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.