Validation of 11 candidate regions of chimp-bonobo-human incomplete lineage sorting.

Note: Results of resequencing of 11 candidate regions of incomplete lineage sorting. We targeted up to 5 kb for resequencing in 4 chimpanzees, 3 bonobos, 3 humans, and 3 orangutans. Divergent sites were filtered to remove sites that overlapped with the ones used to discoverer the regions (Text S9). The counts of the 7 possible classes of divergent sites can be non-integer due to within-species polymorphism.
*We observe an excess of CH sites in regions where chimpanzees and humans cluster, and BH sites in regions where bonobos and humans cluster (6.6% vs. the genome-wide average of 0.3%). Chimpanzee-bonobo genetic divergence in these regions is also inflated: 38.4% on average versus the average of 12.2%.
†Resequencing of region 1298 provided substantially less data than the other 10 regions. Nevertheless, the data showed a substantial excess of BH (n = 6) over CH (n = 2) sites at this locus, supporting the presence of incomplete lineage sorting.