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. 2011 Nov;85(21):11361–11371. doi: 10.1128/JVI.05046-11

Fig. 7.

Fig. 7.

Apobec3DE evolved rapidly in chimpanzee ancestors. Sequences obtained by PCR in this study, as described in Materials and Methods, were analyzed. (A) A maximum-likelihood phylogeny based on primate Apobec3DE and Apobec3F sequences is shown. Statistical support, calculated as aLRT values, is shown for each node. (B) Positive selection analysis of Apobec3DE. Two phylogenies of Apobec3DE, one with the human ortholog as an outgroup to gorilla, chimpanzee, and bonobo Apobec3DE (right) and another with gorilla Apobec3DE as an outgroup to human, chimpanzee, and bonobo Apobec3DE (left), were analyzed. Global dN/dS ratios are indicated above each branch. The numbers of nonsynonymous and synonymous changes along each branch are indicated below each branch in parentheses (NS:S). dN/dS values greater than 1 are indicative of positive selection. (C) Codons in Apobec3DE under positive selection. An alignment of human and chimpanzee Apobec3DE protein sequences is shown with chimpanzee-specific changes highlighted in black. Residues having a high probability of being under positive selection across all primates are marked with asterisks. Residues with BEB values of >0.95 are marked with a single asterisk, and residues with BEB values of >0.99 are marked with two asterisks. The C-terminal domain in Apobec3DE that was tested for antiviral activity is underlined, with the minimal 5 residues that are required for antiviral activity underlined twice.