A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern.

DNA sequences evolving differently in the human and chimpanzee genomes signal recent and regionally limited changes in the process of DNA sequence evolution. Here we present the comparison of 90 kb from the nonrecombining part of the human Y chromosome to the corresponding part of the chimpanzee genome using gorilla as out-group. Our results reveal a significant difference in the region-specific substitution process among the human and chimpanzee lineages. As a consequence, this region experiences a change in its GC content on the human lineage while it resides in compositional equilibrium on the chimpanzee lineage. Based on our analysis, we suggest a recent and species-specific shift in the region's mutation pattern as the cause of its differing evolution in humans and chimpanzees.