Article | Published:

Horizontal gene transfer constrains the timing of methanogen evolution

Nature Ecology & Evolutionvolume 2pages897903 (2018) | Download Citation


Microbial methanogenesis may have been a major component of Earth’s carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun’s lower luminosity at the time. Evaluation of potential solutions to the ‘faint young Sun’ hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use a temporal constraint: a horizontal gene transfer event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown-group fossils. Results of molecular clock analyses calibrated by this horizontal-gene-transfer-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 billion years ago, with methanogenesis itself probably evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from $8.99

All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Battistuzzi, F. U., Feijao, A. & Hedges, S. B. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4, 44 (2004).

  2. 2.

    Haqq-Misra, J. D., Domagal-Goldman, S. D., Kasting, P. J. & Kasting, J. F. A revised, hazy methane greenhouse for the Archean Earth. Astrobiology 8, 1127–1137 (2008).

  3. 3.

    Gao, B. & Gupta, R. S. Phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis. BMC Genom. 8, 86 (2007).

  4. 4.

    Hinrichs, K.-U. Microbial fixation of methane carbon at 2.7 Ga: was an anaerobic mechanism possible? Geochem. Geophys. Geosyst. 3, 1–10 (2002).

  5. 5.

    Ueno, Y., Yamada, K., Yoshida, N., Maruyama, S. & Isozaki, Y. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440, 516–519 (2006).

  6. 6.

    Marin, J., Battistuzzi, F. U., Brown, A. C. & Hedges, S. B. The timetree of prokaryotes: new insights into their evolution and speciation. Mol. Biol. Evol. 34, 437–446 (2017).

  7. 7.

    Battistuzzi, F. U. & Hedges, S. B. A major clade of prokaryotes with ancient adaptations to life on land. Mol. Biol. Evol. 26, 335–343 (2009).

  8. 8.

    Sheridan, P. P., Freeman, K. H. & Brenchley, J. E. Estimated minimal divergence times of the major bacterial and archaeal phyla. Geomicrobiol. J. 20, 1–14 (2003).

  9. 9.

    Blank, C. E. Not so old archaea—the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology 7, 495–514 (2009).

  10. 10.

    Lozano-Fernandez, J., dos Reis, M., Donoghue, P. C. J. & Pisani, D. RelTime rates collapse to a strict clock when estimating the timeline of animal diversification. Genome Biol. Evol. 9, 1320–1328 (2017).

  11. 11.

    Parham, J. F. et al. Best practices for justifying fossil calibrations. Syst. Biol. 61, 346–359 (2012).

  12. 12.

    Brocks, J. J. & Pearson, A. Building the biomarker tree of life. Rev. Mineral. Geochem. 59, 233–258 (2005).

  13. 13.

    Rasmussen, B., Fletcher, I. R., Brocks, J. J. & Kilburn, M. R. Reassessing the first appearance of eukaryotes and cyanobacteria. Nature 455, 1101–1104 (2008).

  14. 14.

    Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).

  15. 15.

    Da Cunha, V., Gaia, M., Gadelle, D., Nasir, A. & Forterre, P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. 13, e1006810 (2017).

  16. 16.

    Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).

  17. 17.

    Gogarten, J. P., Murphey, R. D. & Olendzenski, L. Horizontal gene transfer: pitfalls and promises. Biol. Bull. 196, 359–362 (1999).

  18. 18.

    Huang, J., Xu, Y. & Gogarten, J. P. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol. 22, 2142–2146 (2005).

  19. 19.

    Petitjean, C., Moreira, D., López-García, P. & Brochier-Armanet, C. Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in archaea. BMC Evol. Biol. 12, 226 (2012).

  20. 20.

    Szöllősi, G. J., Boussau, B., Abby, S. S., Tannier, E. & Daubin, V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Natl Acad. Sci. USA 109, 17513–17518 (2012).

  21. 21.

    Szöllősi, G. J., Tannier, E., Lartillot, N. & Daubin, V. Lateral gene transfer from the dead. Syst. Biol. 62, 386–397 (2013).

  22. 22.

    Rothman, D. H. et al. Methanogenic burst in the end-Permian carbon cycle. Proc. Natl Acad. Sci. USA 111, 5462–5467 (2014).

  23. 23.

    Sauquet, H. et al. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst. Biol. 61, 289–313 (2012).

  24. 24.

    Schenk, J. J. Consequences of secondary calibrations on divergence time estimates. PLoS ONE 11, e0148228 (2016).

  25. 25.

    Soppa, J. Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins. Gene 278, 253–264 (2001).

  26. 26.

    Cobbe, N. & Heck, M. M. S. The evolution of SMC proteins: phylogenetic analysis and structural implications. Mol. Biol. Evol. 21, 332–347 (2003).

  27. 27.

    Zheng, Y. & Wiens, J. J. Do missing data influence the accuracy of divergence-time estimation with BEAST? Mol. Phylogenet. Evol. 85, 41–49 (2015).

  28. 28.

    Amard, B. & Bertrand-Sarfati, J. Microfossils in 2000 Ma old cherty stromatolites of the Franceville Group, Gabon. Precambrian Res. 81, 197–221 (1997).

  29. 29.

    Luo, G. et al. Rapid oxygenation of Earth’s atmosphere 2.33 billion years ago. Sci. Adv. 2, e1600134 (2016).

  30. 30.

    Valley, J. W. et al. Hadean age for a post-magma-ocean zircon confirmed by atom-probe tomography. Nat. Geosci. 7, 219–223 (2014).

  31. 31.

    Tomitani, A., Knoll, A. H., Cavanaugh, C. M. & Ohno, T. The evolutionary diversification of cyanobacteria: molecular–phylogenetic and paleontological perspectives. Proc. Natl Acad. Sci. USA 103, 5442–5447 (2006).

  32. 32.

    Butterfield, N. J. Proterozoic photosynthesis—a critical review. Palaeontology 58, 953–972 (2015).

  33. 33.

    Horodyski, R. J. & Donaldson, J. A. Microfossils from the Middle Proterozoic Dismal Lakes Group, Arctic Canada. Precambrian Res. 11, 125–159 (1980).

  34. 34.

    Duchêne, S., Lanfear, R. & Ho, S. Y. W. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol. Phylogenet. Evol. 78, 277–289 (2014).

  35. 35.

    Toussaint, E. F. & Condamine, F. L. To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera: Nicrophorus). Biol. J. Linn. Soc. 117, 686–704 (2016).

  36. 36.

    Shih, P. M., Hemp, J., Ward, L. M., Matzke, N. J. & Fischer, W. W. Crown group Oxyphotobacteria postdate the rise of oxygen. Geobiology 15, 19–29 (2017).

  37. 37.

    Evans, P. N. et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350, 434–438 (2015).

  38. 38.

    Vanwonterghem, I. et al. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat. Microbiol. 1, 16170 (2016).

  39. 39.

    Barker, J. F. & Fritz, P. Carbon isotope fractionation during microbial methane oxidation. Nature 293, 289–291 (1981).

  40. 40.

    Reeburgh, W. S. Oceanic methane biogeochemistry. Chem. Rev. 107, 486–513 (2007).

  41. 41.

    Holler, T. et al. Substantial 13C/12C and D/H fractionation during anaerobic oxidation of methane by marine consortia enriched in vitro. Environ. Microbiol. Rep. 1, 370–376 (2009).

  42. 42.

    Suda, K. et al. Origin of methane in serpentinite-hosted hydrothermal systems: The CH4–H2–H2O hydrogen isotope systematics of the Hakuba Happo hot spring. Earth Planet. Sci. Lett. 386, 112–125 (2014).

  43. 43.

    Blank, C. E. Phylogenomic dating—the relative antiquity of archaeal metabolic and physiological traits. Astrobiology 9, 193–219 (2009).

  44. 44.

    David, L. A. & Alm, E. J. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469, 93–96 (2011).

  45. 45.

    Shih, P. M. & Matzke, N. J. Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Proc. Natl Acad. Sci. USA 110, 12355–12360 (2013).

  46. 46.

    Harmon, L. J. et al. Arbor: comparative analysis workflows for the tree of life. PLoS Curr. 5, (2013).

  47. 47.

    Uyeda, J. C., Harmon, L. J. & Blank, C. E. A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time. PLoS ONE 11, e0162539 (2016).

  48. 48.

    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

  49. 49.

    Melby, T. E., Ciampaglio, C. N., Briscoe, G. & Erickson, H. P. The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge. J. Cell Biol. 142, 1595–1604 (1998).

  50. 50.

    Penn, O. et al. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38, W23–W28 (2010).

  51. 51.

    Tan, G. et al. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Syst. Biol. 64, 778–791 (2015).

  52. 52.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

  53. 53.

    Le, S. Q., Dang, C. C. & Gascuel, O. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol. 29, 2921–2936 (2012).

  54. 54.

    Kück, P. & Meusemann, K. FASconCAT: convenient handling of data matrices. Mol. Phylogenet. Evol. 56, 1115–1118 (2010).

  55. 55.

    Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

  56. 56.

    Quang, L. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).

  57. 57.

    Schirrmeister, B. E., de Vos, J. M., Antonelli, A. & Bagheri, H. C. Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc. Natl Acad. Sci. USA 110, 1791–1796 (2013).

  58. 58.

    Schirrmeister, B. E., Gugger, M. & Donoghue, P. C. J. Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils. Palaeontology 58, 769–785 (2015).

  59. 59.

    Schirrmeister, B. E., Sanchez-Baracaldo, P. & Wacey, D. Cyanobacterial evolution during the Precambrian. Int. J. Astrobiol. 15, 1–18 (2016).

  60. 60.

    Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2006).

  61. 61.

    Warnock, R. C. M., Yang, Z. & Donoghue, P. C. J. Exploring uncertainty in the calibration of the molecular clock. Biol. Lett. 8, 156–159 (2012).

Download references


We thank D. Pisani and M. dos Reis for improving the manuscript with their helpful comments; D. Gruen, C. Magnabosco, D. Rothman and B. Schirrmeister for discussions; and G. Shomo for assistance with the Engaging Cluster at the Massachusetts Green High Performance Computing Center. We acknowledge support from the Simons Foundation Collaboration on the Origin of Life (number 339603 to G.P.F. and NSF EAR-1615426 to G.P.F. and J.M.W).

Author information


  1. Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Joanna M. Wolfe
    •  & Gregory P. Fournier


  1. Search for Joanna M. Wolfe in:

  2. Search for Gregory P. Fournier in:


J.M.W. and G.P.F. designed the research and performed the data analysis. J.M.W. drafted the manuscript with assistance from G.P.F.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Joanna M. Wolfe.

Supplementary information

  1. Supplementary Information

    Supplementary Methods, Supplementary Figs. 1–8, Supplementary Tables 1–4, Supplementary References

  2. Life Sciences Reporting Summary

About this article

Publication history