Resolving the genealogy of life—the phylogenetic relationships that describe the
evolutionary history of species—remains one of the great challenges of systematic biology …

This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …

The COVID-19 pandemic has seen an unprecedented response from the sequencing
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes …

Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the
study of evolution because it enables accounting for discordance among evolutionary …

Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving
factor behind these phylogenomic studies is the promise that the potential discordance …

Introduction Reconstructing species trees for rapid radiations, as in the early diversification
of birds, is complicated by biological processes such as incomplete lineage sorting (ILS) that …

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a
phenomenon known as epistasis. Epistasis can profoundly influence the process of …

Many models of evolution calculate the rate of evolution by multiplying the rate at which new
mutations originate within a population by a probability of fixation. Here we review the …

ABSTRACT Building the Tree of Life (ToL) is a major challenge of modern biology, requiring
advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that …