Abstract Model-based molecular phylogenetics plays an important role in comparisons of
genomic data, and model selection is a key step in all such analyses. We present …

▪ Abstract Investigation into model selection has a long history in the statistical literature. As
model-based approaches begin dominating systematic biology, increased attention has …

In order to have confidence in model-based phylogenetic analysis, the model of nucleotide
substitution adopted must be selected in a statistically rigorous manner. Several model …

2000). For example, we know that sites do not truly evolve independently, that the substitu-
tion process is not completely homogeneous across sites and through time, and that simple …

Almost all studies that estimate phylogenies from DNA sequence data under the maximum-
likelihood (ML) criterion employ an approximate approach. Most commonly, model …

The statistical selection of best-fit models of nucleotide substitution is routine in the
phylogenetic analysis of DNA sequence alignments. The programs ModelTest1 and …

Bayesian inference is becoming a common statistical approach to phylogenetic estimation
because, among other reasons, it allows for rapid analysis of large data sets with complex …

Phylogenetic estimation has largely come to rely on explicitly model-based methods. This
approach requires that a model be chosen and that that choice be justified. To date …

Currently available methods for model selection used in phylogenetic analysis are based on
an initial fixed-tree topology. Once a model is picked based on this topology, a rigorous …

Phylogenetic comparative methods may fail to produce meaningful results when either the
underlying model is inappropriate or the data contain insufficient information to inform the …