Response to comment on "Evidence of abundant purifying selection in humans for recently acquired regulatory functions".

Abstract

Green and Ewing propose corrections to our methodology, which we incorporate and extend here. The improved methodology supports our initial conclusion of extensive lineage-specific constraint concentrated in ENCODE elements. We clarify that our estimate is dependent on the constrained and neutral references used, which can further increase the number of nucleotides involved, because a particularly stringent definition was initially used.