Rapid growth of genome data provides opportunities for updating microbial evolutionaryrelationships, but this is challenged by the discordant evolution of individual genes. Here webuild a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, basedon a comprehensive set of 381 markers, using multiple strategies. Our trees indicateremarkably closer evolutionary proximity between Archaea and Bacteria than previousestimates that were limited to fewer“core”genes, such as the ribosomal proteins. Therobustness of the results was tested with respect to several variables, including taxon and sitesampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, andthe impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide anupdated view of domain-level relationships.
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea / Zhu, Qiyun; Mai, Uyen; Pfeiffer, Wayne; Janssen, Stefan; Asnicar, Francesco; Sanders, Jon G.; Belda-Ferre, Pedro; Al-Ghalith, Gabriel A.; Kopylova, Evguenia; Mcdonald, Daniel; Kosciolek, Tomasz; Yin, John B.; Huang, Shi; Salam, Nimaichand; Jiao, Jian-Yu; Wu, Zijun; Xu, Zhenjiang Z.; Cantrell, Kalen; Yang, Yimeng; Sayyari, Erfan; Rabiee, Maryam; Morton, James T.; Podell, Sheila; Knights, Dan; Li, Wen-Jun; Huttenhower, Curtis; Segata, Nicola; Smarr, Larry; Mirarab, Siavash; Knight, Rob. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 10:1(2019), pp. 5477.1-5477.14. [10.1038/s41467-019-13443-4]
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Asnicar, Francesco;Segata, Nicola;
2019-01-01
Abstract
Rapid growth of genome data provides opportunities for updating microbial evolutionaryrelationships, but this is challenged by the discordant evolution of individual genes. Here webuild a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, basedon a comprehensive set of 381 markers, using multiple strategies. Our trees indicateremarkably closer evolutionary proximity between Archaea and Bacteria than previousestimates that were limited to fewer“core”genes, such as the ribosomal proteins. Therobustness of the results was tested with respect to several variables, including taxon and sitesampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, andthe impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide anupdated view of domain-level relationships.| File | Dimensione | Formato | |
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