I am interested in the analysis performed in the following paper:
They investigated the gene family distribution amongst alphaproteobacteria, reconstructing the genome composition of unknown ancestral lineages. I am stuck to this figure in the paper:
Caption: Analysis of gene loss rate (A), lateral gene transfer rate (B), and gene duplication rate (C) versus amino acid substitution rate on the Roseobacter branches of the alphaproteobacterial phylogeny constructed using P4. For the exterior Roseobacter branches, LGT rate calculations were highly variable and did not exhibit a clock-like pattern (R2 = 0.14; P = 0.02).
I understand what does it mean, but I do not understand what they mean with "Amino Acid substitution rate". They report this "Amino Acid substitution rate" as obtained from RAxML, P4, and PhyloBayes. Am I missing something really basic here?