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Bacterial diversification through geological time

Louca, Stilianos and Shih, Patrick M. and Pennell, Matthew W. and Fischer, Woodward W. and Wegener Parfrey, Laura and Doebeli, Michael (2018) Bacterial diversification through geological time. Nature Ecology & Evolution, 2 (9). pp. 1458-1467. ISSN 2397-334X. doi:10.1038/s41559-018-0625-0.

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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.

Item Type:Article
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URLURL TypeDescription ReadCube access
Louca, Stilianos0000-0001-9216-5619
Shih, Patrick M.0000-0002-2119-3345
Pennell, Matthew W.0000-0002-2886-3970
Fischer, Woodward W.0000-0002-8836-3054
Wegener Parfrey, Laura0000-0001-6959-7616
Additional Information:© 2018 Springer Nature Limited. Received 01 February 2018; Accepted 28 June 2018; Published 30 July 2018. We thank D. H. Parks for providing the 16S rRNA sequences from MAGs. 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 Contributions: 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. The authors declare no competing interests. Data availability: Amplicon sequencing data used to recover de novo OTUs are publicly available under the accession numbers listed in Supplementary File 1. Accession numbers for sequencing data used from the EMP32 are listed in Supplementary File 2. R code used in this study is provided as Supplementary File 3. Timetrees and undated phylogenetic trees constructed in this study are provided as Supplementary File 4. Taxonomic classifications of de novo OTUs are provided as Supplementary File 5.
Funding AgencyGrant Number
Natural Sciences and Engineering Research Council of Canada (NSERC)UNSPECIFIED
University of British ColumbiaUNSPECIFIED
Branco Weiss FellowshipUNSPECIFIED
Simons FoundationUNSPECIFIED
Issue or Number:9
Record Number:CaltechAUTHORS:20180806-081804158
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:88583
Deposited By: Tony Diaz
Deposited On:06 Aug 2018 16:42
Last Modified:16 Nov 2021 00:28

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