Extended Data Fig. 3: Ape MHC organization.

a and b) show schematic representation of MHC locus organization for MHC-I and MHC-II genes, respectively, across the six ape haplotypes (PTR.h1/h2, PPA.h1/h2, GGO.h1/h2, PPY.h1/h2, PAB.h1/h2, SSY.h1/2) and human (HSA.h1). Only orthologs of functional human HLA genes are shown. Loci naming in apes follows human HLA gene names (HSA.h1) with the exception of Gogo-OKO that does not have a human homolog, and orthologs are represented in unique colors across haplotypes and species. Orthologous genes that lack a functional coding sequence are grayed out and their name marked with an asterisk. Two human HLA class I pseudogene (HLA-H, HLA-J) are shown, because functional orthologs of these genes were identified in some apes. c) Pairwise alignment of the 5.31 Mbp MHC region in the genome, with human gene annotations and MHC-I and MHC-II clusters. Below is the variation in phylogenetic tree topologies according to the position in the alignment. The x-axis is the relative coordinate for the MHC region and the y-axis shows topology categories for the trees constructed. The three prominent subregions with highly discordant topologies are shown through shaded boxes. Four subregions (1-4) used to calculate coalescence times are shown with dashed boxes. The phylogenetic tree includes the macaque genome (MFA)⁹⁵ to better estimate the deep coalescence time observed at this locus. Numbers indicate time estimated in millions of years.