Figure 2

Evidence of concerted evolution at ID1 and ID2. (a) Neighbor-joining trees of comparative sequences over three intervals within the AZFa-HERVs (Pt, Pan troglodytes; Hs, Homo sapiens; Gg, Gorilla gorilla). (b) Phylogenetic networks of the same three intervals. (c) Two segments of an ID2 alignment demonstrating alternative directions of gene conversion events. Variant positions within the alignment relative to the human sequences are highlighted in black. In the first panel of the ID2 alignment, multiple variants specific to the proximal paralog in both chimpanzee and gorilla sequences are missing from humans, suggesting gene conversion on the hominid lineage using the distal paralog as a donor. By contrast, the second panel of the same alignment indicates gene conversion of the opposite directionality.