New methods for inferring population dynamics from microbial sequences

Infection, Genetics and Evolution

Volumn 7, Issue 1, 2007, Pages 24-43

  Pérez Losada, Marcos ^a   Porter, Megan L ^a,b   Tazi, Loubna ^a   Crandall, Keith A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

Alignment; Coalescent; Microorganisms; Phylogenetics; Population genetics; Sequences

Indexed keywords

DNA;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BAYES THEOREM; DECISION THEORY; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; HIGH THROUGHPUT SCREENING; MAXIMUM LIKELIHOOD METHOD; MICROBIAL POPULATION DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MONTE CARLO METHOD; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; POPULATION GENETICS; POPULATION GROWTH; POPULATION STRUCTURE; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

BACTERIA; GENOMICS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 33845270141     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2006.03.004     Document Type: Article

References (217)

1. Abascal F., Zardoya R., and Posada D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Abdo Z., Minin V.N., Joyce P., and Sullivan J. Accounting for uncertainty in the tree topology has little effect on the decision-theory approach to model selection in phylogeny estimation. Mol. Biol. Evol. 22 (2005) 691-703
3. Adachi J., and Hasegawa M. MOLPHY version 2.3: Programs for molecular phylogenetics based in maximum likelihood. Comput. Sci. Monogr. 28 (1996) 1-150
4. Adachi J., Waddell P.J., Martin W., and Hasegawa M. Plastid genome phylogeny and a model of amino acid substitution for proteinss encoded by chloroplast DNA. J. Mol. Evol. 50 (2000) 348-358
5. Alfaro M.E., Zoller S., and Lutzoni F. 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 (2003) 255-266
6. Anisimova M., Bielawski J.P., and Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18 (2001) 1585-1592
7. Anisimova M., Bielawski J.P., and Yang Z. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19 (2002) 950-958
8. Anisimova M., Nielsen R., and Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164 (2003) 1229-1236
9. Aris-Brosou S., and Yang Z. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51 (2002) 703-714
10. Bandelt H.J., Forster P., and Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16 (1999) 37-48
11. Bielawski J.P., and Yang Z. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J. Mol. Evol. 59 (2004) 121-132
12. Brauer M.J., Holder M.T., Dries L.A., Zwickl D.J., Lewis P.O., and Hillis D.M. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Mol. Biol. Evol. 19 (2002) 1717-1726
13. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42 (1988) 795-803
14. Browne M. Cross-validation methods. J. Math. Psychol. 44 (2000) 108-132
15. Bruno W.J., and Halpern A.L. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16 (1999) 564-566
16. Buckley T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51 (2002) 509-523
17. Buckley T.R., and Cunningham C.W. The effects of nucleotide substitution model assumptions on estiamts of nonparametric bootstrap support. Mol. Biol. Evol. 19 (2002) 394-405
18. Buckley T.R., Simon C., and Chambers G.K. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: the effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50 (2001) 67-86
19. Burnham K.P., and Anderson D.A. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. 2nd ed. (2002), Springer-Verlag, New York 488 pp
20. Cao Y., Janke A., Waddell P.J., Westerman M., Takenaka O., Murata S., Okada N., Paabo S., and Hasegawa M. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47 (1998) 307-322
21. Carvajal-Rodríguez, A., Crandall, K.A., Posada, D., in press. Recombination estimation under complex evolutionary models with the coalescent composite likelihood method. Mol. Biol. Evol.
22. Cassens I., Mardulyn P., and Milinkovitch M.C. Evaluating intraspecific "network" construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach?. Syst. Biol. 54 (2005) 363-372
23. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
24. Chan M.S., Maiden M.C., and Spratt B.G. Database-driven multi locus sequence typing (MLST) of bacterial pathogens. Bioinformatics 17 (2001) 1077-1083
25. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1659
26. Cooper J.E., and Feil E.J. Multilocus sequence typing-what is resolved?. Trends Microbiol. 12 (2004) 373-377
27. Crandall K.A. Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Mol. Biol. Evol. 13 (1996) 115-131
28. Crandall K.A. The Evolution of HIV (1999), Johns Hopkins University Press, Baltimore, MD
29. Crandall K.A., Kelsey C.R., Imamichi H., Lane H.C., and Salzman N.P. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16 (1999) 372-382
30. Crandall K.A., Pérez-Losada M., Christensen R.G., McClellan D.A., and Viscidi R.P. Phylogenomics and molecular evolution of polyomaviruses. In: Ahsan N. (Ed). Polyomavirus and Human Diseases (2005), Landes BioScience, Georgetown, TX
31. Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1978), National Biomedical Research Foundation, Washington, DC 345-352
32. Desper R., and Gascuel O. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol. 9 (2002) 687-705
33. Dimmic M.W., Rest J.S., Mindell D.P., and Goldstein R.A. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 55 (2002) 65-73
34. Dingle K.E., Colles F.M., Wareing D.R., Ure R., Fox A.J., Bolton F.E., Bootsma H.J., Willems R.J., Urwin R., and Maiden M.C. Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 39 (2001) 14-23
35. Donoghue M.J., Olmstead R.G., Smith J.F., and Palmer J.D. Phylogenetic relationships of dipsacales based on rbcL sequences. Ann. Missouri Bot. Garden 79 (1992) 333-345
36. Douady C.J., Delsuc F., Boucher Y., Doolittle W.F., and Douzery E.J. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20 (2003) 248-254
37. Drummond A.J., Nicholls G.K., Rodrigo A.G., and Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161 (2002) 1307-1320
38. Drummond, A.J., Rambaut, A., 2003. BEAST vl.0. Available from http://www.evolve.zoo.ox.ac.uk/beast/.
39. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
40. Dupanloup I., Schneider S., and Excoffier L. A simulated annealing approach to define the genetic structure of populations. Mol. Ecol. 11 (2002) 2571-2581
41. Duret L., and Abdeddaim S. Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences. In: Higgins D., and Taylor W. (Eds). Bioinformatics, Sequence, Structure and Databanks (2000), Oxford University Press, Oxford 155-167
42. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32 (2004) 1792-1797
43. Emerson B.C., Paradis E., and Thébaud C. Revealing the demographic histories of species using DNA sequences. Trends Ecol. Evol. 16 (2001) 707-716
44. Epperson B.K. Gene genealogies in geographically structured populations. Genetics 152 (1999) 797-806
45. Excoffier L., and Smouse P.E. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136 (1994) 343-359
46. Falush D., Wirth T., Linz B., Pritchard J.K., Stephens M., Kidd M., Blaser M.J., Graham D.Y., Vacher S., Pérez-Pérez G.I., Yamaoka Y., Megraud F., Otto K., Reichard U., Katzowitsch E., Wang X., Achtman M., and Suerbaum S. Traces of human migrations in Helicobacter pylori populations. Science 299 (2003) 1582-1585
47. Fearnhead P., and Donnelly P. Estimating recombination rates from population genetic data. Genetics 159 (2001) 1299-1318
48. Feil E.J., Cooper J.E., Grundmann H., Robinson D.A., Enright M.C., Berendt T., Peacock S.J., Smith J.M., Murphy M., Spratt B.G., Moore C.E., and Day N.P. How clonal is Staphylococcus aureusi?. J. Bacteriol. 185 (2003) 3307-3316
49. Feil E.J., Li B.C., Aanensen D.M., Hanage W.P., and Spratt B.G. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186 (2004) 1518-1530
50. Feil E.J., Smith J.M., Enright M.C., and Spratt B.G. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154 (2000) 1439-1450
51. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401-410
52. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
53. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
54. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Sunderland, MA
55. Fitch W.M., Bush R.M., Bender C.A., and Cox N.J. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 7712-7718
56. Ford M.J. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18 (2001) 639-647
57. Forsberg R., and Christiansen F.B. A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol. Biol. Evol. 20 (2003) 1252-1259
58. Frati F., Simon C., Sullivan J., and Swofford D.L. Evolution of the mitochondrial COII gene in Collembola. J. Mol. Evol. 44 (1997) 145-158
59. Fu Y.X., and Li W.H. Maximum likelihood estimation of population parameters. Genetics 134 (1993) 1261-1270
60. Gatesy J., DeSalle R., and Wheeler W. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2 (1993) 152-157
61. Gaut B.S., and Lewis P.O. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12 (1995) 152-162
62. Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
63. Graur D., and Martin W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20 (2004) 80-86
64. Green P.J. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82 (1995) 711-732
65. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phyhlogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
66. Guindon S., Rodrigo A.G., Dyer K.A., and Huelsenbeck J.P. Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 12957-12962
67. Hendy M.D., and Penny D. Branch and bound algorithms to determine minimal evolutionary trees. Math. BioSci. 59 (1982) 277-290
68. Henikoff S., and Henikoff J.G. Amino acid substitution matrices for protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 10915-10919
69. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
70. Hillis D.M., and Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42 (1993) 182-192
71. Hudson R.R. In: Futuyma D., and Antonovics J. (Eds). Gene Genealogies and the Coalescent Process (1991), Oxford University Press, New York, NY 1-44
72. Hudson R.R. Two-locus sampling distributions and their application. Genetics 159 (2001) 1805-1817
73. Huelsenbeck J.P. Performance of phylogenetic methods in simulation. Syst. Biol. 44 (1995) 17-48
74. Huelsenbeck J.P., and Crandall K.A. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28 (1997) 437-466
75. Huelsenbeck J.P., and Hillis D.M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42 (1993) 247-264
76. Huelsenbeck J.P., Larget B., and Alfaro M.E. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21 (2004) 1123-1133
77. Huelsenbeck J.P., Larget B., Miller R.E., and Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51 (2002) 673-688
78. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
79. Huelsenbeck J.P., Ronquist F., Nielsen R., and Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310-2314
80. Huson D.H., and Steel M. Distances that perfectly mislead. Syst. Biol. 53 (2004) 327-332
81. Janies D.A., and Wheeler W.C. Efficiency of parallel direct optimization. Cladistics 17 (2001) S71-S82
82. Jobb, G., 2005. TREEFINDER version of June 2005, Munich. Distributed by author at http://www.treefinder.de.
83. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comp. Appl. BioSci. 8 (1992) 275-282
84. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.M. (Ed). Mammalian Protein Metabolism (1969), Academic Press, New York, NY 21-132
85. Kass R.E., and Raftery A.E. Bayes factors and model uncertainty. J. Am. Stat. Assoc. 90 (1995) 773-775
86. Katoh K., Kuma K., and Miyata T. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53 (2001) 477-484
87. Katoh K., Kuma K., Toh H., and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl. Acids Res. 33 (2005) 511-518
88. Katoh K., Misawa K., Kuma K., and Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 30 (2002) 3059-3066
89. Kelsey C.R., Crandall K.A., and Voevodin A.F. Different models, different trees: the geographic origin of PTLV-I. Mol. Phylogenet. Evol. 13 (1999) 336-347
90. Kimura M. The Neutral Theory of Molecular Evolution (1983), Cambridge University Press, Cambridge
91. Kishino H., and Hasegawa M. 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 (1989) 170-179
92. Kosakovsky P.S.L., Frost S.D.W., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
93. Kuhner M.K., Yamato J., Beerli P., Smith L.P., Rynes E., Walkup E., Li C., Sloan J., Colacurcio P., and Felsenstein J. LAMARC v 2.0.2 (2005), University of Washington
94. Kuhner M.K., Yamato J., and Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149 (1998) 429-434
95. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
96. Leaché A.D., and Reeder T.W. Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51 (2002) 44-68
97. Lemmon A.R., and Milinkovitch M.C. The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 10516-10521
98. Lewis P.O. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15 (1998) 277-283
99. Li W.H. Molecular Evolution (1997), Sinauer Associates, Sunderland, MA
100. Löytynoja A., and Milinkovitch M.C. A hidden Markov model for progressive multiple alignment. Bioinformatics 19 (2003) 1505-1513
101. Lunter G., Miklos I., Drummond A., Jensen J.L., and Hein J. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinform. 6 (2005) (Art. No. 83)
102. Lutzoni F., Wagner P., Reeb V., and Zoller S. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst. Biol. 49 (2000) 628-651
103. Maddison D.R., and Maddison W.P. MacClade 4: Analysis of Phylogeny and Character Evolution, version 4.0 (2000), Sinauer Associates
104. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., Zhang Q., Zhou J., Zurth K., Caugant D.A., Feavers I.M., Achtman M., and Spratt B.G. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 3140-3145
105. Mansky L.M., and Temin H.M. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69 (1995) 5087-5094
106. Matsuda H. Protein phylogenetic inference using maximum likelihood with a genetic algorithm. Paper presented at Pacific Symposium on Biocomputing. World Scientific, London (1996)
107. Maynard Smith J. Do bacteria have population genetics?. In: Baumberg J.P. (Ed). Population Genetics of Bacteria (1995), Press Syndicate of the University of Cambridge, Cambridge 1-12
108. McClellan D.A., and McCracken K.G. Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol. Biol. Evol. 18 (2001) 917-925
109. McClellan D.A., Palfreyman E.J., Smith M.J., Moss J.L., Christensen R.G., and Sailsbery J.K. Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol. Biol. Evol. 22 (2005) 437-455
110. McVean G., Awadalla P., and Fearnhead P. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160 (2002) 1231-1241
111. McVean G.A.T., and Vieira J. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157 (2001) 245-257
112. Meats E., Feil E.J., Stringer S., Cody A.J., Goldstein R., Kroll J.S., Popovic T., and Spratt B.G. Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J. Clin. Microbiol. 41 (2003) 1623-1636
113. Minin V., Abdo Z., Joyce P., and Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52 (2003) 674-683
114. Miyata T., and Yasunaga T. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol. 16 (1980) 23-36
115. Muller T., and Vingron M. Modeling amino acid replacement. J. Comput. Biol. 7 (2000) 761-776
116. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
117. Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
118. Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analyses. Cladistics 15 (1999) 407-414
119. Nordborg M. Coalescent theory. In: Balding D., Bishop M., and Cannings C. (Eds). Handbook of Statistical Genetics (2001), John Wiley & Sons, Chichester, UK 179-212
120. Notredame C. Recent progress in multiple sequence alignment: a survey. Pharmacogen 3 (2002) 131-144
121. Notredame C., Higgins D.G., and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
122. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
123. O'Sullivan O., Suhre K., Abergel C., Higgins D.G., and Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340 (2004) 385-395
124. Page R.D.M., and Holmes E.C. Molecular Evolution: A Phylogenetic Approach (1998), Blackwell Science
125. Pagel M., and Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence of character-state data. Syst. Biol. 53 (2004) 571-581
126. Pearse D.E., and Crandall K.A. Beyond Fst: analysis of population genetic data for conservation. Conserv. Genet. 5 (2004) 585-602
127. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 2444-2448
128. Penny D., Lockhart P.J., Steel M.A., and Hendy M.D. The role of models in reconstructing evolutionary trees. In: Scotland R.W., Siebert D.J., and Williams D.M. (Eds). Models in Phylogenetic Reconstruction (1994), Clarendon Press, Oxford 211-230
129. Pérez-Losada M., Viscidi R.P., Demma J.C., Zenilman J., and Crandall K.A. Population genetics of Neisseria gonorrhoeae in a high prevalence community using a hyper-variable outer membrane porB and thirteen slowly-evolving housekeeping genes. Mol. Biol. Evol. 22 (2005) 1887-1902
130. Pérez-Losada M., Browne E.B., Madsen A., Wirth T., Viscidi R.P., and Crandall K.A. Population genetics of microbial pathogens estimated from Multilocus Sequence Typing (MLST) data. Infect. Genet. Evol. 6 (2006) 97-112
131. Pond S.L., and Frost S.D. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22 (2005) 478-485
132. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
133. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
134. Posada D., and Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 13757-13762
135. Posada D., and Crandall K.A. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54 (2002) 396-402
136. Posada D., Crandall K.A., and Holmes E.C. Recombination in evolutionary genomics. Annu. Rev. Genet. 36 (2002) 75-97
137. Posada D., Crandall K.A., and Templeton A.R. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol. Ecol. 9 (2000) 487-488
138. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
139. Pupko T., Huchon D., Cao Y., Okada N., and Hasegawa M. Combining multiple data sets in a likelihood analysis: which models are the best?. Mol. Biol. Evol. 19 (2002) 2294-2307
140. Pybus O.G., and Rambaut A. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18 (2002) 1404-1405
141. Raftery A.E. Hypothesis testing and model selection. In: Gilks W.R., Richardson S., and Spiegelhalter D.J. (Eds). Markov Chain Monte Carlo in Practice (1996), Chapman & Hall, London 163-188
142. Rambaut, A., Drummond, A.J., 2003. Tracer version 1.2.1. Available from http://www.evolve.zoo.ox.ac.uk/.
143. Redelings B.D., and Suchard M.A. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54 (2005) 401-418
144. Rivera M.C., and Lake J.A. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431 (2004) 152-155
145. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
146. Rosenberg M.S. Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinform. 6 (2005) (Art. No. 102)
147. Rzhetsky A., and Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10 (1993) 1073-1095
148. Sainudiin R., Wong W.S., Yogeeswaran K., Nasrallah J.B., Yang Z., and Nielsen R. Detecting site-specific physicochemical selective pressures: applications to the class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J. Mol. Evol. 60 (2005) 315-326
149. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
150. Sanderson M.J. Objections to bootstrapping phylogenies: a critique. Syst. Biol. 44 (1995) 299-320
151. Sanderson M.J., and Wojciechowski M.F. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49 (2000) 671-685
152. Schierup M.H., and Hein J. Consequences of recombination on traditional phylogenetic analysis. Genetics 156 (2000) 879-891
153. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler M. TREE-PUZZLE: maximum-likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
154. Schneider S., Roessli D., and Excoffier L. ARLEQUIN version 2.000: A Software for Population Genetics Data Analysis (2000), Genetics and Biometry Laboratory, University of Geneva
155. Schwarz G. Estimating the dimensions of a model. Ann. Stat. 6 (1978) 461-464
156. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
157. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
158. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
159. Shriner D., Nickle D.C., Jensen M.A., and Mullins J.I. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81 (2003) 115-121
160. Simes R.J. An improved Bonferroni procedure for multiple tests of significance. Biometrika 73 (1986) 751-754
161. Simon D., and Larget B. Bayesian Analysis in Molecular Biology and Evolution (BAMBE) version 2.03 Beta (2000), Department of Mathematics and Computer Science, Duquesne University
162. Sinclair, E.A., Pérez-Losada, M., Crandall, K.A., 2005. Molecular phylogenetics for conservation biology. In: Purvis, A., Brooks, T., Gittleman, J. (Eds.), Phylogeny and Conservation. Cambridge University Press, Cambridge, pp.19-58.
163. Sokal R.R., and Sneath P.H.A. Numerical Taxonomy (1963), Freeman WH, San Francisco
164. Spratt B.G., Hanage W.P., Li B., Aanensen D.M., and Feil E.J. Displaying the relatedness among isolates of bacterial species-the eBURST approach. FEMS Microbiol. Lett. 241 (2004) 129-134
165. Stamatakis A., Ludwig T., and Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21 (2005) 456-463
166. Stephens M. Inference under the coalescent. In: Balding D.J., Cannings C., and Bishop M. (Eds). Handbook of Statistical Genetics (2001), Wiley, Chichester 213-238
167. Strimmer K., and Pybus O.G. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol. Biol. Evol. 18 (2001) 2298-2305
168. Strimmer K., and Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc. Biol. Sci. 269 (2002) 137-142
169. Suchard M.A., Weiss R.E., and Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18 (2001) 1001-1013
170. Sullivan J., and Swofford D.L. Are guinea pigs rodents? The importance of adequate models in molecular phylogenies. J. Mamm. Evol. 4 (1997) 77-86
171. Sullivan J., and Swofford D.L. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution patter are violated?. Syst. Biol. 50 (2001) 723-729
172. Sullivan J., and Joyce P. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 36 (2005) 445-466
173. Sullivan J., Markert J.A., and Kilpatrick C.W. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46 (1997) 426-440
174. Suzuki Y., Glazko G.V., and Nei M. Overcredibililty of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 16138-16143
175. Suzuki Y., and Gojobori T. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16 (1999) 1315-1328
176. Suzuki Y., Gojobori T., and Nei M. ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17 (2001) 660-661
177. *. Phylogenetic Analysis Using Parsimony (* and other methods) (2002), Sinauer Associates, Sunderland, MA
178. Swofford D.L., Olsen G.J., Waddell P.J., and Hillis D.M. Phylogenetic Inference. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates, Sunderland, MA 407-514
179. Tamura K. Model selection in the estimation of the number of nucleotide substitutions. Mol. Biol. Evol. 11 (1994) 154-157
180. Tamura K., Nei M., and Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 11030-11035
181. Taylor S.D., de la Cruz K.D., Porter M.L., and Whiting M.F. Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: does a flea see?. Mol. Biol. Evol. 22 (2005) 1165-1174
182. Templeton A.R. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol. Ecol. 7 (1998) 381-397
183. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-810
184. Templeton A.R., Crandall K.A., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132 (1992) 619-633
185. Templeton A.R., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134 (1993) 659-669
186. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25 (1997) 4876-4882
187. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
188. Thompson J.D., Plewniak F., and Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15 (1999) 87-88
189. Thompson J.D., Plewniak F., and Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucl. Acids Res. 27 (1999) 2682-2690
190. Tibayrenc M. Bridging the gap between molecular epidemiologists and evolutionists. Trends Microbiol. 13 (2005) 575-580
191. Tierney L. Markov-chains for exploring posterior distributions. Ann. Stat. 22 (1994) 1701-1728
192. Urwin R., and Maiden M.C. Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol. 11 (2003) 479-487
193. Wain-Hobson S., Renoux-Elbe C., Vartanian J.P., and Meyerhans A. Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways. J. Gen. Virol. 84 (2003) 885-895
194. Wall J.D. A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17 (2000) 156-163
195. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (1975) 256-276
196. Wernersson R., and Pedersen A.G. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucl. Acids Res. 31 (2003) 3537-3539
197. Wheeler W.C. Optimization alignment: the end of multiple alignment in phylogenetics?. Cladistics 12 (1996) 1-9
198. Wheeler, W.C., Gladstein, D., De Laet, J., 2003. POY: phylogeny reconstruction via optimization of DNA and other data. American Museum of Natural History, New York. Available from http://www.research.amnh.org/scicomp/projects/poy.php.
199. Whelan S., and Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18 (2001) 691-699
200. Wiedmann M. Subtyping of bacterial foodborne pathogens. Nutr. Rev. 60 (2002) 201-208
201. Williamson S., and Orive M.E. The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evol. 19 (2002) 1376-1384
202. Wong W.S., Yang Z., Goldman N., and Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168 (2004) 1041-1051
203. Wooding S., and Rogers A. The matrix coalescent and an application to human single-nucleotide polymorphisms. Genetics 161 (2002) 1641-1650
204. Woolley S., Johnson J., Smith M.J., Crandall K.A., and McClellan D.A. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 19 (2003) 671-672
205. Xia X., and Li W.H. What amino acid properties affect protein evolution?. J. Mol. Evol. 47 (1998) 557-564
206. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. BioSci. 13 (1997) 555-556
207. Yang Z., and Bielawski J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15 (2000) 496-503
208. Yang Z., Goldman N., and Friday A. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44 (1995) 384-399
209. Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
210. Yang Z., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 (2002) 908-917
211. Yang Z., Nielsen R., Goldman N., and Pedersen A.M. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449
212. Yang Z., and Rannala B. Branch-length prior influences Bayesian posterior probabilities of phylogeny. Syst. Biol. 54 (2005) 455-470
213. Yang Z., and Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19 (2002) 49-57
214. Yang Z., Wong W.S., and Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22 (2005) 1107-1118
215. Zhang J. Performance of likelihood rate tests of evolutionary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16 (1999) 868-875
216. Zhang J., and Nei M. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44 (1997) S139-S146
217. Zwickl D.J., and Holder M.T. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53 (2004) 877-888