The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for each gene group and region

Classical genes within the Major Histocompatibility Complex (MHC) are responsible for peptide presentation to T cells, thus playing a central role in immune defense against pathogens. These genes are subject to strong selective pressures, including both balancing and directional selection, resulting in exceptional genetic diversity—thousands of alleles per gene in humans. Moreover, some allelic lineages appear to be shared between primate species, a phenomenon known as trans-species polymorphism (TSP) or incomplete lineage sorting, which is rare in the genome overall. However, despite the clinical and evolutionary importance of MHC diversity, we currently lack a full picture of primate MHC evolution. In particular, we do not know to what extent genes and allelic lineages are retained across speciation events. To start addressing this gap, we used Bayesian phylogenetic methods to determine the extent of TSP at 17 MHC genes, including classical and non-classical Class I and Class II genes. This dataset contains 38 sets of posterior trees which are outputs of BEAST2 (one for each gene group and exon studied). Each file is a .zip archive containing one file in NEXUS format. Each NEXUS file lists the alleles/sequences involved in the tree and then lists the trees (one for each state in the chain) in Newick format. We calculated Bayes factors using each set of posterior trees and found strong support for ancient TSP in 7 of 10 classical genes. This dataset can be used to explore the relationships between MHC alleles within and between species. It could also be connected to other information, such as disease susceptibility or allele frequency. All of the sequences that went into this dataset was publicly available, so there are no additional ethical or legal considerations for its use.