Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B. Yin, Shi Huang, Nimaichand Salam, Jian Yu Jiao, Zijun Wu, Zhenjiang Z. Xu, Kalen Cantrell, Yimeng Yang, Erfan SayyariMaryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight

Research output: Contribution to journalArticlepeer-review

60 Scopus citations


Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Original languageEnglish (US)
Article number5477
JournalNature communications
Issue number1
StatePublished - Dec 1 2019

Bibliographical note

Funding Information:
We are grateful to Victor Nizet, Eric Allen, Milton Saier, Jürgen Schulze, Toni Gabaldó Estevan, Benjamin Hillmann, Arturo Medrano-Soto, Madhusudan Gujral, Monika Kumaraswamy, Jeff Dereus, Anupriya Tripathi, Amnon Amir, Serene Jiang, Yoshiki Vázquez-Baeza, Thant H. Zaw for insightful discussions on this study and additional assistance. This study was supported in part by National Science Foundation grant 1565057 and the Alfred P. Sloan Foundation under grant number G-2017-9838 awarded to R.K. This work used the Comet supercomputer at the San Diego Supercomputer Center through allocation BIO150043, awarded to R.K., L.S. and S.M. through the Extreme Science and Engineering Discovery Environment (XSEDE). Both Comet and XSEDE are funded by the National Science Foundation. S.M., U.M., and M.R. were supported by the National Science Foundation grant III-1845967 to S.M. W.L. was supported by National Natural Science Foundation of China (91951205).

Publisher Copyright:
© 2019, The Author(s).


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