The accrual of genomic data from both cultured and uncultured microorganisms provides
new opportunities to develop systematic taxonomies based on evolutionary relationships. …

INTRODUCTION Bacteria are the most diverse and abundant cellular organisms on Earth,
and in recent years environmental genomics has revealed the existence of an enormous …

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the
origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have …

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is
generally assumed that it has had less influence among eukaryotes. To explore this …

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria,
archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of …

ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on
a common underlying statistical model of how gene trees evolve along species trees, these …

Species tree-aware phylogenetic methods model how gene trees are generated along the
species tree by a series of evolutionary events, including the duplication, transfer and loss of …

Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences
in silico, that considers for the first time the evolution of genomes in extinct lineages. It also …

Motivation A reconciliation is an annotation of the nodes of a gene tree with evolutionary
events—for example, speciation, gene duplication, transfer, loss, etc.—along with a mapping …

Lateral gene transfers between ancient species contain information about the relative timing
of species diversification. Specifically, the ancestors of a donor species must have existed …