Journal article
Authors list: 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
Publication year: 2019
Journal: Nature Communications
Volume number: 10
eISSN: 2041-1723
Open access status: Gold
DOI Link: https://doi.org/10.1038/s41467-019-13443-4
Publisher: Nature Research
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.
Citation Styles
Harvard Citation style: Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J., et al. (2019) Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea, Nature Communications, 10, Article 5477. https://doi.org/10.1038/s41467-019-13443-4
APA Citation style: Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J., Belda-Ferre, P., Al-Ghalith, G., Kopylova, E., McDonald, D., Kosciolek, T., Yin, J., Huang, S., Salam, N., Jiao, J., Wu, Z., Xu, Z., Cantrell, K., Yang, Y., ...Knight, R. (2019). Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications. 10, Article 5477. https://doi.org/10.1038/s41467-019-13443-4
Keywords
GENE TREE
