Fig. 2

Evolutionary rates based on observed protein divergence (a, b) and phylogenetic analysis (c, d). a For each pairwise species comparison (total of 120 comparisons), divergence time (obtained from timetree.org) versus average protein divergence was plotted. Average protein divergence was the average divergence of all orthologous proteins. Data points are colored according to clade comparisons as indicated in the legend. The best regression line (dashed) was fitted to the data; b Boxplots of individual protein divergences; c Proof-of-concept phylogenetic analysis (detailed in the methods section) for the NSMF gene, with branches annotated with their inferred evolutionary rate (in substitutions per site per million years); d Mean evolutionary rates for Eutheria (black) and Metatheria (red) estimated through phylogenetic analysis, conducted on three sets of 16 genes with complete protein sequence information available for all species. Set 1: Eutherian subtelomeric genes located in landscape windows with highest protein divergence rates in eutherian comparisons; set 2: Metatherian subtelomeric genes in windows with highest protein divergence rates for intra-Metatherian comparisons; set 3: genes that were not in subtelomeric of Eutherian and Metatherian genomes with low protein divergence rates for intra-Metatherian and intra-Eutherian comparisons