A new view of the tree of life

TLDR

The tree of life is a fundamental organizing principle in biology, yet its full scale remains elusive because previous depictions focused on deep relationships or well‑classified eukaryotes, overlooking the dramatic changes revealed by genomic sampling of previously unexamined environments. The authors aim to infer a dramatically expanded tree of life that includes Bacteria, Archaea, and Eukarya by integrating new genomic data from over 1,000 uncultivated and little‑known organisms with published sequences. They employed novel genome‑sequencing methods to generate and analyze genomes from these uncultivated organisms, placing them in community and ecosystem contexts to reconstruct the expanded phylogeny. The resulting tree provides a global overview and snapshot of diversity, revealing bacterial diversification dominance, underrepresentation of certain lineages in biogeochemical models, and major radiations that may be pivotal for future evolutionary analyses.

Abstract

The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts(7,8). Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.