The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for the whole-class multi-gene alignments

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.