A 20-state empirical amino-acid substitution model for green plant chloroplasts

Molecular Phylogenetics and Evolution

Volumn 68, Issue 2, 2013, Pages 218-220

  Cox, Cymon J ^a   Foster, Peter G ^b  

^a UNIVERSITY OF ALGARVE   (Portugal)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Chloroplast; CpREV; Empirical protein model; GcpREV; Green plant; Phylogeny reconstruction

Indexed keywords

CHLOROPLAST PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETICS; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; PLANT; PROBABILITY; SEQUENCE HOMOLOGY; STATISTICAL MODEL;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CHLOROPLAST PROTEINS; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; PLANTS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

VIRIDIPLANTAE;

EID: 84878115695     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.03.030     Document Type: Article

References (14)

1. Adachi J., Waddell P.J., Martin W., Hasegawa M. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 2000, 50:348-358.
2. Clarke J.T., Warnock R.C.M., Donoghue P.C.J. Establishing a time-scale for plant evolution. New Phytol. 2011, 192:266-301.
3. Foster P.G. Modeling compositional heterogeneity. Syst. Biol. 2004, 53:485-495.
4. Karol K.G., Arumuganathan K., Boore J.L., Duffy A.M., Everett K.D.E., Hall J.D., Hansen S.K., Kuehl J.V., Mandoli D.F., Mishler B.D., Olmstead R.G., Renzaglia K.S., Wolf P.G. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol. Biol. 2010, 10:321.
5. Lartillot N., Lepage T., Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25:2286-2288.
6. Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
7. Lewis P.O., Holder M.T., Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 2005, 54:241-253.
8. Qiu Y.-L., Li L., Wang B., Chen Z., Knoop V., Groth-Malonek M., Dombrovska O., Lee J., Kent L., Rest J., Estabrook G.F., Hendry T.A., Taylor D.W., Testa C.M., Ambros M., Crandall-Stotler B., Duff R.J., Stech M., Frey W., Quandt D., Davis C.C. The deepest divergences in land plants inferred from phylogenomic evidence. Proc. Natl. Acad. Sci. USA 2006, 103:15511-15516.
9. Rodriguez-Ezpeleta N., Philippe H., Brinkmann H., Becker B., Melkonian M. Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the streptophyta. Mol. Biol. Evol. 2007, 24:723-731.
10. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
11. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
12. Whelan S., Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 2001, 18:691-699.
13. Wolf P.G., Karol K.G., Mandolib D.F., Kuehl J., Arumuganathane K., Ellis M.W., Mishler B.D., Kelch D.G., Olmstead R.G., Boore J.L. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 2005, 350:117-128.
14. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2004, 24:1586-1591.