Origin & Evolution of Life

An Evolutionary Timescale For Bacteria Calibrated Using The Great Oxidation Event

By Keith Cowing

Status Report

biorxiv.org

August 16, 2023

Filed under aerobic respiration, Anaerobic, atmosphere, Bacteria, biorxiv.org, evolution, fossils, Great Oxidation Event, microbiology

An Evolutionary Timescale For Bacteria Calibrated Using The Great Oxidation Event — Bacterial evolution through geological time. (a) The early evolution of bacterial genetic diversity in the Archaean (David and Alm 2010) is reflected by rapid increase in gene content disparity (see Supplementary Material). (b) A persistent higher diversification rate of aerobes since the GOE. The line charts the relative diversification rate (the ratio of the inverse of the waiting time to the next speciation event) for aerobic and anaerobic lineages, revealing a persistent higher diversification rate of aerobes for most of the Earth’s history since the GOE. Rates equilibrated prior to the NOE, before a return to higher diversification rates for aerobes since the GOE. The dotted line denotes a ratio of 1, where the diversification rate of aerobic and anaerobic lineages is equal. Terminal branches were omitted and ratios since 100 Mya were not calculated do to a low number of nodes. (c) Spread of aerobic metabolism by HGT. Transitions from anaerobic to aerobic lifestyles have outnumbered transitions in the reverse direction/back transitions/returns to anaerobicity for most of Earth history since the GOE. The plots show the ratio of aerobic to anaerobic transition rates on the dated species tree during each time period. The dotted line denotes a ratio of 1, where transitions occur in both directions at the same rate. The small number of nodes since ~200 Ma greatly increases uncertainty for both analyses, as reflected in the wide confidence intervals of posterior node age estimates. Ratios since 100 Mya were not calculated due to a low number of nodes. (d) shows the number of aerobic lineages according to Figure 2, e) qualitative sketch of atmospheric oxygen levels through time based on (Lyons, Reinhard, and Planavsky 2014; Poulton et al. 2021; Krause et al. 2022). The grey line shows the Moon-forming impact at ~4.52 Ga; the green line at ~3.23 Ga reflects the presence of fossil and isotopic evidence for oxygenic photosynthesis; the red line at ~2.33 Ga reflects the end of the GOE (see calibrations in Supplementary Material). — biorxiv.org

Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time.

However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ∼2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earth’s biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution.

Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE.

Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial diversity over hundreds of millions of years. Our analyses demonstrate that the diversification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O2 at the dawn of the Palezoic (Krause et al. 2022).

A dated phylogeny of Bacteria. a) dated phylogenetic tree of Bacteria. Branch colours represent anaerobic (blue) and aerobic lineages (red). Mitochondrial branches are colored in orange while chloroplast branches are coloured in green. Branch lengths are proportional to geological time (Ga). 95% highest posterior densities are shown for the root, and the two major bacterial divisions Gracilicutes and Terrabacteria. The grey line shows the Moon-forming impact at ~4.52 Ga; the green line at ~3.23 Ga reflects the presence of fossil and isotopic evidence for oxygenic photosynthesis; the red line at ~2.33 Ga reflects the end of the GOE (see calibrations in Supplementary Material). The bottom panel shows the ages of taxonomic groups. The names of phyla represented by 8 or more genomes are shown. We show the age of the last common ancestors of major taxa (phyla, class, order and family) represented in our 1007 genomes dataset by at least 3 genomes. The median ages are: phyla: 2115 Ma; class: 1524 Ma; order: 11120 Ma; family: 655 Ma. Black dots denote nodes that were directly calibrated in molecular clock analyses. — biorxiv.org

https://www.biorxiv.org/content/10.1101/2023.08.08.552427v1

Astrobiology

Keith Cowing

Explorers Club Fellow, ex-NASA Space Station Payload manager/space biologist, Away Teams, Journalist, Lapsed climber, Synaesthete, Na’Vi-Jedi-Freman-Buddhist-mix, ASL, Devon Island and Everest Base Camp veteran, (he/him) 🖖🏻

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