Fig. 1

Predictions and results of phylogenetic analysis. a The hypothetical pattern expected if balancing selection on supertypes maintains TSP, but alleles within supertypes experience rapid turnover. Hypothetical supertypes are marked with diamonds of the same colour, and the species-specific branches are in turquoise and deep blue. Supertype lineages should be shared between species, but sharing of identical alleles (dashed line) should be rare. b Neighbour-joining tree of 539 MHC class II exon 2 alleles reported by Lighten et al.¹. The tree was constructed from a matrix of Jukes–Cantor distances calculated using all 209 nucleotide positions. Alleles from each supertype are marked with the same colour as in Lighten at al. Supertype 9 is marked yellow; the asterisk indicates that it is the only monophyletic supertype (bootstrap support 97%)