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.
Kamath and Getz BMC Evolutionary Biology 2011 11:128 doi:10.1186/1471-2148-11-128