Abstract The interface of protein structural biology, protein biophysics, molecular evolution,
and molecular population genetics forms the foundations for a mechanistic understanding of …

Simple Summary In a broad sense, genomic signature refers to characteristics associated to
DNA sequences. Many studies analyze genotype–phenotype patterns in a group of genes …

A number of evolutionary hypotheses can be tested by comparing selective pressures
among sets of branches in a phylogenetic tree. When the question of interest is to identify …

Motivation: The accurate inference of gene trees is a necessary step in many evolutionary
studies. Although the problem of accurate gene tree inference has received considerable …

Substitutions between chemically distant amino acids are known to occur less frequently
than those between more similar amino acids. This knowledge, however, is not reflected in …

One of the key evolutionary events on the scale of the biosphere was an endosymbiosis
between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid …

Evolutionary studies usually use a two-step process to investigate sequence data. Step one
estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods …

As species richness varies along the tree of life, there is a great interest in identifying factors
that affect the rates by which lineages speciate or go extinct. To this end, theoretical …

A central objective in biology is to link adaptive evolution in a gene to structural and/or
functional phenotypic novelties. Yet most analytic methods make inferences mainly from …

Phylogenomic analyses can be performed by analysing gene trees separately and using
coalescent or supertree analyses to retrieve a tree or using the supermatrix approach. In the …