A New Analysis of Archaea-Bacteria Domain Separation : Variable Phylogenetic Distance and the Tempo of Early Evolution

© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution..

Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.

Medienart:	E-Artikel

Erscheinungsjahr:	2020
Erschienen:	2020

Enthalten in:	Zur Gesamtaufnahme - volume:37
Enthalten in:	Molecular biology and evolution - 37(2020), 8 vom: 01. Aug., Seite 2332-2340

Sprache:	Englisch

Beteiligte Personen:	Berkemer, Sarah J [VerfasserIn] McGlynn, Shawn E [VerfasserIn]

Links:	Volltext

Themen:	Archaeal Proteins Bacterial Proteins Conserved orthologous groups of proteins Journal Article LUCA Microbial physiology Orthology Progenote Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Anmerkungen:	Date Completed 02.04.2021 Date Revised 02.04.2021 published: Print Citation Status MEDLINE

doi:	10.1093/molbev/msaa089

funding:
Förderinstitution / Projekttitel:

PPN (Katalog-ID):	NLM309004632