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. 2018 Aug 2;103(2):261–275. doi: 10.1016/j.ajhg.2018.07.007

Figure 6.

Figure 6

The Reference Amplicon State Has Been Selected For throughout Human Evolution

(A) Distribution of mutation events over the phylogenetic tree. Blue curve: branches of the phylogenetic tree of males in our dataset, sorted by branch age. Red diagonal line: expected distribution if CNVs were selectively neutral. Gray lines: branches of the phylogenetic tree shuffled at random. 1,000 shuffles were performed. See Figure S9 for an in-depth description of this method.

(B) Mutation events versus number of males with CNVs. Each point represents one simulation over the phylogenetic tree of males in our dataset.

(C and D) Amplicon rescue in gr/gr (C) and b2/b3 (D) deletions. Top: a chromosome with the deletion undergoes a blue-to-blue duplication that restores most of the amplicons to the reference copy number. The blue arc shows the targets of NAHR on a single copy of the AZFc region. Middle: males with the pre-rescue and post-rescue AZFc structures. Bottom: phylogenetic trees containing the rescued males. Males in red have the gr/gr (C) or b2/b3 (D) deletion; males in green have the respective rescue amplicon copy number states.