A geological timescale for bacterial evolution and oxygen adaptation

Adrián A. Davín; Ben J. Woodcroft; Rochelle M. Soo; Benoit Morel; Ranjani Murali; Dominik Schrempf; James W  Clark; Sandra Alvarez-Carretero; Bastien Boussau; Edmund R R Moody; Lenard Szantho; Etienne M A M Richy; Davide Pisani; James Hemp; Woodward Fischer; Philip C J Donoghue; Anja Spang; Philip Hugenholtz; Tom Williams; Gergely J. Szollosi

doi:10.1126/science.adp1853

A geological timescale for bacterial evolution and oxygen adaptation

Adrián A. Davín^*, Ben J. Woodcroft^*, Rochelle M. Soo, Benoit Morel, Ranjani Murali, Dominik Schrempf, James W Clark, Sandra Alvarez-Carretero, Bastien Boussau, Edmund R R Moody, Lenard Szantho, Etienne M A M Richy, Davide Pisani, James Hemp, Woodward Fischer, Philip C J Donoghue, Anja Spang, Philip Hugenholtz^*, Tom Williams^*, Gergely J. Szollosi^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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Abstract

Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ~2.33 billion years ago (Ga). Here, we combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial timetree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Cambrian. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, aerobic metabolism likely pre-dated the GOE in the cyanobacterial ancestor, which may have facilitated the evolution of oxygenic photosynthesis.

Original language	English
Article number	eadp1853
Pages (from-to)	eadp1853
Number of pages	12
Journal	Science
Volume	388
Issue number	6742
DOIs	https://doi.org/10.1126/science.adp1853
Publication status	Published - 4 Apr 2025

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© 2025 American Association for the Advancement of Science. All rights reserved.

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Accepted author manuscript, 25 MBLicence: CC BY

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Efficient computational technologies to resolve the Timetree of Life: from ancient DNA to species-rich phylogenies
Donoghue, P. C. J. (Principal Investigator)
1/08/24 → 31/07/27
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Davín, A. A., Woodcroft, B. J., Soo, R. M., Morel, B., Murali, R., Schrempf, D., Clark, J. W., Alvarez-Carretero, S., Boussau, B., Moody, E. R. R., Szantho, L., Richy, E. M. A. M., Pisani, D., Hemp, J., Fischer, W., Donoghue, P. C. J., Spang, A., Hugenholtz, P., Williams, T., & Szollosi, G. J. (2025). A geological timescale for bacterial evolution and oxygen adaptation. Science, 388(6742), eadp1853. Article eadp1853. https://doi.org/10.1126/science.adp1853

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title = "A geological timescale for bacterial evolution and oxygen adaptation",

abstract = "Microbial life has dominated Earth{\textquoteright}s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ~2.33 billion years ago (Ga). Here, we combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial timetree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Cambrian. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, aerobic metabolism likely pre-dated the GOE in the cyanobacterial ancestor, which may have facilitated the evolution of oxygenic photosynthesis. ",

author = "Dav{\'i}n, {Adri{\'a}n A.} and Woodcroft, {Ben J.} and Soo, {Rochelle M.} and Benoit Morel and Ranjani Murali and Dominik Schrempf and Clark, {James W} and Sandra Alvarez-Carretero and Bastien Boussau and Moody, {Edmund R R} and Lenard Szantho and Richy, {Etienne M A M} and Davide Pisani and James Hemp and Woodward Fischer and Donoghue, {Philip C J} and Anja Spang and Philip Hugenholtz and Tom Williams and Szollosi, {Gergely J.}",

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doi = "10.1126/science.adp1853",

language = "English",

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Davín, AA, Woodcroft, BJ, Soo, RM, Morel, B, Murali, R, Schrempf, D, Clark, JW, Alvarez-Carretero, S, Boussau, B, Moody, ERR, Szantho, L, Richy, EMAM, Pisani, D, Hemp, J, Fischer, W, Donoghue, PCJ, Spang, A, Hugenholtz, P, Williams, T & Szollosi, GJ 2025, 'A geological timescale for bacterial evolution and oxygen adaptation', Science, vol. 388, no. 6742, eadp1853, pp. eadp1853. https://doi.org/10.1126/science.adp1853

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T1 - A geological timescale for bacterial evolution and oxygen adaptation

AU - Davín, Adrián A.

AU - Woodcroft, Ben J.

AU - Soo, Rochelle M.

AU - Morel, Benoit

AU - Murali, Ranjani

AU - Schrempf, Dominik

AU - Clark, James W

AU - Alvarez-Carretero, Sandra

AU - Boussau, Bastien

AU - Moody, Edmund R R

AU - Szantho, Lenard

AU - Richy, Etienne M A M

AU - Pisani, Davide

AU - Hemp, James

AU - Fischer, Woodward

AU - Donoghue, Philip C J

AU - Spang, Anja

AU - Hugenholtz, Philip

AU - Williams, Tom

AU - Szollosi, Gergely J.

PY - 2025/4/4

Y1 - 2025/4/4

N2 - Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ~2.33 billion years ago (Ga). Here, we combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial timetree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Cambrian. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, aerobic metabolism likely pre-dated the GOE in the cyanobacterial ancestor, which may have facilitated the evolution of oxygenic photosynthesis.

AB - Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ~2.33 billion years ago (Ga). Here, we combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial timetree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Cambrian. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, aerobic metabolism likely pre-dated the GOE in the cyanobacterial ancestor, which may have facilitated the evolution of oxygenic photosynthesis.

U2 - 10.1126/science.adp1853

DO - 10.1126/science.adp1853

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SP - eadp1853

JO - Science

JF - Science

IS - 6742

M1 - eadp1853

ER -

A geological timescale for bacterial evolution and oxygen adaptation

Abstract

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Efficient computational technologies to resolve the Timetree of Life: from ancient DNA to species-rich phylogenies

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