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Molecular clocks provide little information to date methanogenic Archaea

Nature Ecology & Evolution volume 2, pages 1676–1677 (2018)Cite this article

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To the Editor — Wolfe and Fournier describe a lateral gene transfer (LGT) of ‘structural maintenance of chromosomes’ (SMC) genes from methanogenic euryarchaeote Archaea to an ancestor of the Cyanobacteria1. They conducted a relaxed molecular clock (RMC) analysis using a phylogeny estimated from the SMC proteins concatenated with ribosomal proteins from Archaea and Cyanobacteria calibrated with two dates based on microfossils and isotopic data from ancient rocks. Based on their analyses they conclude that extant euryarchaeal methanogens diversified prior to 3.51 billion years ago (Ga) creating an ancient ‘microbial methane greenhouse’ on Earth. Here we highlight several problems with the analyses.

In the RMC analysis, the calibration prior distribution for the archaeal root had a mean of 3.9 Ga and 95% probability interval 3.44–4.36 Ga. The lower value, 3.44 Ga, roughly matches the age of the first isotopic evidence for microbial methanogenesis (3.46 Ga)2. The authors assume methanogenesis originated within the euryarchaeote phylum of Archaea, so the archaeal root must be older than the first signatures of this process.

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Fig. 1: A plausible origin of methanogenesis and phylogeny of Archaea.

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Acknowledgements

We thank L. Eme for constructive comments. Financial support comes from Discovery Grants from the Natural Sciences and Engineering Research Council of Canada awarded to A.J.R. and E.S. A.J.R. acknowledges support from the Canada Research Chairs Program.

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Authors and Affiliations

  1. Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada

    Andrew J. Roger & Edward Susko

  2. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

    Andrew J. Roger

  3. Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada

    Edward Susko

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  1. Andrew J. Roger
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Correspondence to Andrew J. Roger.

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Roger, A.J., Susko, E. Molecular clocks provide little information to date methanogenic Archaea. Nat Ecol Evol 2, 1676–1677 (2018). https://doi.org/10.1038/s41559-018-0687-z

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