DOI: 10.5061/dryad.zcrjdfnrz
title: The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for each gene group and region

description: 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.
description: # 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
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-A group, exon 3. #### File:
 Agroup_exon4_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-A group,
 exon 4. #### File: Bgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-B group, exon 2. #### File:
 Bgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-B group,
 exon 3. #### File: Cgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-C group, exon 2. #### File:
 DMAgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DMA
 group, exon 3. #### File: Cgroup_exon3_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-C group, exon 3. #### File:
 DMBgroup_exon2_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DMB
 group, exon 2. #### File: DMAgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DMA group, exon 2. #### File:
 DOAgroup_exon2_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DOA
 group, exon 2. #### File: DOAgroup_exon3_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DOA group, exon 3. #### File:
 DMBgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DMB
 group, exon 3. #### File: DOBgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DOB group, exon 2. #### File:
 Cgroup_exon4_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-C group,
 exon 4. #### File: Bgroup_exon4_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-B group, exon 4. #### File:
 DOBgroup_exon3_all_posterior_treesd.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DOB
 group, exon 3. #### File: DPAgroup_exon3_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DPA group, exon 3. #### File:
 DPAgroup_exon2_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DPA
 group, exon 2. #### File: DPBgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DPB group, exon 2. #### File:
 DPBgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DPB
 group, exon 3. #### File: DQAgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DQA group, exon 2. #### File:
 DQAgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DQA
 group, exon 3. #### File: DQBgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DQB group, exon 2. #### File:
 DQBgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DQB
 group, exon 3. #### File: DRAgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DRA group, exon 2. #### File:
 DRAgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DRA
 group, exon 3. #### File: DRBgroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-DRB group, exon 2. #### File:
 DRBgroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-DRB
 group, exon 3. #### File: Egroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-E group, exon 2. #### File:
 Egroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-E group,
 exon 3. #### File: Egroup_exon4_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-E group, exon 4. #### File:
 Fgroup_exon2_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-F group,
 exon 2. #### File: Fgroup_exon3_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-F group, exon 3. #### File:
 Fgroup_exon4_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-F group,
 exon 4. #### File: Ggroup_exon2_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-G group, exon 2. #### File:
 Ggroup_exon3_all_posterior_trees.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the MHC-G group,
 exon 3. #### File: Ggroup_exon4_all_posterior_trees.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the MHC-G group, exon 4. ## Code/software You can unzip the
 .zip files with no extra software and can read the NEXUS files in any text
 editor.