Jump to ContentJump to Main Navigation

Cellular and Molecular Biology Letters

Editor-in-Chief: /

4 Issues per year


Impact Factor 2013: 1.782

SCImago Journal Rank (SJR): 0.673
Source Normalized Impact per Paper (SNIP): 0.530

VolumeIssuePage

Molecular systematics: A synthesis of the common methods and the state of knowledge

1The Natural History Museum

2University of Navarra

© 2010 Versita Warsaw. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. (CC BY-NC-ND 3.0)

Citation Information: Cellular and Molecular Biology Letters. Volume 15, Issue 2, Pages 311–341, ISSN (Online) 1689-1392, DOI: 10.2478/s11658-010-0010-8, March 2010

Publication History

Published Online:
2010-03-25

Abstract

The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.

Keywords: Molecular systematics; Phylogenetic inference; Molecular evolution; Phylogeny; Evolutionary analysis; Evolutionary hypothesis; Divergence time

  • [1] Page, R.D.M. and Holmes, E.C. Molecular evolution: a phylogenetic approach, Blackwell Science, Oxford, 1998.

  • [2] Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B.H., Wolinsky, S. and Bhattacharya, T. Timing the Ancestor of the HIV-1 Pandemic Strains. Science 288 (2000) 1789–1796. http://dx.doi.org/10.1126/science.288.5472.1789 [CrossRef]

  • [3] Smith, G.J.D., Vijaykrishna, D., Bahl, J., Lycett, S.J., Worobey, M., Pybus, O.G., Ma, S.K., Cheung, C.L., Raghwani, J., Bhatt, S., Peiris, J.S.M., Guan, Y. and Rambaut, A. Origins and evolutionary genomics of the 2009 swineorigin H1N1 influenza A epidemic. Nature 459 (2009) 1122–1125. http://dx.doi.org/10.1038/nature08182 [CrossRef]

  • [4] Rokas, A. and Holland, P.W.H. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15 (2000) 454–459. http://dx.doi.org/10.1016/S0169-5347(00)01967-4 [CrossRef]

  • [5] Hillis, D.M., Moritz, C. and Mable, B.K., Eds. Molecular systematics. Sinauer Associates, Inc., Sunderland, MA, 1996.

  • [6] Hillis, D.M. and Wiens, J.J. Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. in: Phylogenetic analysis of morphological data (Wiens, J.J., Ed.), Smithsonian Institution Press, Washington, DC, 2000, 1–19.

  • [7] Maley, L.E. and Marshall, C.R. The coming of age of molecular systematics. Science 279 (1998) 505–506. http://dx.doi.org/10.1126/science.279.5350.505 [CrossRef]

  • [8] Stevens, J.R. and Schofield, C.J. Phylogenetics and sequence analysis — some problems for the unwary. Trends Parasitol. 19 (2003) 582–588. http://dx.doi.org/10.1016/j.pt.2003.10.004 [CrossRef]

  • [9] Doyle, J.J. Gene trees and species trees: molecular systematics as onecharacter taxonomy. Syst. Bot. 17 (1992) 144–163. http://dx.doi.org/10.2307/2419070 [CrossRef]

  • [10] Rokas, A., Williams, B.L., King, N. and Carroll, S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425 (2003) 798–804. http://dx.doi.org/10.1038/nature02053 [CrossRef]

  • [11] Cummings, M.P., Otto, S.P. and Wakeley, J. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12 (1995) 814–822.

  • [12] Graybeal, A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47 (1998) 9–17. http://dx.doi.org/10.1080/106351598260996 [CrossRef]

  • [13] Huelsenbeck, J.P. Performance of phylogenetic methods in simulation.. Syst. Biol. 44 (1995) 17–48.

  • [14] Maddison, W.P. Gene trees in species trees. Syst. Biol. 46 (1997) 523–536. [CrossRef]

  • [15] Pääbo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L. and Hofreiter, M. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38 (2004) 645–679. http://dx.doi.org/10.1146/annurev.genet.37.110801.143214 [CrossRef]

  • [16] Organ, C.L., Schweitzer, M.H., Zheng, W., Freimark, L.M., Cantley, L.C. and Asara, J.M. Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science 320 (2008) 499. http://dx.doi.org/10.1126/science.1154284 [CrossRef]

  • [17] Tautz, D., Arctander, P., Minelli, A., Thomas, R.H. and Vogler, A.P. A plea for DNA taxonomy. Trends Ecol. Evol. 18 (2003) 70–74. http://dx.doi.org/10.1016/S0169-5347(02)00041-1 [CrossRef]

  • [18] Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D. and Vogler, A.P. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55 (2006) 595–609. http://dx.doi.org/10.1080/10635150600852011 [CrossRef]

  • [19] Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270 (2003) 313–321. http://dx.doi.org/10.1098/rspb.2002.2218 [CrossRef]

  • [20] Swofford, D.L., Olse, G.J., Waddell, P.J. and Hillis, D.M. Phylogenetic inference. in: Molecular systematics (Hillis, D.M., Moritz, C. and Mable, B.K., Eds.), Sinnauer Associates, Sunderland, MA, 1996, 407–514.

  • [21] Whelan, S., Liò, P. and Goldman, N. Molecular phylogentics: state-of-theart methods for looking into the past. Trends Genet. 17 (2001) 262–272. http://dx.doi.org/10.1016/S0168-9525(01)02272-7 [CrossRef]

  • [22] Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368–376. http://dx.doi.org/10.1007/BF01734359 [CrossRef]

  • [23] Posada, D. Selecting models of evolution. in: The phylogenetic handbook (Salemi, M. and Vandamme, A.-M., Eds.), Cambridge University Press, Cambridge, 2003, 256–282.

  • [24] Yang, Z. Estimating the pattern of of nucleotide substitution. J. Mol. Evol. 39 (1994) 105–111.

  • [25] Fitch, W.M. and Margoliash, E. A method for estimating the number of invariant amino acid coding positions in a gene, using cytochrome c as a model case. Biochem. Genet. 1 (1967) 65–71. http://dx.doi.org/10.1007/BF00487738 [CrossRef]

  • [26] Wakeley, J. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37 (1993) 613–623. http://dx.doi.org/10.1007/BF00182747

  • [27] Reeves, J.H. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J. Mol. Evol. 35 (1992) 17–31. http://dx.doi.org/10.1007/BF00160257 [CrossRef]

  • [28] Hasegawa, M., Kishino, H. and Yano, T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160–174. http://dx.doi.org/10.1007/BF02101694 [CrossRef]

  • [29] Yang, Z. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10 (1993) 1396–1401.

  • [30] Yang, Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306–314. http://dx.doi.org/10.1007/BF00160154 [CrossRef]

  • [31] Felsenstein, J. Inferring phylogenies. Sinauer Associates, Inc., Sunderland, MA, 2004.

  • [32] Adachi, J. and Hasegawa, M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42 (1996) 459–468. http://dx.doi.org/10.1007/BF02498640 [CrossRef]

  • [33] 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.

  • [34] Rodríguez, F., Oliver, J.F., Marín, A. and Medina, J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485–501. http://dx.doi.org/10.1016/S0022-5193(05)80104-3 [CrossRef]

  • [35] Ren, F., Tanaka, H. and Yang, Z. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst. Biol. 54 (2005) 808–818. http://dx.doi.org/10.1080/10635150500354688 [CrossRef]

  • [36] Tavaré, S., Adams, D.C., Fedrigo, O. and Naylor, G.J.P. A model for phylogenetic inference using structural and chemical covariates. in: Pacific Symposium on Biocomputing (Altman, R.B., Dunker, A.K., Hunter, L., Lauderdale, K. and Klein, T.E., Eds.), World Scientific, Singapore, 2001, 215–225.

  • [37] Galtier, N. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18 (2001) 866–873. [CrossRef]

  • [38] Huelsenbeck, J.P. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19 (2002) 698–707. [CrossRef]

  • [39] Cunningham, C.W., Zhu, H. and Hillis, D.M. Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52 (1998) 978–987. http://dx.doi.org/10.2307/2411230 [CrossRef]

  • [40] Bruno, W.J. and Halpern, A.L. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16 (1999) 564–566. [CrossRef]

  • [41] Huelsenbeck, J.P. and Hillis, D.M. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42 (1993) 247–264. [CrossRef]

  • [42] Holder, M. and Lewis, P.O. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4 (2003) 275–284. http://dx.doi.org/10.1038/nrg1044 [CrossRef]

  • [43] Posada, D. and Crandall, K.A. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50 (2001) 580–601. http://dx.doi.org/10.1080/106351501750435121 [CrossRef]

  • [44] Huelsenbeck, J.P. and Crandall, K.A. Phylogeny estimation and hypothesis testing using maximum likelihood. Ann. Rev. Ecol. Syst. 28 (1997) 437–466. http://dx.doi.org/10.1146/annurev.ecolsys.28.1.437 [CrossRef]

  • [45] Akaike, H. Information theory as an extension of the maximum likelihood principle. in: Second international symposium of information theory (Petrov, B.N. and Csaki, F., Eds.), Akademiai Kiado, Budapest, Hungary, 1973.

  • [46] Schwarz, G. Estimating the dimensions of a model. Ann. Stat. 6 (1978) 461–464. http://dx.doi.org/10.1214/aos/1176344136 [CrossRef]

  • [47] 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. http://dx.doi.org/10.1080/10635150490522304 [CrossRef]

  • [48] Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Wheeler, D.L. GenBank. Nucleic Acids Res. 35 (2007) D21–D25. http://dx.doi.org/10.1093/nar/gkl986 [CrossRef]

  • [49] Kitching, I.L., Forey, P.L., Humphries, C.J. and Williams, D.M. Cladistics. ed. 2. The theory and practice of parsimony analysis, Oxford University Press, Oxford, 1998.

  • [50] Smith, A.B. Rooting molecular trees: problems and strategies. Biol. J. Linn. Soc. 51 (1994) 279–292. http://dx.doi.org/10.1111/j.1095-8312.1994.tb00962.x [CrossRef]

  • [51] Phillips, A., Janies, D. and Wheeler, W. Multiple sequence alignment in phylogenetic analysis. Mol. Phylogenet. Evol. 16 (2000) 317–330. http://dx.doi.org/10.1006/mpev.2000.0785 [CrossRef]

  • [52] Goldman, N. Effects of sequence alignment procedures on estimates of phylogeny. BioEssays 20 (1998) 287–290. http://dx.doi.org/10.1002/(SICI)1521-1878(199804)20:4<287::AID-BIES4>3.0.CO;2-N [CrossRef]

  • [53] Ogden, T.H. and Rosenberg, M.S. Multiple sequence alignment accuracy and phylogenetic inference. Syst. Biol. 55 (2006) 314–328. http://dx.doi.org/10.1080/10635150500541730 [CrossRef]

  • [54] Edgar, R.C. and Batzoglou, S. Multiple sequence alignment. Curr. Opin. Struct. Biol. 16 (2006) 368–373. http://dx.doi.org/10.1016/j.sbi.2006.04.004 [CrossRef]

  • [55] Notredame, C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol. 3 (2007) e123. http://dx.doi.org/10.1371/journal.pcbi.0030123 [CrossRef]

  • [56] Thompson, J.D., Plewniak, F. and Poch, O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 7 (1999) 2682–2690. http://dx.doi.org/10.1093/nar/27.13.2682 [CrossRef]

  • [57] Feng, D.F. and Doolittle, R.F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25 (1987) 351–361. http://dx.doi.org/10.1007/BF02603120 [CrossRef]

  • [58] Morrison, D.A. Why would phylogeneticists ignore computerized sequence alignment? Syst. Biol. 58 (2009) 150–158. http://dx.doi.org/10.1093/sysbio/syp009 [CrossRef]

  • [59] Hickson, R.E., Simon, C. and Perrey, S.W. The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol. Biol. Evol. 17 (2000) 530–539. [CrossRef]

  • [60] Hofacker, I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31 (2003) 3429–3431. http://dx.doi.org/10.1093/nar/gkg599 [CrossRef]

  • [61] Wong, K.M., Suchard, M.A. and Huelsenbeck, J.P. Alignment uncertainty and genomic analysis. Science 319 (2008) 473–476. http://dx.doi.org/10.1126/science.1151532 [CrossRef]

  • [62] Löytynoja, A. and Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320 (2008) 1632–1635. http://dx.doi.org/10.1126/science.1158395 [CrossRef]

  • [63] Thorne, J.L., Kishino, H. and Felsenstein, J. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33 (1991) 114–124. http://dx.doi.org/10.1007/BF02193625 [CrossRef]

  • [64] Fitch, W.M. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20 (1971) 406–416. http://dx.doi.org/10.2307/2412116 [CrossRef]

  • [65] Farris, J.S. The logical basis of phylogenetic systematics. in: Advances in Cladistics (Platnick, N.I. and Funk, V.A., Eds.), Columbia University Press, New York, 1983, 7–36.

  • [66] Hennig, W. Grundzüge einer theorie der phylogenetischen systematik, Deutsche Zentral Verlag, Berlin, 1950.

  • [67] Felsenstein, J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401–410. http://dx.doi.org/10.2307/2412923 [CrossRef]

  • [68] Huelsenbeck, J.P. Is Felsenstein zone a fly trap? Syst. Biol. 46 (1997) 69–74. [CrossRef]

  • [69] Goldman, N. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Syst. Zool. 39 (1990). [CrossRef]

  • [70] Cavalli-Sforza, L.L. and Edwards, A.W.F. Phylogenetic analysis: Models and estimation procedures. Evolution 21 (1967) 550–570. http://dx.doi.org/10.2307/2406616 [CrossRef]

  • [71] Fitch, W.M. and Margoliash, E. Construction of phylogenetic trees. Science 155 (1967) 279–284. http://dx.doi.org/10.1126/science.155.3760.279 [CrossRef]

  • [72] Sneath, P.H.A. and Sokal, R.R. Numerical taxonomy, W.H. Freeman, San Francisco, 1973.

  • [73] Saitou, N. and Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406–425.

  • [74] Rzhetsky, A. and Nei, M. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9 (1992) 945–967.

  • [75] Nei, M. and Kumar, S. Molecular evolution and phylogenetics, Oxford University Press, Oxford, 2000.

  • [76] Edwards, A.W.F. Likelihood, Cambridge University Press, Cambridge, 1972.

  • [77] Edwards, A.W.F. and Cavalli-Sforza, L.L. Reconstruction of evolutionary trees. in: Phenetic and phylogenetic classification (Heywood, V.H. and McNeill, J., Eds.), Systematics Association Publ. No. 6, London, 1964, 67–76.

  • [78] Neyman, J. Molecular studies of evolution: a source of novel statistical problems. in: Statistical decision theory and related topics (Gupta, S.S. and Yackel, J., Eds.), Academic Press, New York, 1971, 1–27.

  • [79] Swofford, D.L. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0, Sinauer Associates, Inc., Sunderland, MA, USA, 1998.

  • [80] Kosakovsky Pond, S.L., Frost, S.D.W. and Muse, S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676–679. http://dx.doi.org/10.1093/bioinformatics/bti079 [CrossRef]

  • [81] Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (2006) 2688–2690. http://dx.doi.org/10.1093/bioinformatics/btl446 [CrossRef]

  • [82] Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 (2007) 1586–1591. http://dx.doi.org/10.1093/molbev/msm088 [CrossRef]

  • [83] Yang, Z. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14 (1997) 105–108. [CrossRef]

  • [84] Guindon, S. and Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696–704. http://dx.doi.org/10.1080/10635150390235520 [CrossRef]

  • [85] Huelsenbeck, J.P., Ronquist, F.R., Nielsen, R. and Bollback, J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310–2314. http://dx.doi.org/10.1126/science.1065889 [CrossRef]

  • [86] Rannala, B. and Yang, Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43 (1996) 304–311. http://dx.doi.org/10.1007/BF02338839 [CrossRef]

  • [87] Larget, B. and Simon, D.L. Markov chain Monet Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16 (1999) 750–759. [CrossRef]

  • [88] Gilks, W.R., Richardson, S. and Spiegelhalter, D.J., Eds. Markov Chain Monte Carlo in Practice. Chapman & Hall, London, 1996.

  • [89] Hastings, W.K. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57 (1970) 97–109. http://dx.doi.org/10.1093/biomet/57.1.97 [CrossRef]

  • [90] Metropolis, N., Rosenbluth, A.W., Teller, A.H. and Teller, E. Equations of state calculations by fast computing machines. J. Chem. Phys. 21 (1953) 1087–1091. http://dx.doi.org/10.1063/1.1699114 [CrossRef]

  • [91] Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. and Swofford, D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24 (2008) 581–583. http://dx.doi.org/10.1093/bioinformatics/btm388 [CrossRef]

  • [92] Goldman, N., Anderson, J.P. and Rodrigo, A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652–670. http://dx.doi.org/10.1080/106351500750049752 [CrossRef]

  • [93] Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783–791. http://dx.doi.org/10.2307/2408678 [CrossRef]

  • [94] Hedges, S.B. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol. Biol. Evol. 9 (1992) 366–369.

  • [95] Zharkikh, A. and Li, W.-H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock. J. Mol. Evol. 35 (1992) 356–366. http://dx.doi.org/10.1007/BF00161173 [CrossRef]

  • [96] 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. [CrossRef]

  • [97] Suzuki, Y., Glazko, G.V. and Nei, M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99 (2002) 16138–16143. http://dx.doi.org/10.1073/pnas.212646199 [CrossRef]

  • [98] Huelsenbeck, J.P. and Rannala, B. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53 (2004) 904–913. http://dx.doi.org/10.1080/10635150490522629 [CrossRef]

  • [99] Erixon, P., Svennblad, B., Britton, T. and Oxelman, B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52 (2003) 665–673. http://dx.doi.org/10.1080/10635150390235485 [CrossRef]

  • [100] 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) 255–256. http://dx.doi.org/10.1093/molbev/msg028 [CrossRef]

  • [101] Lewis, P.O., Holder, M.T. and Holsinger, K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54 (2005) 241–253. http://dx.doi.org/10.1080/10635150590924208 [CrossRef]

  • [102] Templeton, A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and the apes. Evolution 37 (1983) 221–244. http://dx.doi.org/10.2307/2408332 [CrossRef]

  • [103] Wilks, S.S. The large-sample distribution of the likelihood ratio for testing composite hypotheses. Ann. Math. Statist. 9 (1938) 60–62. http://dx.doi.org/10.1214/aoms/1177732360 [CrossRef]

  • [104] Huelsenbeck, J.P., Hillis, D.M. and Jones, R. Parametric bootstrapping in molecular phylogenetics: Applications and performance. in: Molecular Zoology: Advances, Strategies, and Protocols (Ferarris, J.D. and Palumbi, S.R., Eds.), Wiley-Liss, New York, 1996, 19–45.

  • [105] Goldman, N. Statistical tests of models of DNA substitution. J. Mol. Evol. 36 (1993) 182–198. http://dx.doi.org/10.1007/BF00166252 [CrossRef]

  • [106] Efron, B. Bootstrap confidence intervals for a class of parametric problems. Biometrika 72 (1985) 45–58. http://dx.doi.org/10.1093/biomet/72.1.45 [CrossRef]

  • [107] 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. http://dx.doi.org/10.1007/BF02100115 [CrossRef]

  • [108] Shimodaira, H. and Hasegawa, M. Multiple comparisons of Log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114–1116. [CrossRef]

  • [109] Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492–508. http://dx.doi.org/10.1080/10635150290069913 [CrossRef]

  • [110] Buckley, T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51 (2002) 509–523. http://dx.doi.org/10.1080/10635150290069922 [CrossRef]

  • [111] Aris-Brosou, S. Least and most powerful tests to elucidate the origin of seed plants in the presence of conflicting signals under misspecified models. Syst. Biol. 52 (2003) 781–793. [CrossRef]

  • [112] Gissi, C., San Mauro, D., Pesole, G. and Zardoya, R. Mitochondrial phylogeny of Anura (Amphibia): A case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters. Gene 366 (2006) 228–237. http://dx.doi.org/10.1016/j.gene.2005.07.034 [CrossRef]

  • [113] San Mauro, D., Gower, D.J., Oommen, O.V., Wilkinson, M. and Zardoya, R. Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol. Phylogenet. Evol. 33 (2004) 413–427. http://dx.doi.org/10.1016/j.ympev.2004.05.014 [CrossRef]

  • [114] Strimmer, K. and Rambaut, A. Inferring confidence sets of possible misspecified gene trees. Proc. R. Soc. London B 269 (2001) 137–142. http://dx.doi.org/10.1098/rspb.2001.1862 [CrossRef]

  • [115] Zuckerkandl, E. and Pauling, L. Evolutionary divergence and convergence in proteins. in: Evolving genes and proteins (Bryson, V. and Vogel, H., Eds.), Academic Press, New York, 1965, 97–166.

  • [116] Li, W.-H. and Graur, D. Fundamentals of Molecular Evolution, Sinauer, Sunderland, MA., 1991.

  • [117] Nei, M. Molecular evolutionary genetics, Columbia University Press, New York, 1987.

  • [118] Kimura, M. The neutral theory of molecular evolution, Cambridge University Press, Cambridge, 1983. http://dx.doi.org/10.1017/CBO9780511623486 [CrossRef]

  • [119] Kimura, M. Evolutionary rate at the molecular level. Nature 217 (1968) 624–626. http://dx.doi.org/10.1038/217624a0 [CrossRef]

  • [120] Benton, M.J. and Ayala, F.J. Dating the tree of life. Science 300 (2003) 1698–1700. http://dx.doi.org/10.1126/science.1077795 [CrossRef]

  • [121] Rodríguez-Trelles, F., Tarrío, R. and Ayala, F.J. A methodological bias toward overstimation of molecular evolutionary time scales. Proc. Natl. Acad. Sci. USA 99 (2002) 8112–8115. http://dx.doi.org/10.1073/pnas.122231299 [CrossRef]

  • [122] Bromham, L. and Penny, D. The modern molecular clock. Nat. Rev. Genet. 4 (2003) 216–224. http://dx.doi.org/10.1038/nrg1020 [CrossRef]

  • [123] Wu, C.I. and Li, W.H. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82 (1985) 1741–1745. http://dx.doi.org/10.1073/pnas.82.6.1741 [CrossRef]

  • [124] Ohta, T. Near-neutrality in evolution of genes and in gene regulation. Proc. Natl. Acad. Sci. USA 99 (2002) 16134–16137. http://dx.doi.org/10.1073/pnas.252626899 [CrossRef]

  • [125] Martin, A.P. and Palumbi, S.R. Body size, metabolic rate, generation time and the molecular clock. Proc. Natl. Acad. Sci. USA 90 (1993) 4087–4091. http://dx.doi.org/10.1073/pnas.90.9.4087 [CrossRef]

  • [126] Ota, R. and Penny, D. Estimating changes in mutational mechanisms of evolution. J. Mol. Evol. 57 (2003) S233–S240. http://dx.doi.org/10.1007/s00239-003-0032-1 [CrossRef]

  • [127] Welch, J.J. and Bromham, L. Molecular dating when rates vary. Trends Ecol. Evol. 20 (2005) 320–327. http://dx.doi.org/10.1016/j.tree.2005.02.007 [CrossRef]

  • [128] Ho, S.Y.W. An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 5 (2009) 421–424. http://dx.doi.org/10.1098/rsbl.2008.0729 [CrossRef]

  • [129] Douzery, E.J.P., Snell, E.A., Baptese, E., Delsuc, F. and Philippe, H. The timing of eukaryotic evolution: Does a realxed molecular clock reconcile proteins and fossils? Proc. Natl. Acad. Sci. USA 101 (2004) 15386–15391. http://dx.doi.org/10.1073/pnas.0403984101 [CrossRef]

  • [130] Sanderson, M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101–109. [CrossRef]

  • [131] Sanderson, M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14 (1997) 1218–1231. [CrossRef]

  • [132] Kishino, H., Thorne, J.L. and Bruno, W.J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18 (2001) 352–361. [CrossRef]

  • [133] Thorne, J.L., Kishino, H. and Painter, I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15 (1998) 1647–1657. [CrossRef]

  • [134] Thorne, J.L. and Kishino, H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51 (2002) 689–702. http://dx.doi.org/10.1080/10635150290102456 [CrossRef]

  • [135] Drummond, A.J., Ho, S.Y.W., Phillips, M.J. and Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biology 4 (2006) 699–710. http://dx.doi.org/10.1371/journal.pbio.0040088 [CrossRef]

  • [136] Drummond, A.J. and Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214. http://dx.doi.org/10.1186/1471-2148-7-214 [CrossRef]

  • [137] Sanderson, M.J. R8S: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19 (2003) 301–302. http://dx.doi.org/10.1093/bioinformatics/19.2.301 [CrossRef]

  • [138] Lepage, T., Bryant, D., Philippe, H. and Lartillot, N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24 (2007) 2669–2680. http://dx.doi.org/10.1093/molbev/msm193 [CrossRef]

  • [139] Donoghue, P.C. and Benton, M.J. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 22 (2007) 424–431. http://dx.doi.org/10.1016/j.tree.2007.05.005 [CrossRef]

  • [140] 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. http://dx.doi.org/10.1016/j.tig.2003.12.003 [CrossRef]

  • [141] Hedges, S.B. and Kumar, S. Precision of molecular time estimates. Trends Genet. 20 (2004) 242–247. http://dx.doi.org/10.1016/j.tig.2004.03.004 [CrossRef]

  • [142] Ho, S.Y.W. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 38 (2007) 409–414. [CrossRef]

  • [143] Ho, S.Y.W. and Phillips, M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. DOI:10.1093/sysbio/syp035 (2009). [CrossRef]

  • [144] Yang, Z. and Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23 (2006) 212–226. http://dx.doi.org/10.1093/molbev/msj024 [CrossRef]

  • [145] Avise, J.C. Molecular Markers, Natural History and Evolution, Chapman & Hall, New York, 1994.

  • [146] Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S., Higuchi, R., Horn, G.T., Mullis, K.B. and Erlich, H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239 (1988) 487–491. http://dx.doi.org/10.1126/science.2448875 [CrossRef]

  • [147] Cummings, M.P. and Meyer, A. Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology 108 (2005) 329–336. http://dx.doi.org/10.1016/j.zool.2005.09.006 [CrossRef]

  • [148] Rokas, A. and Carroll, S.B. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22 (2005) 1337–1344. http://dx.doi.org/10.1093/molbev/msi121 [CrossRef]

  • [149] Wiens, J.J. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52 (2003) 528–538. http://dx.doi.org/10.1080/10635150390218330 [CrossRef]

  • [150] Wiens, J.J. Missing data and the design of phylogenetic analyses. J. Biomed. Inform. 39 (2006) 34–42. http://dx.doi.org/10.1016/j.jbi.2005.04.001 [CrossRef]

  • [151] Hillis, D.M. Taxonomic sampling, phylogenetic accuracy, and investigatior bias. Syst. Biol. 47 (1998) 3–8. http://dx.doi.org/10.1080/106351598260987 [CrossRef]

  • [152] Poe, S. and Swofford, D.L. Taxon sampling revisited. Nature 398 (1999) 299–300. http://dx.doi.org/10.1038/18592 [CrossRef]

  • [153] Pollock, D.D. and Bruno, W.J. Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition. Mol. Biol. Evol. 17 (2000) 1854–1858. [CrossRef]

  • [154] Pollock, D.D., Zwickl, D.J., McGuire, J.A. and Hillis, D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51 (2002) 664–671. http://dx.doi.org/10.1080/10635150290102357 [CrossRef]

  • [155] Rannala, B., Huelsenbeck, J.P., Yang, Z. and Nielsen, R. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47 (1998) 702–710. http://dx.doi.org/10.1080/106351598260680 [CrossRef]

  • [156] Zwickl, D.J. and Hillis, D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51 (2002) 588–598. http://dx.doi.org/10.1080/10635150290102339 [CrossRef]

  • [157] Kim, J. Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47 (1998) 43–60. http://dx.doi.org/10.1080/106351598261021 [CrossRef]

  • [158] Rosenberg, M.S. and Kumar, S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98 (2001) 10751–10756. http://dx.doi.org/10.1073/pnas.191248498 [CrossRef]

  • [159] Palumbi, S.R., Martin, A., Romano, S., Owen MacMillan, W., Stice, L. and Grabowski, G. The simple fool’s guide to PCR, Department of Zoology, University of Hawaii, Honolulu, 1991.

  • [160] Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X. and Wilson, A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196–6200. http://dx.doi.org/10.1073/pnas.86.16.6196 [CrossRef]

  • [161] Ballard, J.W.O. and Rand, D.M. The population biology of mitochondrial DNA and its phylogenetics implications. Annu. Rev. Ecol. Evol. Syst. 36 (2005) 621–642. http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175513 [CrossRef]

  • [162] Russo, C.A.M., Takezaki, N. and Nei, M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13 (1996) 525–536. [CrossRef]

  • [163] Zardoya, R. and Meyer, A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13 (1996) 933–942. [CrossRef]

  • [164] Delsuc, F., Brinkmann, H. and Philippe, H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6 (2005) 361–375. http://dx.doi.org/10.1038/nrg1603 [CrossRef]

  • [165] Philippe, H., Delsuc, F., Brinkmann, H. and Lartillot, N. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 36 (2005) 541–562. http://dx.doi.org/10.1146/annurev.ecolsys.35.112202.130205 [CrossRef]

  • [166] Springer, M.S., DeBry, R.W., Douady, C.J., Amrine, H.M., Madsen, O., deJong, W.W. and Stanhope, M.J. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol. Biol. Evol. 18 (2001) 132–143. [CrossRef]

  • [167] Groth, J.G. and Barrowclough, G.F. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12 (1999) 115–123. http://dx.doi.org/10.1006/mpev.1998.0603

  • [168] Liolios, K., Tavernarakis, N., Hugenholtz, P. and Kyrpides, N.C. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucl. Acids. Res. 34 (2006) D332–D334. http://dx.doi.org/10.1093/nar/gkj145 [CrossRef]

  • [169] AToL initiative. (Assembling the Tree of Life). http://atol.sdsc.edu/.

  • [170] Boore, J.L. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol. Evol. 21 (2006) 439–446. http://dx.doi.org/10.1016/j.tree.2006.05.009 [CrossRef]

  • [171] Rannala, B. and Yang, Z. Phylogenetic inference using whole genomes. Annu. Rev. Genomics Hum. Genet. 9 (2008) 217–231. http://dx.doi.org/10.1146/annurev.genom.9.081307.164407 [CrossRef]

  • [172] Sanderson, M.J., Boss, D., Chen, D., Cranston, K.A. and Wehe, A. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Syst. Biol. 57 (2008) 335–346. http://dx.doi.org/10.1080/10635150802158688 [CrossRef]

  • [173] Beaumont, M.A. and Rannala, B. The Bayesian revolution in genetics. Nat. Rev. Genet. 5 (2004) 251–261. http://dx.doi.org/10.1038/nrg1318 [CrossRef]

  • [174] Cyberinfrastructure for Phylogenetic Research (CIPRES). Available at http://www.phylo.org/.

  • [175] Goldman, N. Phylogenetic information and experimental design in molecular systematics. Proc. R. Soc. Lond. B 265 (1998) 1779–1786. http://dx.doi.org/10.1098/rspb.1998.0502 [CrossRef]

  • [176] Geuten, K., Massingham, T., Darius, P., Smets, E. and Goldman, N. Experimental design criteria in phylogenetics: where to add taxa. Syst. Biol. 56 (2007) 609–622. http://dx.doi.org/10.1080/10635150701499563 [CrossRef]

  • [177] San Mauro, D., Gower, D.J., Massingham, T., Wilkinson, M., Zardoya, R. and Cotton, J.A. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Syst. Biol. 58 (2009) 425–438. http://dx.doi.org/10.1093/sysbio/syp043 [CrossRef]

  • [178] Cotton, J.A. and Page, R.D.M. Tangled trees from molecular markers: reconciling conflict between phylogenies to build molecular supertrees. in: Phylogenetic supertrees: combining information to reveal the Tree of Life (Bininda-Emonds, O.R.P., Ed.), Kluwer Academic, Dordrecht, the Netherlands, 2004, 107–125.

  • [179] Maddison, W.P. and Knowles, L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55 (2006) 21–30. http://dx.doi.org/10.1080/10635150500354928 [CrossRef]

  • [180] de Queiroz, A. and Gatesy, J. The supermatrix approach to systematics. Trends Ecol. Evol. 22 (2007) 34–41. http://dx.doi.org/10.1016/j.tree.2006.10.002 [CrossRef]

  • [181] Kearney, M. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Syst. Biol. 51 (2002) 369–381. http://dx.doi.org/10.1080/10635150252899824 [CrossRef]

  • [182] Campbell, V. and Lapointe, F.-J. The use and validity of composite taxa in phylogenetic analysis. Syst. Biol. 58 (2009) 560–572. http://dx.doi.org/10.1093/sysbio/syp056 [CrossRef]

  • [183] Hartmann, S. and Vision, T.J. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol. Biol. 8 (2008) 95. http://dx.doi.org/10.1186/1471-2148-8-95 [CrossRef]

  • [184] Wheeler, W.C. Search-based optimization. Cladistics 19 (2003) 348–355. http://dx.doi.org/10.1111/j.1096-0031.2003.tb00378.x [CrossRef]

  • [185] Wheeler, W.C. Homology and the optimization of DNA sequence data. Cladistics 17 (2001) S3–S11. http://dx.doi.org/10.1111/j.1096-0031.2001.tb00100.x [CrossRef]

  • [186] Simmons, M.P. Independence of alignment and tree search. Mol. Phylogenet. Evol. 31 (2004) 874–879. http://dx.doi.org/10.1016/j.ympev.2003.10.008 [CrossRef]

  • [187] Bininda-Emonds, O.R.P. The evolution of supertrees. Trends Ecol. Evol. 19 (2004) 315–322. http://dx.doi.org/10.1016/j.tree.2004.03.015 [CrossRef]

  • [188] Sanderson, M.J., Purvis, A. and Henze, C. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13 (1998) 105–109. http://dx.doi.org/10.1016/S0169-5347(97)01242-1 [CrossRef]

  • [189] Gatesy, J., Matthee, C., DeSalle, R. and Hayashi, C. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51 (2002) 652–664. http://dx.doi.org/10.1080/10635150290102311 [CrossRef]

  • [190] Wilkinson, M., Cotton, J.A., Creevey, C., Eulenstein, O., Harris, S.R., Lapointe, F.-J., Levasseur, C., McInerney, J.O., Pisani, D. and Thorley, J.L. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst. Biol. 54 (2005) 419–431. http://dx.doi.org/10.1080/10635150590949832 [CrossRef]

  • [191] Roshan, U., Moret, B.M.E., Williams, T.L. and Warnow, T. Performance of supertree methods on various data set decompositions. in: Phylogenetic supertrees: Combining information to reveal the Tree of Life (Bininda-Emonds, O.R.P., Ed.), Kluwer Academic, Dordrecht, The Netherlands, 2004, 301–328.

  • [192] Wilkinson, M. and Cotton, J.A. Supertree methods for building the Tree of Life: Divide-and-conquer approaches to large phylogenetic problems. in: Reconstructing the Tree of Life. Taxonomy and systematics of species rich taxa (Hodkinson, T.R. and Parnell, J.A.N., Eds.), The Systematics Association and CRC Press, London, 2007, 61–75.

  • [193] Ren, F., Tanaka, H. and Yang, Z. A likelihood look at the supermatrix-supertree controversy. Gene 441 (2009) 119–125. http://dx.doi.org/10.1016/j.gene.2008.04.002 [CrossRef]

  • [194] Smith, S.A., Beaulieu, J.M. and Donoghue, M.J. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. 9 (2009) 37. http://dx.doi.org/10.1186/1471-2148-9-37 [CrossRef]

  • [195] http://evolution.gs.washington.edu/phylip/software.html.

  • [196] 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. Nucleic Acids Res. 22 (1994) 4673–4680. http://dx.doi.org/10.1093/nar/22.22.4673 [CrossRef]

  • [197] Katoh, K., Kuma, K., Toh, H. and Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33 (2005) 511–518. http://dx.doi.org/10.1093/nar/gki198 [CrossRef]

  • [198] Katoh, K., Misawa, K., Kuma, K. and Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 (2002) 3059–3066. http://dx.doi.org/10.1093/nar/gkf436 [CrossRef]

  • [199] 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. http://dx.doi.org/10.1006/jmbi.2000.4042 [CrossRef]

  • [200] Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540–552. [CrossRef]

  • [201] Posada, D. and Crandall, K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817–818. http://dx.doi.org/10.1093/bioinformatics/14.9.817 [CrossRef]

  • [202] Posada, D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25 (2008) 1253–1256. http://dx.doi.org/10.1093/molbev/msn083 [CrossRef]

  • [203] Abascal, F., Zardoya, R. and Posada, D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104–2105. http://dx.doi.org/10.1093/bioinformatics/bti263 [CrossRef]

  • [204] Felsenstein, J. PHYLIP — Phylogeny inference package (Version 3.2.). Cladistics 5 (1989) 164–166.

  • [205] Tamura, K., Dudley, J., Nei, M. and Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596–1599. http://dx.doi.org/10.1093/molbev/msm092

  • [206] Zwickl, D.J. (2006) Garli. Available from the author at http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html.

  • [207] Ronquist, F. and Huelsenbeck, J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572–1574. http://dx.doi.org/10.1093/bioinformatics/btg180 [CrossRef]

  • [208] Huelsenbeck, J.P. and Ronquist, F.R. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754–755 http://dx.doi.org/10.1093/bioinformatics/17.8.754 [CrossRef]

  • [209] Shimodaira, H. and Hasegawa, M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246–1247. http://dx.doi.org/10.1093/bioinformatics/17.12.1246 [CrossRef]

  • [210] Maddison, W.P. and Maddison, D.R. MacClade: analysis of phylogeny and character evolution, Sinauer Associates Inc., Sunderland, Massachusetts, USA, 1992.

  • [211] Maddison, W.P. and Maddison, D.R. (2009) Mesquite: a modular system for evolutionary analysis. Available from the authors at http://mesquiteproject.org.

  • [212] Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555–556.

  • [213] Foster, P.G. (2009) P4. Available from the author at http://www.bmnh.org/~pf/p4.html.

  • [214] Thorne, J.L. and Kishino, H. (2003) Multidivtime. Available from the authors at http://statgen.ncsu.edu/thorne/multidivtime.html.

  • [215] Page, R.D.M. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12 (1996) 357–358.

  • [216] Rambaut, A. (2006) FigTree. Available from the author at http://tree.bio.ed.ac.uk/software/figtree/.

Comments (0)

Please log in or register to comment.