Diversity and positive selection analysis of avian ZAP. (A) Using an alignment of 13 avian ZAP sequences (Supplemental Data Table S4A) and following trimming to remove a region of no homology between the fourth and fifth zinc-finger motifs, a sliding-window analysis of sequence diversity was conducted using 100 bp windows and 1 bp increment size. Diversity was calculated as the average pairwise number of variant sites per 100 bp window. The four domains of ZAP are shown in colored blocks, including the NAD+ binding sites in the PARP domain (yellow). Superimposed in red points are positively selected sites as determined by M2a in PAML. Nucleotide position refers to the position in the alignment following trimming—original coordinates of the chicken sequence can be found in Supplemental Data Table S4B. (B) Using the same alignment, the free-ratios model in PAML was implemented to determine along which branches positive selection has been strongest. Each branch is labeled with its respective dN/dS value, and branches are colored according to dN/dS.
