A rooted phylogeny resolves early bacterial evolution

Bacteria are the most diverse and abundant cellular organisms on Earth, and in recent years environmental genomics has revealed the existence of an enormous diversity of previously unknown lineages. Despite the abundance of genomic sequence data, the root of the bacterial tree and the nature of the most recent common ancestor of Bacteria have remained elusive. The problem is that even with the help of new data, tracing billions of years of bacterial evolution back to the root has remained challenging because standard phylogenetic models do not account for the full range of evolutionary processes that shape bacterial genomes. In particular, standard models treat horizontal gene transfer as an impediment to the reconstruction of the tree of life thatmust be removed fromanalyses. But if horizontal gene transfer is modeled appropriately, it can provide information about the deep past that is unavailable to standard methods.