Journal of Molecular Evolution

, Volume 73, Issue 3, pp 188–208

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


DOI: 10.1007/s00239-011-9467-y

Cite this article as:
Blank, C.E. J Mol Evol (2011) 73: 188. doi:10.1007/s00239-011-9467-y


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 solfataricusSulfolobus 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.


Archaea Microbial evolution Phylogenomic dating Relaxed molecular clock Chitinase Chitin degradation Lignin degradation 



Ancestral character state reconstruction


Giga-anna (billion years) before present


Mega-anna (million years) before present


Mr. Bayes, Bayesian method of phylogenetic reconstruction


Maximum parsimony method of phylogenetic reconstruction


Relaxed molecular clock

Supplementary material

239_2011_9467_MOESM1_ESM.docx (326 kb)
Supplementary material 1 (DOCX 326 kb)

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of GeosciencesUniversity of MontanaMissoulaUSA

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