Bayesian reconstruction of unique DQA alleles in Equidae. Sequence data (205 bp) was partitioned by codon position and a GTR nucleotide substitution model was used, with gamma-distributed rates across sites. Analyses were run with 6 chains for 16,000,000 generations, burnin = 40,000 trees. Posterior probabilities > 50% are reported at the nodes. Identical alleles across multiple species are indicated by the appropriate colored bars (see legend) and names were omitted from the tree: Eqbu-DQA*02 = Eqze-DQA*02; Eqpr-DQA*01 = Eqca-DQA*05; Eqbu-DQA*01 = Eqca-DQA*08 = Eqgr-DQA*01 = Eqze-DQA*01; Eqbu-DQA*07 = Eqze-DQA*04; Eqbu-DQA*09 = Eqca-DQA*07. Eqbu-DQA*21 has a stop codon, but was included in this analysis. Sequences from B. taurus (AB548942), O. aries (M33304) and S. scrofa (EU195146) were used as outgroups.