An index of substitution saturation and its application
Tài liệu tham khảo
Archie, 1989, A randomization test for phylogenetic information in systematic data, Syst. Zool., 38, 219, 10.2307/2992285
Baldauf, 1996, The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny, Proc. Natl. Acad. Sci. USA, 93, 7749, 10.1073/pnas.93.15.7749
Chang, 1996, Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters, Math. Biosci., 134, 189, 10.1016/0025-5564(95)00172-7
Cho, 1995, A highly conserved nuclear gene for low-level phylogenetics: elongation factor-1α recovers morphology-based tree for heliothine moths, Mol. Biol. Evol., 12, 650
Faith, 1991, Cladistic permutation tests for monophyly and nonmonophyly, Syst. Zool., 40, 366, 10.2307/2992329
Felsenstein, J., 1993. PHYLIP 3.5 (phylogeny inference package). Department of Genetics, University of Washington
Fitch, 1971, Rate of change of concomitantly variable codons, J. Mol. Evol., 1, 84, 10.1007/BF01659396
Fitch, 1970, An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution, Biochem. Genet., 4, 579, 10.1007/BF00486096
Friedlander, 1998, Two nuclear genes yield concordant relationships within Attacini (Lepidoptera: Saturniidae), Mol. Phylogenet. Evol., 9, 131, 10.1006/mpev.1997.9999
Galtier, 2001, Maximum-likelihood phylogenetic analysis under a covarion-like model, Mol. Biol. Evol., 18, 866, 10.1093/oxfordjournals.molbev.a003868
Graessmann, 1992, Characterization of the elongation factor 1-α gene of Rhynchosciara americana, Nucleic Acids Res., 20, 3780, 10.1093/nar/20.14.3780
Kuhner, 1994, A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol. Biol. Evol., 11, 459
Lake, 1994, Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances, Proc. Natl. Acad. Sci. USA, 91, 1455, 10.1073/pnas.91.4.1455
Lenstra, 1986, Genes coding for the elongation factor EF-1α in Artemia, Eur. J. Biochem., 155, 475, 10.1111/j.1432-1033.1986.tb09514.x
Lockhart, 1994, Recovering evolutionary trees under a more realistic model of sequence evolution, Mol. Biol. Evol., 11, 605
Lockhart, 1998, A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages, Mol. Biol. Evol., 15, 1183, 10.1093/oxfordjournals.molbev.a026025
Lockhart, 2000, How molecules evolve in eubacteria, Mol. Biol. Evol., 17, 835, 10.1093/oxfordjournals.molbev.a026363
Lopez, 1999, The root of the tree of life in the light of the covarion model, J. Mol. Evol., 49, 496, 10.1007/PL00006572
Lyons-Weiler, 1996, Relative Apparent Synapomorphy Analysis (RASA) I: the statistical measurement of phylogenetic signal, Mol. Biol. Evol., 13, 749, 10.1093/oxfordjournals.molbev.a025635
Miyamoto, 1995, Testing the covarion hypothesis of molecular evolution, Mol. Biol. Evol., 12, 503
Penny, 2001, Mathematical elegance with biochemical realism: the covarion model of molecular evolution, J. Mol. Evol., 53, 711, 10.1007/s002390010258
Philippe, 1999, The rooting of the universal tree of life is not reliable, J. Mol. Evol., 49, 509, 10.1007/PL00006573
Pupko, 2002, A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes, Proc. R. Soc. Lond. B. Bio, 269, 1313, 10.1098/rspb.2002.2025
Regier, 1997, Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods, Mol. Biol. Evol., 14, 902, 10.1093/oxfordjournals.molbev.a025833
Ritland, 1990, Optimal DNA sequence divergence for testing phylogenetic hypotheses, 289
Steel, 1995, A frequency-dependent significance test for parsimony, Mol. Phylogenet. Evol., 4, 64, 10.1006/mpev.1995.1006
Steel, 1993, Confidence in evolutionary trees from biological sequence data, Nature, 364, 440, 10.1038/364440a0
Swofford, 1993
Uzzel, 1971, Fitting discrete probability distributions to evolutionary events, Science, 172, 1089, 10.1126/science.172.3988.1089
Walldorf, 1990, Apis mellifera cytoplasmic elongation factor 1α (EF-1α) is closely related to Drosophila melanogaster EF-1α, FEBS, 267, 245, 10.1016/0014-5793(90)80936-D
Xia, 1998, The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes, Mol. Biol. Evol., 15, 336, 10.1093/oxfordjournals.molbev.a025930
Xia, 2000
Xia, 2001, DAMBE: data analysis in molecular biology and evolution, J. Hered., 92, 371, 10.1093/jhered/92.4.371
Xia, 1996, On transition bias in mitochondrial genes of pocket gophers, J. Mol. Evol., 43, 32, 10.1007/BF02352297
Yang, 1996, Maximum-likelihood models for combined analyses of multiple sequence data, J. Mol. Evol., 42, 587, 10.1007/BF02352289
Yang, 1996, Among-site rate variation and its impact on phylogenetic analysis, TREE, 11, 367
Yang, 2000