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• W2012184427 abstract "Kelchner and Thomas addressed nine key questions regarding the use of stochastic models in phylogenetics [ 2 Kelchner S.A. Thomas M.A. Model use in phylogenetics: nine key questions. Trends Ecol. Evol. 2007; 22: 87-94 Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar ]. A tenth crucial question was not explored in detail in their TREE review: ‘In modern systematic studies, how often is the fit between model and data absolutely poor?’ At their best, models should provide adequate explanations of complex biological patterns. Yet until now, systematists have been preoccupied primarily with the relative fit of competing models to DNA datasets [ 3 Posada D. Crandall K. Model test: testing the model of DNA substitution. Bioinformatics. 1998; 14: 817-818 Crossref PubMed Scopus (18096) Google Scholar ]. Simple methods for detecting an absolutely poor fit between DNA sequence data and a particular model have existed for some time [ 1 Reeves J.H. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J. Mol. Evol. 1992; 35: 17-31 Crossref PubMed Scopus (113) Google Scholar , 4 Goldman N. Statistical tests of models of DNA substitution. J. Mol. Evol. 1993; 36: 182-198 Crossref PubMed Scopus (582) Google Scholar , 5 Bollback J.P. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 2002; 19: 1171-1180 Crossref PubMed Scopus (161) Google Scholar , 6 Waddell P.J. Measuring the fit of sequence data to phylogenetic model: allowing for missing data. Mol. Biol. Evol. 2005; 22: 395-401 Crossref PubMed Scopus (13) Google Scholar ], but, unfortunately, these tests have been implemented in relatively few cases [ 7 Sullivan J. Joyce P. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 2005; 36: 445-466 Crossref Scopus (308) Google Scholar ]. Perhaps either buoyed by studies that asserted the robustness of model-based methods [ 8 Sullivan J. Swofford D. Should we use model–based methods for phylogenetic inference when we know assumptions about among–site rate variation and nucleotide substitution patterns are violated?. Syst. Biol. 2001; 50: 723-729 Crossref PubMed Scopus (123) Google Scholar ] or daunted by computational demands, systematists have hidden their heads in the sand for ∼15 years." @default.
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• W2012184427 title "A tenth crucial question regarding model use in phylogenetics" @default.
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• W2012184427 doi "https://doi.org/10.1016/j.tree.2007.08.002" @default.
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