Consistent with previous findings, we do not observe genome-wide evidence for pan-mammalian selection of novel RNA sequences (Panel D). There are also a large number of elements without mammalian constraint, between 17–90% for TF-binding regions as well as DHSs and FAIRE regions. Previous studies could not determine whether these sequences are either biochemically active, but with little overall impact on the organism, or are under lineage specific selection. By isolating sequences preferentially inserted into the primate lineage, which is only feasible given the genome-wide scale of this data, we are able to specifically examine this issue. The majority of primate-specific sequence is due to retrotransposon activity, but an appreciable proportion is non-repetitive primate-specific sequence. Of 104,343,413 primate-specific bases (excluding repetitive elements), 67,769,372 (65%) are found within ENCODE-identified elements. Examination of 227,688 variants segregating in these primate specific regions revealed that all classes of elements (RNA and regulatory) show depressed derived allele frequencies, consistent with recent negative selection occurring in at least some of these regions (Figure 1E). An alternative approach examining sequences that are not clearly under pan-mammalian constraint showed
