Figure 4

Positively selected amino-acid sites identified from the coding sequences of Maleae S-alleles. The profile hidden Markov model for Maleae S-alleles was created by skylign (http://skylign.org/). The height of a stack corresponds to the conservation at that position, and the height of a letter within a stack relies on the frequency of that letter occurred at that position. The five conserved (C1–C5) and two hypervariable regions (HVa and HVb) were highlighted following Long et al. (2010). Dots indicate amino acids identified as being under positive selection, with the first line by codeml, the second line by omegaMap and the third line by Vieira et al. (2010). For codeml analyses, the grey and black dots represent selection sites with posterior probability >0.95 and >0.99, respectively. For omegaMap analyses, the amino acids with posterior probability >0.95 were reported as positively selected sites.