Nonparallel accumulation of synonymous and non-synonymous substitutions on human and chimpanzee chromosomes

To reveal the evolutionary dynamics of primate chromosomes, using mice and dogs as backgrounds, we analyzed a total of 61949 pairs of genes by comparative genomics and bioinformatics methods, which included 16 427, 15 161, 15 802 and 14 559 ortholog pairs identified, from human-mouse, human-dog, chimpanzee-mouse and chimpanzee-dog phylogenies respectively. The results show that, in humans and chimpanzees, genes on chromosomes 16, 19, 21 and 22 have featured significantly higher synonymous substitution rates (dS). Analysis of human-mouse-dog and chimpanzee-mouse-dog ortholog trios also indicates dS and non-synonymous substitution rates (dN) to be homogeneous across different phylogeny branches, suggesting that the relevant genes have been subjected to similar selection for base substitution rates. The analysis also suggests that local chromatin environment, such as GC content and gene density, may contribute to the accumulation of both types of substitutions on human chromosomes. Furthermore, recombination rates seem to have a significant influence on the dS of human chromosomes.