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An Expansion of Age Constraints for Microbial Clades that Lack a Conventional Fossil Record Using Phylogenomic Dating

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Abstract

Most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. Building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. Using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and genetic data, showed that members of the Halobacteriales and Thermococcales are able to metabolize chitin. Ancestral state reconstruction combined with phylogenetic analysis of the genes underlying chitin degradation predicted that the ancestors of these two groups were also likely able to metabolize chitin or chitin-related compounds. These two clades were therefore assigned a maximum age of 1.0 Ga (when chitin likely first appeared). Similar analyses also predicted that the ancestor to the Sulfolobus solfataricus–Sulfolobus islandicus clade was able to metabolize phenol using catechol dioxygenase, so this clade was assigned a maximum age of 475 Ma. Inferred ages of archaeal clades using relaxed molecular clocks with the new age constraints were consistent with those inferred with the oxygen age constraints. This work expands our current toolkit to include Paleoproterozoic, Neoproterozoic, and Paleozoic age constraints, and should aid in our ability to phylogenetically reconstruct the antiquity of a wide array of microbial clades and their associated morphological and biogeochemical traits, spanning deep geologic time. Such hypotheses—although built upon evolutionary inferences—are fundamentally testable.

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Abbreviations

ASR:

Ancestral character state reconstruction

Ga:

Giga-anna (billion years) before present

Ma:

Mega-anna (million years) before present

MB:

Mr. Bayes, Bayesian method of phylogenetic reconstruction

MP:

Maximum parsimony method of phylogenetic reconstruction

RMC:

Relaxed molecular clock

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Acknowledgments

The author would like to acknowledge helpful comments by two anonymous reviewers as well as support provided by Nancy Hinman and Bill Woessner. Additional assistance and inspiration came from Robin Brigmon, Michael Ceballos, Robert Kelly, Heiko Langner, Lindsay MacKenzie, Julie Maupin-Furlow, Brent Mishler, Penny Morris-Smith, and James Staub. Portions of this work were funded by a research initiation grant from the NASA Montana Space Grant Consortium.

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    Carrine E. Blank

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Blank, C.E. An Expansion of Age Constraints for Microbial Clades that Lack a Conventional Fossil Record Using Phylogenomic Dating. J Mol Evol 73, 188–208 (2011). https://doi.org/10.1007/s00239-011-9467-y

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