Feb 6, 2020

The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets

Systematic Biology
Xiaodong JiangLiang Liu

Abstract

A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation...Continue Reading

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Mentioned in this Paper

Insecta
Study
Phylogenetic Analysis
Statistical Test
Logistic Regression
Validation
Multilocus Sequence Typing
Locus
Aves
Genetic Pedigree

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