In the quest to reconstruct the Tree of Life, researchers have increasingly turned to
phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box …

The comparative approach is routinely used to test for possible correlations between
phenotypic or life-history traits. To correct for phylogenetic inertia, the method of …

Congruence is a broadly applied notion in evolutionary biology used to justify multigene
phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and …

Modeling the interplay between mutation and selection at the molecular level is key to
evolutionary studies. To this end, codon-based evolutionary models have been proposed as …

The physical sciences have long recognized the distinction between formal descriptions of
observations versus explanations for observations, with the canonical example embodied in …

Motivation: In recent years, there has been an increasing interest in the potential of codon
substitution models for a variety of applications. However, the computational demands of …

Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists,
systematists, ecologists, and epidemiologists to obtain answers to very detailed …

The use of amino acid substitution matrices to model protein evolution has yielded important
insights into both the evolutionary process and the properties of specific protein families. In …

Codon-based models of evolution are a relatively new addition to the toolkit of
computational biologists, and in recent years remarkable progress has been made in this …

Chloridoideae (chloridoid grasses) are a subfamily of ca. 1700 species with high diversity in
arid habitats. Until now, their evolutionary relationships have primarily been studied with …