Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …

Models of character evolution underpin all phylogeny estimations, thus model adequacy
remains a crucial issue for phylogenetics and its many applications. Although progress has …

Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed
many key mechanisms of molecular evolution. One criticism of the approach is an inability to …

Background Explicit evolutionary models are required in maximum-likelihood and Bayesian
inference, the two methods that are overwhelmingly used in phylogenetic studies of DNA …

The use of modelbased methods to infer a phylogenetic tree from a given data set is
frequently motivated by the truism that under certain circumstances the parsimony approach …

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 …

It is now well known that incomplete lineage sorting can cause serious difficulties for
phylogenetic inference, but little attention has been paid to methods that attempt to …

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 …

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 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 …