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 Sayyari, Maryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab and Rob Knight ()
Additional contact information
Qiyun Zhu: University of California San Diego
Uyen Mai: University of California San Diego
Wayne Pfeiffer: University of California San Diego
Stefan Janssen: University of California San Diego
Francesco Asnicar: University of Trento
Jon G. Sanders: University of California San Diego
Pedro Belda-Ferre: University of California San Diego
Gabriel A. Al-Ghalith: University of Minnesota
Evguenia Kopylova: University of California San Diego
Daniel McDonald: University of California San Diego
Tomasz Kosciolek: University of California San Diego
John B. Yin: University of California San Diego
Shi Huang: University of California San Diego
Nimaichand Salam: Sun Yat-sen University
Jian-Yu Jiao: Sun Yat-sen University
Zijun Wu: University of California San Diego
Zhenjiang Z. Xu: University of California San Diego
Kalen Cantrell: University of Minnesota
Yimeng Yang: University of Minnesota
Erfan Sayyari: University of California San Diego
Maryam Rabiee: University of California San Diego
James T. Morton: University of California San Diego
Sheila Podell: University of California San Diego
Dan Knights: University of Minnesota
Wen-Jun Li: Sun Yat-sen University
Curtis Huttenhower: Harvard T. H. Chan School of Public Health
Nicola Segata: University of Trento
Larry Smarr: University of California San Diego
Siavash Mirarab: Jagiellonian University
Rob Knight: University of California San Diego

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract 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.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13443-4

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DOI: 10.1038/s41467-019-13443-4

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