Abstract

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

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Acknowledgements

G.J.Sz. received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 714774. This project was supported by the French Agence Nationale de la Recherche through grant no. ANR-10-BINF-01–01 ‘Ancestrome’. Computations were performed using the Curie supercomputer thanks to PRACE project 2013081661 and the computing facilities of the CC LBBE/PRABI. T.A.W. is supported by a Royal Society University Research Fellowship. We thank N. Lartillot, T. Warnow, M. Paris, I. Derényi, L. Nagy and J. Miguel Blanca Postigo for discussions, comments on the manuscript and additional computing resources.

Author information

Affiliations

  1. Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France

    • Adrián A. Davín
    • , Eric Tannier
    • , Bastien Boussau
    •  & Vincent Daubin
  2. Inria Grenoble Rhône–Alpes, Montbonnot, France

    • Eric Tannier
  3. School of Biological Sciences, University of Bristol, Bristol, UK

    • Tom A. Williams
  4. MTA-ELTE ‘Lendulet’ Evolutionary Genomics Research Group, Budapest, Hungary

    • Gergely J. Szöllősi
  5. Department of Biological Physics, Eotvos Lorand University, Budapest, Hungary

    • Gergely J. Szöllősi

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Contributions

E.T., B.B., V.D. and G.J.Sz. conceived the study. A.A.D., B.B., E.T. and G.J.Sz. developed the computational tools, T.A.W. contributed datasets, and A.A.D., E.T., B.B., T.A.W., V.D. and G.J.Sz. analysed the data, interpreted the results and wrote the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Vincent Daubin or Gergely J. Szöllősi.

Supplementary information

  1. Supplementary Information

    Supplementary Methods, Supplementary Figures 1–29, Supplementary Tables 1–4.

  2. Life Sciences Reporting Summary

  3. Supplementary Table 5

    Constraints and their support in cyanobacteria.

  4. Supplementary Table 6

    Constraints and their support in archaea.

  5. Supplementary Table 7

    Constraints and their support in fungi.

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DOI

https://doi.org/10.1038/s41559-018-0525-3