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Bacterial diversification through geological time

Abstract

Numerous studies have estimated plant and animal diversification dynamics; however, no comparable rigorous estimates exist for bacteria—the most ancient and widespread form of life on Earth. Here, we analyse phylogenies comprising up to 448,112 bacterial lineages to reconstruct global bacterial diversification dynamics. To handle such large phylogenies, we developed methods based on the statistical properties of infinitely large trees. We further analysed sequencing data from 60 environmental studies to determine the fraction of extant bacterial diversity missing from the phylogenies—a crucial parameter for estimating speciation and extinction rates. We estimate that there are about 1.4–1.9 million extant bacterial lineages when lineages are defined by 99% similarity in the 16S ribosomal RNA gene, and that bacterial diversity has been continuously increasing over the past 1 billion years (Gyr). Recent bacterial extinction rates are estimated at 0.03–0.05 per lineage per million years (lineage–1 Myr–1), and are only slightly below estimated recent bacterial speciation rates. Most bacterial lineages ever to have inhabited this planet are estimated to be extinct. Our findings disprove the notion that bacteria are unlikely to go extinct, and provide a valuable perspective on the evolutionary history of a domain of life with a sparse and cryptic fossil record.

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Acknowledgements

We thank D. H. Parks for providing the 16S rRNA sequences from MAGs48. S.L. was supported by an NSERC grant and a postdoctoral fellowship from the Biodiversity Research Centre, University of British Columbia. M.W.P., M.D. and L.W.P. were supported by NSERC Discovery Grants. P.M.S. was supported by The Branco Weiss Fellowship – Society in Science. W.W.F. acknowledges support from the Simons Collaboration on the Origins of Life and NASA Exobiology award number NNX16AJ57G.

Author information

S.L., L.W.P. and M.D. conceived the project. S.L. developed the mathematical methods, performed the diversification analyses and wrote the first draft of the manuscript. P.M.S. performed the molecular clock analyses of the BEAST trees, provided the cyanobacterial multigene tree and contributed to the development of the project ideas. All authors helped to interpret the results, advised on methodological improvements and contributed to writing the manuscript.

Competing interests

The authors declare no competing interests.

Correspondence to Stilianos Louca.

Supplementary information

  1. Supplementary Information

    Supplementary methods, figures and tables.

  2. Reporting Summary

  3. Supplementary file 1

    Accession numbers and summaries of amplicon sequencing data used to recover de novo OTUs.

  4. Supplementary file 2

    Accession numbers and summaries of sequencing data used from the Earth Microbiome Project.

  5. Supplementary file 3

    R code used for analysing diversification dynamics, including required input files.

  6. Supplementary file 4

    Time trees and undated phylogenetic trees constructed in this study.

  7. Supplementary file 5

    Taxonomic classifications of de novo OTUs.

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Fig. 1: Non-parametric methods capture complex diversification scenarios.
Fig. 2: Bacterial, cyanobacterial and bird diversification dynamics through time.
Fig. 3: Estimated recent speciation, extinction and diversification rates.