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

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

There is an expectation that analyses of molecular sequences might be able to distinguish
between alternative hypotheses for ancient relationships, but the phylogenetic methods …

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle
of harmful metal (loids), including that of arsenic, which doubtlessly imposed substantial …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

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 …

Glycopeptide antibiotics are produced by Actinobacteria through biosynthetic gene clusters
that include genes supporting their regulation, synthesis, export and resistance. The …

We describe eMPRess, a software program for phylogenetic tree reconciliation under the
duplication-transfer-loss model that systematically addresses the problems of choosing …

In recent years, phylogenetic reconciliation has emerged as a promising approach for
studying microbial ecology and evolution. The core idea is to model how gene trees evolve …

The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms,
regulating the Earth's redox state, and affecting climate. However, geochemical …