Maximum-likelihood tree with MHC-IIB exon 2 or partial exon 3 sequences from <i>Nipponia nippon</i> and other bird species.

Abstract

<p>The best-fitting nucleotide substitution model for each codon position was evaluated using Find Best DNA/Protein Models (ML) in MEGA version 5.2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108506#pone.0108506-Tamura1" target="_blank">[28]</a> according to the Akaike information criterion. (A) The tree of exon 2 was constructed by using a Kimura 2-parameter model with gamma distribution in MEGA. (B) The tree of partial exon 3 was constructed by using a Tamura 3-parameter model with gamma distribution in MEGA. Bird species used for the analyses were shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108506#pone.0108506.s005" target="_blank">Table S3</a>. In both analyses, bootstrap values were evaluated with 1000 replications. Bootstrap values>60 are shown in this tree. Branch lengths represent the number of changes per site.</p