A rooted phylogeny resolves early bacterial evolution

Abstract

Bacteria are the most abundant and metabolically diverse cellular lifeforms on Earth. A rooted bacterial phylogeny provides a framework to interpret this diversity and to understand the nature of early life. Inferring the position of the bacterial root is complicated by incomplete taxon sampling and the long branch to the archaeal outgroup. To circumvent these limitations, we model bacterial genome evolution at the level of gene duplication, transfer and loss events, allowing outgroup-free inference of the root1. We infer a rooted bacterial tree on which 68% of gene transmission events are vertical. Our analyses reveal a basal split between Terrabacteria and Gracilicutes, which together encompass almost all known bacterial diversity. However, the position of one phylum, Fusobacteriota, could not be resolved in relation to these two major clades. In contrast to recent proposals, our analyses strongly reject a root between the Candidate Phyla Radiation (CPR) and all other Bacteria. Instead, we find that the CPR is a sister lineage to the Chloroflexota within the Terrabacteria. We predict that the last bacterial common ancestor was a free-living flagellated, rod-shaped cell featuring a double membrane with a lipopolysaccharide outer layer, a Type III CRISPR-Cas system, Type IV pili, and the ability to sense and respond via chemotaxis.