Figure 3

Phylogenetic tree of ARD genes. Phylogenetic tree showing that the speciation resulting in the marsupials, probably precedes the gene duplication that resulted in ARDs. All identifiers are from Ensembl, except for 061219 (UniProt), 12718517 and 28422364 (GenBank GI numbers), Opossum (Ensembl prediction 'Built_from_P41227_and_others_1') and Kangaroo (which is a consensus sequence of all the Kangaroo sequences described in this paper). The protein sequences were aligned using T-Coffee, a coding sequence alignment was produced from this, the best aligned section was extracted (positions 53–214 in the protein alignment, positions 157–642 in the coding sequence alignment), and from this a new tree was generated using MrBayes (3000000 generations, 250000 burn-in, different rates for transitions and transversions, gamma distributed rates across sites). This tree was then rooted by mapping it to the NCBI tree of life whilst miniming the number of gene duplication and loss events when allowing poorly supported branches to be rearranged (Berglund, Steffansson, Betts and Liberles, Manuscript submitted). The figures on the branches are posterior probabilities produced by MrBayes. The two branches marked 'X' are the result of rearrangements during the rooting of the tree.