Fig. 3: Estimated origin of phosphorus-cycling genes in the Tree of Life assuming relative event costs of 3:2:1:0 for transfer, duplication, loss, and speciation respectively.
From: Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics
Results of other event costs are available in the supplementary information Figs. 15 and 16. Coloured shapes represent speciations (asterisks), horizontal gene transfers (filled circles), duplications (filled squares) and losses (empty triangles) of genes underlying phosphate utilisation (yellow), phosphonate usage (pink), phosphonate production (green), phosphite usage (blue) and hypophosphite usage (black). Each transfer, duplication and loss is estimated to have occurred on either an internal (bright colours) or terminal (faded colours) branch of our time-calibrated tree-of-life, made using the Cox-Ingersoll-Ross clock model. Our methods do not predict whether transfers, duplications and losses happened at the start or end of the branch, so we summarise them by plotting the midpoints. Speciations are plotted on the node where they occur. For a full representation of branch lengths and uncertainties, see supplementary information Figs. 1–14.
