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

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.

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

“…1 and 2; Additional file 3: Table S3). However, an alternative plausible model for the origin of chromalveolate CHS could imply several independent horizontal gene transfers at different times during the chromalveolate evolutionary history [48], as we suggested for the chs of the rhizaria Plasmodiophora brassicae (see above in Update of CHS fungi classification). Diatom chs genes from Thalassiosira pseudonana (division 2) and Phaeodactylum tricornutum (division 1), were probably acquired by an HGT from Opistokonta (fungi or metazoa; Fig.…”

Genome sequences as the type material for taxonomic descriptions of prokaryotes

“…Second, sequence identity has clock-like properties and provides the promise of correlation with times of divergence (25). Discovery of divergence times of prokaryotic groups will enable correlation of the formation of species with the fossil record, the established evolutionary record of eukaryotes and the geological record (4,6). Third, sequence identity has been used to proposed thresholds for higher taxa in addition to species (29,62).…”

Low Rates of Lateral Gene Transfer among Metabolic Genes Define the Evolving Biogeochemical Niches of Archaea through Deep Time

“…The branch lengths are scaled to geologic time, using age constraints for the archaeal domain of life developed by Blank [11, 19], and the likelihood that the ancestral genomes have cytochrome oxidase is indicated on the nodes of the tree using ancestral state reconstruction. This approach inferred that the ancestor to the Halobacteriales likely contained cytochrome oxidase in its genome.…”

“…The methods for calculating the genomic tree and converting the branch lengths to ages have been published in detail elsewhere [10, 11]. In brief, the backbone genomic tree topology for the archaeal domain of life was calculated with Bayesian and maximum parsimony methods using a concatenated genomic dataset containing 98 protein and 2 ribosomal RNA sequences.…”