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

Dataset DOI: [10.5061/dryad.zcrjdfnrz](10.5061/dryad.zcrjdfnrz)

## Description of the data and file structure

This data is part of our manuscript \"Ancient Trans-Species Polymorphism at the Major Histocompatibility Complex in Primates,\" in which we assess evidence for trans-species polymorphism at several MHC Class I and Class II genes. To build allele and gene phylogenies, we used Bayesian phylogenetics software BEAST2 with the package SubstBMA. This software produces a large set of phylogenies sampled from the posterior, which are included here. There is one file for each gene group and gene region, e.g., \"MHC-A group, exon 2.\"

### Files and variables

#### File: Agroup_exon2_all_posterior_trees.trees.zip

**Description:** Zip archive containing the posterior tree file (in NEXUS format) for the MHC-A group, exon 2.

#### File: Agroup_exon3_all_posterior_trees.trees.zip...,