The archaeal domain is currently divided into two major phyla, the Euryarchaeota and
Crenarchaeota. During the past few years, diverse groups of uncultivated mesophilic archaea …

Progress in genome sequencing now enables the large-scale generation of reference genomes.
Various international initiatives aim to generate reference genomes representing global …

The availability of public genomic resources can greatly assist biodiversity assessment,
conservation, and restoration efforts by providing evidence for scientifically informed …

To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite
of models. Consequently, users of these software packages are simultaneously forced to …

Comparisons of gene trees and species trees are key to understanding major processes of
genome evolution such as gene duplication and loss. Because current methods to …

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 improving …

Fossils of organisms dating from the origin and diversification of cellular life are scant and
difficult to interpret 1 , for this reason alternative means to investigate the ecology of the last …

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 …

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early
cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated …