Abstract
We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of beta-tubulin. Our analysis identified one amino acid substitution--beta-tubulin F224--which was highly lineage specific. Investigation of beta-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for "supergroups" other than the unikonts. To understand why, we analysed the beta-tubulin Neighbor-Net and demonstrated a fundamental division between core beta-tubulins (plant-like) and divergent beta-tubulins (animal and fungal). F224 was almost completely restricted to the core beta-tubulins, while divergent beta-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of beta-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core beta-tubulins and Y-type, divergent beta-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins.