DOI: 10.5061/dryad.37pvmcvz7
title: The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for the whole-class multi-gene alignments

description: Gene families are groups of evolutionarily-related genes. One large gene
 family that has experienced rapid evolution lies within the Major
 Histocompatibility Complex (MHC), whose proteins serve critical roles in
 innate and adaptive immunity. Across the ~60 million year history of the
 primates, some MHC genes have turned over completely, some have changed
 function, some have converged in function, and others have remained
 essentially unchanged. Past work has typically focused on identifying MHC
 alleles within particular species or comparing gene content, but more work
 is needed to understand the overall evolution of the gene family across
 species. Thus, despite the immunologic importance of the MHC and its
 peculiar evolutionary history, we lack a complete picture of MHC evolution
 in the primates. We readdress this question using sequences from dozens of
 MHC genes and pseudogenes spanning the entire primate order, building a
 comprehensive set of gene and allele trees with modern methods. This
 dataset contains 7 sets of posterior trees which are outputs of BEAST2
 (one each for Class I exon 2, Class I exon 3, Class I exon 4, Class IIA
 exon 2, Class IIA exon 3, Class IIB exon 2, and Class IIB exon 3). 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 also included
 3 summary trees for the genes in the Class I alpha-block (one each for
 exon 2, exon 3, and exon 4). These trees are also in NEXUS format.
 Overall, we find that the Class I gene subfamily is evolving much more
 quickly than the Class II gene subfamily, with the exception of the Class
 II MHC-DRB genes. We also pay special attention to the often-ignored
 pseudogenes, which we use to reconstruct different events in the evolution
 of the Class I region. This dataset can be used to explore the
 relationships between MHC genes within and between species. It could also
 be connected to other information, such as MHC diversity in different
 species or haplotype frequencies. All of the sequences that went into this
 dataset are 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 the whole-class multi-gene alignments Dataset DOI:
 [10.5061/dryad.37pvmcvz7](10.5061/dryad.37pvmcvz7) ## Description of the
 data and file structure This data is part of our manuscript "The
 Primate Major Histocompatibility Complex: A Case Study of Gene Family
 Evolution," in which we explore the evolutionary relationships
 between the MHC Class I and Class II genes and pseudogenes. 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 multi-gene set and gene region, e.g., "Class I,
 exon 2." ### Files and variables #### File:
 classIIB_exon3_rdpm_uc_combined_forbf.trees.zip **Description:** Zip
 archive containing the posterior tree file (in NEXUS format) for the Class
 IIB group, exon 3. #### File:
 classIIB_exon2_rdpm_uc_combined_forbf.trees.zip **Description:** Zip
 archive containing the posterior tree file (in NEXUS format) for the Class
 IIB group, exon 2. #### File:
 alphablock_exon2_rdpm_uc_combined_maxcctree.txt **Description:** NEXUS
 file containing the maximum clade credibility tree for the alpha-block
 gene group, exon 2. #### File:
 alphablock_exon4_rdpm_uc_combined_maxcctree.txt **Description:** NEXUS
 file containing the maximum clade credibility tree for the alpha-block
 gene group, exon 4. #### File:
 alphablock_exon3_rdpm_uc_combined_maxcctree.txt **Description:** NEXUS
 file containing the maximum clade credibility tree for the alpha-block
 gene group, exon 3. #### File:
 classIIA_exon3_rdpm_uc_combined_forbf.trees.zip **Description:** Zip
 archive containing the posterior tree file (in NEXUS format) for the Class
 IIA group, exon 3. #### File:
 classIIA_exon2_rdpm_uc_combined_forbf.trees.zip **Description:** Zip
 archive containing the posterior tree file (in NEXUS format) for the Class
 IIA group, exon 2. #### File:
 classI_exon4_rdpm_uc_combined_forbf.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the Class I
 group, exon 4. #### File: classI_exon3_rdpm_uc_combined_forbf.trees.zip
 **Description:** Zip archive containing the posterior tree file (in NEXUS
 format) for the Class I group, exon 3. #### File:
 classI_exon2_rdpm_uc_combined_forbf.trees.zip **Description:** Zip archive
 containing the posterior tree file (in NEXUS format) for the Class I
 group, exon 2. ## Code/software You can unzip the .zip files with no extra
 software and can read the NEXUS files in any text editor.