chronograms

In order to determine the evolutionary history of each COG of interest identified above, we first had to create a tree of life that is representative of the diversity of life on Earth, and anchor this tree in time to create a molecular clock. For this analysis, we used the phylogenetic tree and molecular clock previously described in Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics (Boden et al.). Briefly, the tree includes 865 different genomes chosen to represent the full diversity of bacteria and archaea. We used sixteen ribosomal genes that have been used previously to reconstruct the evolutionary history of life to create the alignment that served as the basis for the final tree, as implemented in GToTree. The tree was created using maximum likelihood methodology implemented in IQ-Tree 2.2.0.3. A relaxed Bayesian molecular clock was implemented in PhyloBayes 4.1 with eight calibration points and a uniform root prior between 4.4 and 3.5 Ga.