Figure 1

Positive selection detected in primate tehterin.

(a) Amino acid sequences of primate tetherin. RCM tetherin (GenBank accession number AB907706; determined in this study), SM tetherin (FJ864713), RM tetherin (FJ943432), African green monkey (Chlorocebus aethiops; AGM) tetherin (FJ943430), CPZ tetherin (NM_001190480), HU tetherin (NM_004335) and night monkey (Aotus vociferans; NM) tetherin (FJ638415) are respectively shown. The numbers indicate the amino acid positions in NM tetherin. The two positively selected sites (positioned at 9 and 14), which are determined by both site model of PAML (Figure 1d) and REL method of HyPhy (Figure 1e), are indicated with green asterisks. The six amino acids (positioned at 10, 14, 39, 93, 103 and 187) inferred to be under positive selection in Cercocebus tetherin (the clade of RCM and SM tetherins) (Figure 1f) are indicated with pink asterisks. The amino acids, which are putatively associated with the ability to induce NFκB-dependent signaling³⁶, are indicated with shading in pale blue. (b) Phylogenic tree of 47 primate tetherins reconstructed using ML method. The tree was rerooted with the NWM clade. The dN/dS ratios are shown on each branch and the numbers in parenthesis represent nonsynonymous (left) and synonymous (right) changes, respectively. (c) The positive selection detected in different regions of the tetherin gene. The regions inferred to be under positive selection with statistical significance are represented in red. ND, not detected (2Δl = −0.000002). (d and e) Positively selected sites identified in our analyses. In panel d, the codons under positive selection identified by PAML with posterior probability > 0.95 are shown in bold. In panel e, the codons under positive selection inferred by HyPhy with Bayes factor > 50 are shown in bold. (f) The result obtained from the twobranch-site analyses for RCM and Cercocebus clades. All PAML analyses were performed under two models of codon usage, F61 and F3x4 and they yield consistent results. ^a, All nodes/branches within RCM and the Cercocebus clades were respectively designated as the foreground branches. ^b, The number in parenthesis represents posterior probability.