Interview with the authors: Associations between MHC class II variation and phenotypic traits in a free-living sheep population

In a recent paper in Molecular Ecology, Huang, Dicks and colleagues analysed variation in the major histocompatibility complex (MHC) and phenotypic traits in an unmanaged population of sheep living on an island off the coast of Scotland. This population of sheep has been studied closely for more around 70 years, providing a very rare level of insight and statistical power to evolutionary genetic studies. The MHC is among the most variable parts of mammalian genomes and has long been known to be encode proteins central to the adaptive immune system. Through their analyses, Huang, Dicks and colleagues found associations with levels of circulating antibodies and variation at MHC loci.

We sent some questions to the corresponding author of this work, Wei Huang, to get more detail on this new study.

Rams in St Kilda. Photo credit, Martin Adam Stoffel.

Can you describe the significance of this research for the general scientific community in one sentence?

This study demonstrated the direct link between immune genes and antibody levels in wild populations.

What led to your interest in this topic / what was the motivation for this study? 

The major histocompatibility complex (MHC) contains a number of genes linked with immune defence in vertebrates. Associations between MHC variation and phenotypic traits or pathogens have been identified in many species. Also, selection on MHC genes has also been demonstrated in some studies. However, many previous studies only examined associations between MHC variation and a limited number of phenotypic traits or pathogens. Few of them have examined both MHC-fitness associations and MHC-trait associations. The longitudinal study of Soay sheep in St Kilda is a great system to study the associations between MHC variation and phenotypic traits and how the associations are linked with selection on MHC genes. Using three representative phenotypic traits monitored in thousands of sheep over decades, we are able to provide a full picture of MHC-trait associations in wild populations.

Can you describe the significance of this research for your scientific community in one sentence?

This study suggests associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits and highlights the association between MHC variation and antibodies in wild populations.

What difficulties did you run into along the way? 

It is extremely hard to monitor populations and collect longitudinal data over decades. Thanks to our great field assistants and volunteers, the Soay sheep data has provided a good foundation. In terms of the specific study, the first difficulty is to genotype MHC in a large number of sheep. We used two steps to genotype the MHC genes. We first used genotype-by-sequencing to genotype hundreds of sheep. Then, benefiting from the high-density sheep SNP chip, we were able to use 13 SNPs to genotype MHC in the other thousands of sheep successfully.

Additionally, it is hard to choose the appropriate model. Some of our traits are not normally distributed and are also not closed to other common error structures. We instead used Bayesian statistical methods to run the analysis.

What is the biggest or most surprising innovation highlighted in this study? 

We used three representative traits to examine the associations between MHC variation and phenotypic traits. The traits included a fitness-related integrative trait, body weight, a measure of gastrointestinal parasites, faecal egg count, and level of three antibodies. All of the three traits are related to fitness. We only found associations between MHC variation and antibodies. Such results reflect the important role of MHC in immune defence in wild populations. Our study is one of the first studies to examine associations between MHC variation and multiple phenotypic traits. 

How do you think your results generalize to other systems?
Our study is based on the longitudinal study of Soay sheep. The large sample size provides great statistical power. Therefore, our results are reliable and solid. Also, we investigated phenotypic traits that have different links with immune defence. Therefore, our results can reflect the general pattern of MHC-trait associations.  

You conclude from your study that MHC variation is more likely to be associated with immune traits. How would you validate your findings for species with less rich data?

First, it is possible to use experiments to test the associations. In terms of wild populations, future studies can investigate multiple populations or multiple traits in a single population if they are restricted by the study length.

Moving forward, what are the next steps in this area of research?

Our study demonstrates that it is important to study MHC-antibody associations. Future studies should focus on immune traits rather than only examine MHC-pathogen associations. Also, previous studies are often restrained by small sample size. It would be nice if future studies could increase their sample size to strength the statistical power.

Huang, W.*, Dicks, K. L.*, Ballingall, K. T., Johnston, S. E., Sparks, A. M., Watt, K., Pilkington, J. G., & Pemberton, J. M. (2022). Associations between MHC class II variation and phenotypic traits in a free-living sheep population. Molecular Ecology, 31, 902– 915. 

*These authors contributed equally to this work

Interview with the authors: Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones

Hybridization is a mechanism by which adaptive alleles can cross species boundaries and possibly boost the adaptive potential of hybridizing species. This may be especially true for alleles that confer a selective advantage when rare, which is common among major histocompatibility complex (MHC) genes involved in pathogen defense. We therefore would expect MHC genes to introgress across hybridizing species relatively easily, though there exists relatively few examples supporting this hypothesis. In this paper from Molecular Ecology, Katarzyna Dudek, Tomasz Gaczorek, Piotr Zieliński, and Wiesław Babik document the extent of introgression in MHC variants across two hybridizing European newts across replicated transects. Read below for a behind-the-scenes look at their paper!

Link to the study:

F1 hybrid male. Photo from M. Niedzicka

What led to your interest in this topic / what was the motivation for this study? 
The evolutionary significance of adaptive introgression is increasingly appreciated and many examples have been described, but few generalizations are available. There is a relatively well understood mechanism – novel/rare allele advantage – which should promote introgression of genes evolving under balancing selection (a prime example of these are MHC genes). However balancing selection itself produces signatures resembling introgression, so convincing demonstration of introgression in genes under balancing selection is difficult. Hybrid zones, especially in the form of replicated transect, are among the best tools you can imagine for such a project. And we’ve been studying these newts for some time – in a way this study was motivated by our long standing interest in adaptive introgression, but it’s an off-shoot of another project (see the paper in the same issue of Mol. Ecol.).

What difficulties did you run into along the way? 
The most difficult part was the design and justification of simulations that we used to rule out explanations alternative to introgression. Because MHC in newts is multi-locus and shows extensive copy number variation, it’s been difficult to design simulations that would at the same be time realistic and feasible. This may sound surprising, but genotyping and interpretation of MHC variation has not been a major problem, although the system is quite complicated. It seems that the field has matured enough that exon-based genotyping of MHC variation has become a standard. Another frontier would be population genetic analysis of entire MHC haplotypes, extremely interesting but currently beyond reach in non-model (and most model) taxa.

Field sampling. Photo from M. Liana

What is the biggest or most surprising finding from this study? 
The scale of apparently adaptive introgression. It’s not only that MHC variants introgress – we have suspected this before. One could expect that a single or a handful of novel, introgressed MHC haplotypes would be favoured in the recipient species, but we found massive introgression, apparently involving tens or more haplotypes, most likely in both directions. It’s been quite a surprise for us – this suggests that introgression can really remodel MHC variation in hybridizing species – an influx of large amount of variation may cause species to share, at least locally, pool of MHC variation.

Moving forward, what are the next steps for this research?
A natural next step is to test generality of our findings. The mechanism of novel/rare allele advantage should operate rather universally. If so, we expect that MHC genes will be among the last genes to stop introgressing between species that still hybridize, but are strongly reproductively isolated genome-wide. In other words we expect MHC introgression should be detectable (and perhaps strong) in systems, where despite hybridization, there is very little genome-wide introgression. We’ve been lucky to obtain funding for a collaborative project, in which we are going to test this prediction using over twenty hybrid zones from major vertebrate groups. We’d also like to look at the process at the level of entire haplotypes, but this would need to wait until technologies mature.

Albino L. montandoni male. Photo from W. Babik

What would your message be for students about to start their first research projects in this topic?
The most important would probably be: have your questions worked out and if you find a system that is good to address them – go for it. Try to understand the available theory, there’s nothing more practical than good theory to guide you and to save countless hours of your precious time. And finally, start writing before you think you’re ready. Writing is the best way to have your ideas clear, to spot weak points and see things you didn’t realized before.

What have you learned about science over the course of this project? 
Over and over again – that science is unpredictable. That reality mocks your well laid out ideas and plans, twisting and turning your paths, but if you recognize and follow the opportunities that appear on the way, everything will be fine :). For example something that appears as an offshoot of a major project may turn out at least equally interesting and important. Two key components are good and diverse collaboration and the scale of research appropriate to your question – that is just large enough to provide sound answers, but not necessarily larger.

Field sampling pt 2. Photo from W. Babik

Describe the significance of this research for the general scientific community in one sentence.
Our research suggests that MHC introgression may be a widespread process that introduces novel and restores previously lost variation, boosting the adaptive potential of hybridizing taxa.

Dudek, K., Gaczorek, T.S., Zieliński, P. and Babik, W., 2019. Massive introgression of MHC genes in newt hybrid zones. Molecular Ecology. 28(21). 4798-4810.