What is the "Amino Acid substitution rate"?

Question

[dago]

I am interested in the analysis performed in the following paper:

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria, Haiwei Luo, Miklós Csűros, Austin L. Hughes, Mary Ann Moran

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?

Any suggestions?

Answer 1

[DG]

The Substitution rate is a measure of evolutionary rate. In this case it is the estimated empirical rate of substitution from the dataset and should be in the same measure as branch lengths in phylogenetic trees which is basically the expected number of substitutions per site. It is sort of a combined time/rate of evolution measurement and always relates back to the phylogenetic tree.

[dago]

Thank you. So basically what the AASR stand for are the branch lengths in the trees obtained with the different algorithms (for example: ((((A:0.19841173,B:0.23483478):0.0404971, ...))?

[DG]

In this case that would be my assumption of what they mean. It would likely be a sum of ancestral branches for the overall rate. Not sure what they mean by exterior branches in this case though.