Supplementary material from "Effect of genetic drift on determinants of protein evolution"

A number of previous studies reported that gene expression, tissue specificity, gene essentiality and the number of protein–protein interactions influence the rate of protein evolution. Here we investigated the influence of effective population size (N_e) on these determinants of protein evolution. For this purpose, we compared the ratio of non-synonymous-to-synonymous diversities (π_N/π_S) estimated for protein-coding genes of Mus musculus castaneus and Mus musculus musculus: populations with high and low N_e respectively. Our results revealed that the difference between π_N/π_S estimated for genes with high and low expression levels was significantly smaller for M. m. musculus compared to that observed for M. m. castaneus. The difference between the π_N/π_S of broadly expressed and tissue specific genes was much higher for M. m. castaneus compared to that of M. m. musculus. Furthermore, the difference between the π_N/π_S computed for essential and non-essential genes was much smaller for M. m. musculus than M. m. castaneus. A similar pattern was observed for genes involved in many protein–protein interactions versus those involved in one. These results suggest that the effects of the determinants on protein evolution were much reduced for the population with small N_e due to increased genetic drift.