A new view of the tree of life

By L. Hug, B. Baker, Karthik Anantharaman, C. Brown, Alexander J. Probst, C. Castelle, Cristina N Butterfield, Alex W Hernsdorf, Y. Amano, K. Ise and 7 more. 2016

1,983 citations recorded by the source corpus.

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, 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 relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. 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 contexts7,8. 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.

Subfields: Ecology, Genetics, Molecular Biology

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Citations in the corpus

The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics (2017, background): “They span a continuum from recent divergences at the phylogeographic level (Hickerson et al. 2010, Edwards et al. 2016a) to ancient diversification among the major lineages of life (Hinchliff et al. 2015, Hug et al. 2016).”
25 years of serving the community with ribosomal RNA gene reference databases and tools. (2017, background): “The numbers of bacterial and archaeal phyla are currently under a dramatic expansion (Hug et al., 2016; Rinke et al., 2013; Seitz et al., 2016; Zaremba-Niedzwiedzka et al., 2017).”
New CRISPR-Cas systems from uncultivated microbes (2016, background): “We identified another new class 2 Cas protein encoded in the genomes of certain candidate phyla radiation (CPR) bacteria 6,29 (Fig.”
The Transporter Classification Database (TCDB): 2021 update (2020, background): “In addition, we have ongoing projects on probiotic and pathogenic Lactobacillus species, seven species of sulfur reducing proteobacteria, four different phyla of the recently discovered ‘Candidatus Phylum Radiation’ (CPR) nanobacteria (19,20), and four phyla of the newly discovered Asgard archaeal s”