Ancient Trans-Species Polymorphism at the Major Histocompatibility Complex in Primates

Reviewer #1 (Public review):

Summary:

MHC (Major Histocompatibility Complex) genes have long been mentioned as cases of trans-species polymorphism (TSP), where alleles might have their most recent common ancestor with alleles in a different species, rather than other alleles in the same species (e.g., a human MHC allele might coalesce with a chimp MHC allele, more recently than the two coalesce with other alleles in either species). This paper provides a more complete estimate of the extent and ages of TSP in primate MHC loci. The data clearly support deep TSP linking alleles in humans to (in some cases) old world monkeys, but the amount of TSP varies between loci.

Strengths:

The authors use publicly available datasets to build phylogenetic trees of MHC alleles and loci. From these trees they are able to estimate whether there is compelling support for Trans-species polymorphisms (TSPs) using Bayes Factor tests comparing different alternative hypotheses for tree shape. The phylogenetic methods are state-of-the-art and appropriate to the task.

The authors supplement their analyses of TSP with estimates of selection (e.g., dN/dS ratios) on motifs within the MHC protein. They confirm what one would suspect: classical MHC genes exhibit stronger selection at amino acid residues that are part of the peptide binding region, and non-classical MHC exhibit less evidence of selection. The selected sites are associated with various diseases in GWAS studies.

Weaknesses:

An implication drawn from this paper (and previous literature) is that MHC has atypically high rates of TSP. However, rates of TSP are not estimated for other genes or gene families, so readers have no basis of comparison. No framework to know whether the depth and frequency of TSP is unusual for MHC family genes, relative to other random genes in the genome, or immune genes in particular. I expect (from previous work on the topic), that MHC is indeed exceptional in this regard, but some direct comparison would provide greater confidence in this conclusion.

Given the companion paper's evidence of genic gain/loss, it seems like there is a real risk that the present study under-estimates TSP, if cases of TSP have been obscured by the loss of the TSP-carrying gene paralog from some lineages needed to detect the TSP. Are the present analyses simply calculating rates of TSP of observed alleles, or are you able to infer TSP rates conditional on rates of gene gain/loss?

Figure 5 (and 6) provide regression model fits (red lines in panel C) relating evolutionary rates (y axis not labeled) to site distance from the peptide binding groove, on the protein product. This is a nice result. I wonder, however, whether a linear model (as opposed to non-linear) is the most biologically reasonable choice, and whether non-linear functions have been evaluated. The authors might consider generalized additive models (GAMs) as an alternative that relaxes linearity assumptions.

The connection between rapidly evolving sites, and disease associations (lines 382-3) is very interesting. However, this is not being presented as a statistical test of association. The authors note that fast-evolving amino acids all have at least one association: but is this really more disease-association than a random amino acid in the MHC? Or, a randomly chosen polymorphic amino acid in MHC? A statistical test confirming an excess of disease associations would strengthen this claim.

Reviewer #2 (Public review):

Summary

In this study, the authors characterized population genetic variation in the MHC locus across primates and looked for signals of long-term balancing selection (specifically trans-species polymorphism, TSP) in this highly polymorphic region. To carry out these tasks, they used Bayesian methods for phylogenetic inference (i.e. BEAST2) and applied a new Bayesian test to quantify evidence supporting monophyly vs. transspecies polymorphism for each exon across different species pairs. Their results, although mostly confirmatory, represent the most comprehensive analyses of primate MHC evolution to date and novel findings or possible discrepancies are clearly pointed out. However, as the authors discuss, the available data are insufficient to fully capture primates' MHC evolution.

Strengths of the paper include: using appropriate methods and statistically rigorous analyses; very clear figures and detailed description of the results methods that make it easy to follow despite the complexity of the region and approach; a clever test for TSP that is then complemented by positive selection tests and the protein structures for a quite comprehensive study.

That said, weaknesses include: lack of information about how many sequences are included and whether uneven sampling across taxa might results in some comparisons without evidence for TSP; frequent reference to the companion paper instead of summarizing (at least some of) the critical relevant information (e.g., how was orthology inferred?); no mention of the quality of sequences in the database and whether there is still potential effects of mismapping or copy number variation affecting the sequence comparison.

Reviewer #3 (Public review):

Summary

The study uses publicly available sequences of classical and non-classical genes from a number of primate species to assess the extent and depth of TSP across the primate phylogeny. The analyses were carried out in a coherent and, in my opinion, robust inferential framework and provided evidence for ancient (even > 30 million years) TSP at several classical class I and class II genes. The authors also characterise evolutionary rates at individual codons, map these rates onto MHC protein structures, and find that the fastest evolving codons are extremely enriched for autoimmune and infectious disease associations.

Strengths

The study is comprehensive, relying on a large data set, state-of-the-art phylogenetic analyses and elegant tests of TSP. The results are not entirely novel, but a synthesis and re-analysis of previous findings is extremely valuable and timely.

Weaknesses

I've identified weaknesses in several areas (details follow in the next section):
- Inadequate description and presentation of the data used
- Large parts of the results read like extended figure captions, which breaks the flow.
- Older literature on the subject is duly cited, but the authors don't really discuss their findings in the context of this literature.
- The potential impact of mechanisms other than long-term maintenance of allelic lineages by balancing selection, such as interspecific introgression and incorrect orthology assessment, needs to be discussed.