Fluxes of amino acids in 12 Drosophila genomes. A: Loser and gainer amino acids in the whole phylogeny (red bars) and terminal branches of different depth leading to sister species (blue bars; colour darkness increases with the depth of terminal branches). D_pseper – substitutions in D. pseudoobscura and D. persimulans branches; D_simsec – in D. simulans and D. sechelia branches; D_yakere – in D. yakuba and D. erecta branches; D_virmoj – in D. virilis and D. mojavensis branches. Relative amino acid gain D = (Gain-Loss)/(Gain+Loss) . B: Relationship between relative amino acid gain (D) and frequency of each amino acid in 12 Drosophila genomes. Red circles – all 12 genomes, blue circles – only substitutions in the most shallow branches (in D. pseudoobscura and D. persimulans). C. Relationship between relative amino acid gain (D) and gain-loss rank in Ref . Symbols as on Fig 1B. D. Rank (Spearman) correlation between relative amino acid gain (D) in branches of different depths in this study and in Ref  (ρ; black circles); Pearson coefficient of correlation between D and amino acid frequency in 12 Drosophila genomes (r, green diamonds). E. Mean pair-wise asymmetry of reciprocal substitutions (|D|, red squares). Branch depth (Ks) on parts D and E is in synonymous substitutions per 4-fold degenerative site .
Yampolsky and Bouzinier BMC Genomics 2010 11(Suppl 4):S10 doi:10.1186/1471-2164-11-S4-S10