Figure 3

Evolution patterns of nonsynonymous sites in bird genomes. (A-C) We show sequence patterns in nonsynonymous sites of coding regions divided in different chromosome sets or different evolutionary strata of Z chromosomes. Chr4 and chr5, which have a similar size and gene number with Z chromosome, are shown, and we also performed the comparison between Z chromosome vs. all macrochromosomes. We show pairs of comparison with significant difference labeled with asterisks. ^***:P-value < 0.001. dN: lineage specific nonsynonymous substitution rate. Intron SNP densities were measured in SNP number per kb region. (D) For each species, we calculated the ratio of median intron SNP density of Z linked genes vs. macrochromosome linked genes as a proxy for relative effective population size. We also calculated the ratio of median evolutionary rate (dN/dS) of the two, as a measurement of fast-Z evolution.