Fig. 4.

Phylogenetic relationships of MHC-I exon 2 and MHC-IIA exon 2 alleles among other avian orders. Approximately-maximum-likelihood phylogenetic trees were created for common buzzard (Buteo buteo) MHC alleles to infer the evolutionary history of gene duplication for class I and class II. Scale bars indicate the number of substitutions per site. Bootstrap values > 0.8 are shown. See Methods for accension numbers. a) MHC class I exon 2 alleles cluster by order, with common buzzard alleles clustering with Accipitriformes. Vertical red bars show the locus location of the alleles based on haplotype-aware long-read contigs. b) MHC class IIA exon 2 alleles tend to cluster by isotype (such as mammalian DRA and DQA and avian DBA) instead of order. Common buzzard alleles cluster with Accipitriformes, Pelecaniformes, and Procellariiformes (the DRA/DAA isotype) and locally by species with very short branch lengths. Together this suggests common buzzards share a DRA/DAA isotype with other orders, and recent duplications occurred in common buzzards