Fig. 1. Experimental validation of duplication map.

a) A computationally predicted orangutan-specific duplication (blue=excess depth of coverage of aligned WGS sequence) is confirmed by interspecific FISH and arrayCGH (oligonucleotide relative log₂ ratios are depicted as red/green histograms and correspond to an increase and decrease in signal intensity when test/reference are reverse labeled) (see Supplementary Note for additional details). b) A comparison of duplication copy number as predicted by WSSD sequence analysis versus oligonucleotide arrayCGH between nonhuman and human primates showed a good correlation (r=0.77). Relative duplication copy number was computed as the log₂ ratio of the number of aligned nonhuman primate reads against the human reference genome over the number of reads mapping to known single copy BACs.