Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

Abstract

Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth’s history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053–1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.

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Fig. 1: Posterior time estimates under different parameters.
Fig. 2: Changes in divergence times (Ga) that result from applying alternative parameters.
Fig. 3: A tree combining uncertainties from approaches using uncorrelated and autocorrelated clock models and different calibration density distributions.

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Acknowledgements

H.C.B. was supported by a NERC GW4 PhD studentship. J.W.C. was supported by a BBSRC SWBio PhD studentship. M.N.P. was supported by an 1851 Royal Commission Fellowship. P.C.J.D. was supported by BBSRC grant BB/N000919/1. T.A.W. is supported by a Royal Society Fellowship and NERC grant NE/P00251X/1.

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D.P., P.C.J.D. and T.A.W. designed the study. H.C.B. assembled the datasets and performed the phylogenetic and molecular clock analyses. M.N.P. and J.W.C. contributed further molecular clock analyses. H.C.B., D.P., P.C.J.D. and T.A.W. wrote the manuscript. All authors edited the manuscript and approved the final version.

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Correspondence to Davide Pisani.

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Betts, H.C., Puttick, M.N., Clark, J.W. et al. Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin. Nat Ecol Evol 2, 1556–1562 (2018). https://doi.org/10.1038/s41559-018-0644-x

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