Fig. 4

Phylogenetic trees of MHC-II genes. a MHC-II A gene Maximum likelihood phylogeny based on alignment of nucleotide sequences corresponding to the α1 and α2 domains. b MHC-II B gene Maximum likelihood phylogeny based on nucleotide sequences corresponding to the β1 and β2 domains. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.5470)). The tree is drawn to scale, with branch lengths representing the number of substitutions per site. Branch support is indicated as percentage of trees out of 1000 bootstrap replicates that produce the same branching order. ψ represents putative pseudogenes. HLA – human leucocyte antigen; SLA – swine leucocyte antigen; Eqca – Equus caballus; Ovar – Ovis aries; Mumu – Mus musculus; Orcu – Oryctolagus cuniculus; Gaga – Gallus gallus