gascuel O. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25(7):1307-1320. (Pubitemid 351882003)
30. Le S.Q., Gascuel O. 2010. Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly benefcial. Syst. Biol. 59(3):277-287.
31. Lio P., Goldman N. 1999. Using protein structural information in evolutionary inference: transmembrane proteins. Mol. Biol. Evol. 16(12):1696-1710.
32. Lio P., Goldman N., Jones D.T. 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics. 14(8):726-733. (Pubitemid 28504998)
33. Mateiu L., Rannala B. 2006. Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Syst. Biol. 55(2):259-269.
34. Meller J., Elber R. 2001. Linear programming optimization and a double statistical flter for protein threading protocols. Proteins. 45(3):241-261. (Pubitemid 32988586)
35. Misura K.M.S., Baker D. 2005. Progress and challenges in high-resolution refnement of protein structure models. Proteins. 59(1): 15-29. (Pubitemid 40316474)
36. Nielsen R. 2001. Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics. 159(1):401-411. (Pubitemid 32917387)
37. Pedersen A.M.K., Jensen J.L. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol. 18(5):763-776. (Pubitemid 32372947)
38. Pollock D., Taylor W.R., Goldman N. 1999. Coevolving protein residues: maximum likelihood identifcation and relationship to structure. J. Mol. Biol. 287(1):187-198. (Pubitemid 29134806)
39. Pollock D., Zwickl D., McGuire J., Hillis D.M. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51(4):664-671. (Pubitemid 35180695)
40. Pollock D.D., Chang B.S.W. 2007. Dealing with uncertainty in ancestral reconstruction: sampling from the posterior distribution. In: Liberles D.A., editor. Ancestral sequence reconstruction. Chapter 8. Oxford: Oxford University Press. p. 85-94.
41. Pollock D.D., Taylor W.R. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10(6):647-657. (Pubitemid 27332071)
42. Rivas E., Eddy S.R. 2008. Probabilistic phylogenetic inference with insertions and deletions. PLoS Comput. Biol. 4(9):e1000172.
43. Robinson D., Jones D.T., Kishino H., Goldman N., Thorne J.L. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20(10):1692-1704. (Pubitemid 41070832)
44. Rodrigue N., Lartillot N., Bryant D., Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene. 347(2):207-217. (Pubitemid 40403760)
45. Rodrigue N., Philippe H., Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol. Biol. Evol. 23(9):1762-1775. (Pubitemid 44309770)
46. Rodrigue N., Philippe H., Lartillot N. 2007. Exploring fast computational strategies for probabilistic phylogenetic analysis. Syst. Biol. 56(5):711-726. (Pubitemid 47402905)
47. Rodrigue N., Philippe H., Lartillot N. 2008. Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. Bioinformatics. 24(1):56-62.
48. Rohl C.A., Strauss C.E.M., Misura K.M.S., Baker D. 2004. Protein structure prediction using Rosetta. Meth. Enzymol. 383:66-93. (Pubitemid 38401787)
49. Sanderson M.J., Donoghue M.J., Piel W., Eriksson T. 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am. J. Bot. 81(6): 183.
50. Simons K.T., Kooperberg C., Huang E., Baker D. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268(1):209-225. (Pubitemid 27192690)
51. Thorne J.L. 2007. Protein evolution constraints and model-based techniques to study them. Curr. Opin. Struct. Biol. 17(3):337-341. (Pubitemid 47021360)
52. Wang Z.O., Pollock D.D. 2005. Context dependence and coevolution among amino acid residues in proteins. Meth. Enzymol. 395:779-790. (Pubitemid 40754397)
53. Whelan S., Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18(5):691-699. (Pubitemid 32372940)
54. Williams P.D., Pollock D.D., Blackburne B.P., Goldstein R.A. 2006. Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput. Biol. 2(6):e69.
55. Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10(6):1396-1401. (Pubitemid 23352619)
56. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39(3):306-314. (Pubitemid 24283346)
57. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24(8):1586-1591. (Pubitemid 47236688)
58. Yang Z., Wang T. 1995. Mixed model analysis of DNA sequence evolution. Biometrics. 51(2):552-561.
59. Yang Z., Nielsen R., Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15(12):1600-1611. (Pubitemid 28550985)
60. Zwickl D., Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51(4):588-598. (Pubitemid 35180690)