Discussion
This study represents an effort to comprehensively evaluate multiple
major hypotheses concerning the maintenance of MHC diversity, using
observational data from 26 stickleback populations. Despite the large
scale of sampling, we did not find strong support for any of the three
popular parasite-mediated selection hypotheses, namely heterozygote
advantage, frequency-dependent selection, and fluctuating selection. In
contrast, neutral processes seem to best explain MHC diversity in this
system, both in terms of allelic richness and between-population
divergence.
Consistent with previous studies in other vertebrates (Kaufman, 2018),
MHC IIβ genes are highly polymorphic in the surveyed stickleback
metapopulation. We found 1115 unique MHC IIβ alleles from 1277
individuals, with a majority of alleles only present in one population.
However, although on average fish from lake habitats are infected with
more diverse parasite species than the ones from river and estuary
habitats (Bolnick et al., 2020), lake stickleback have less MHC allelic
diversity than others. The extremely high level of polymorphism in MHC
genes is often attributed to parasite-mediated selection; however, the
discrepancy between parasite richness and MHC allelic diversity among
habitat types suggests that parasite-mediated selection alone is
unlikely to explain the high level of MHC polymorphism in the studied
stickleback populations. This finding contradicts previous results from
studies of stickleback inhabiting different habitats in Germany (K. M.
Wegner, Reusch, & Kalbe, 2003), where lake fish had higher parasite
diversity (as in this study), and higher MHC diversity (unlike this
study).
The above finding is further supported through testing specific
predictions derived from heterozygote advantage model. The heterozygote
advantage hypothesis predicts that the number of MHC alleles in the host
genome would be maximized to recognize a wide range of parasites.
But previous studies (K. Mathias Wegner et al., 2003) in stickleback
found support for the theoretical model that the number of MHC alleles
should be optimized at an intermediate level, rather thanmaximized . The argument is that too many MHC alleles would reduce
the T cell portfolio due to negative selection of self-recognition T
cell receptors. In this study, we applied similar analytical approaches
as Wegner et al. (2003) to a larger sample size and many more
populations. Contrary to those previous results, we did not find support
for either the maximizing or optimizing hypothesis.
Negative frequency-dependent selection suggests that the frequency of
MHC alleles might experience a cyclical pattern through time, with
different low frequency alleles playing the role of conferring
resistance at different time points. For negative frequency dependence
to be effective, on average, it must be true that currently rare alleles
exhibit an advantage over common ones. In this study, we found that
allele prevalence in general is not associated with whether an allele is
effective in parasite resistance. We further examined whether alleles
have consistent effects across sites. We found inconsistent allele
effects in some cases, but we also found consistent effects in a larger
fraction of cases. So negative frequency-dependent selection might be
able to explain a limited number of allele-parasite dynamics in our
study. But, in most cases MHC alleles confer equivalent protection in
multiple isolated populations, inconsistent with cyclic changes due to
coevolution. Ideally, to demonstrate negative frequency-dependent
selection, one would need to carry out a longitudinal study that samples
parasite genotypes and host genotypes through time. However, this type
of study is very challenging to implement in a field setting, especially
for annually reproducing animals.
Finally, fluctuating selection, either temporally or spatially, is
frequently invoked to explain the maintenance of genetic diversity
across a landscape (Charbonnel & Pemberton, 2005; Schemske &
Bierzychudek, 2007). Our sampling sites on Vancouver Island differ in
many physical parameters, such as water area, depth, temperature, flow
speed, etc . It is also documented that parasite communities
differ significantly among different sites (Bolnick et al., 2020). This
spatial heterogeneity in parasite communities is due to abiotic and
biotic variables (e.g., lake size, fish diet; Bolnick et al. (2019)),
and could generate spatially fluctuating selection that maintains MHC
diversity. However, we did not find significant correlation between the
parasite distance matrix and the MHC distance matrix, suggesting that
the spatial heterogeneity in parasite community could not explain the
observed spatial variation in MHC diversity.
Interestingly, we found that neutral processes could contribute to MHC
diversity in two different analyses: (a). populations with higher
genomic heterozygosity also have higher MHC allelic richness, and (b).
less divergent populations (low genomic Fst) have similar MHC genotypes
and frequencies. Similar to analysis (a), a previous study in
stickleback (K. M. Wegner et al., 2003) also found a positive, albeit
weak, association between neutral genetic diversity and population MHC
allelic diversity. The role of neutral processes in the maintenance of
MHC diversity has often been studied in the context of conservation,
which is usually concerned with small and isolated populations (Miller
& Lambert, 2004; Seddon & Ellegren, 2004). Our result suggested that
at larger scales, neutral processes are also important factors in
explaining MHC diversity within- and between-population, even when there
is no specific evidence for past bottlenecks.
Parasite-mediated selection is believed to have an important role in
maintaining MHC polymorphism. Consistent with this, we found some
associations between certain parasites and individual MHC allele.
However, we did not find strong support for parasite-mediated selection
hypotheses in the scale of metapopulations. There are several possible
explanations. First, in this study, we examined the three hypotheses
separately, but in reality, the mechanisms are not mutually exclusive.
For example, low frequency alleles are more likely to be in a
heterozygous state in a population. Therefore, if an allele were
effective in resistance at low frequency, it would be consistent with
both negative frequency-dependent selection and heterozygote advantage.
Furthermore, if these mechanisms work in combination in different
MHC-parasite pairs or in different populations, we may not detect a
clear signal of each mechanism when combining data from multiple
MHC-parasite pairs and many populations. Second, parasites are not the
only selective agents that act upon MHC loci. MHC genes are also
involved in interactions with other species, such as symbionts
comprising the gut microbiome (Bolnick et al., 2014), and within species
interactions, such as mate choice (Milinski et al., 2005). It is unknown
which MHC genes are relevant to which selective forces. If other
selective forces are also at work, the influences of parasite-mediated
selection on MHC diversity could be obscured. Third, we only measured
parasite richness and MHC allelic richness in this study to represent
parasite diversity and MHC diversity, respectively, so the detailed
differences among individual parasite and individual MHC alleles were
not considered. In the future, it is worthwhile to test the
parasite-mediated selection hypotheses with diversity measurements that
take into account of nuances such as the phylogenetic relationship of
parasite taxa and the sequence divergence between distinct MHC alleles.
Finally, our survey does not span multiple seasons, so we cannot
evaluate how MHC variation is shaped across time by temporally
fluctuating selection.
To summarize, we used a large-scale field survey to evaluate the three
popular parasite-mediated selection hypotheses on MHC diversity, namely,
heterozygote advantage, negative frequency-dependent selection, and
fluctuating selection. We found that neutral processes best explain MHC
diversity (allelic richness and population divergence), instead of those
parasite-mediated selection mechanisms. Because MHC diversity can be
influenced by many selective forces, and the outcome of this selection
could be further shaped by spatial and temporal heterogeneity, our study
suggests it may not be possible to parse out how each selective force
influences MHC diversity at large scales directly from observational
data. We propose that it is worthwhile to instead investigate how each
selective force acts upon MHC diversity with experimental approaches
(e.g. controlling other selective forces) at smaller scales.
Combining insights from these small-scale controlled studies in a
step-wise manner can be a fertile future direction to understand the
complex process of MHC evolution and diversification.