The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate
oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing …

In the last decade, we witnessed the ascent of reconciliations as an important tool to model
and study the evolution of gene families. Reconciliations model discordance between gene …

Trace metals have been an important ingredient for life throughout Earth's history. Here, we
describe the genome-guided cultivation of a member of the elusive archaeal lineage …

A gene tree-species tree reconciliation explains the evolution of a gene tree within the
species tree given a model of gene-family evolution. We describe ecceTERA, a program that …

Mavericks are virus-like mobile genetic elements found in the genomes of eukaryotes.
Although Mavericks encode capsid morphogenesis homologs, their viral particles have not …

Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we
investigate the evolution and function of Asgard thymidylate synthases and other folate …

The evolutionary history of gene families can be complex due to duplications and losses.
This complexity is compounded by the large number of genomes simultaneously considered …

In phylogenetics, reconciliation is an approach to connect the history of two or more
coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree …

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 …

Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family
evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile …