Introduction
Genetic variation is the raw material for natural selection to act upon.
Hence, there is a long history of evolutionary studies on how genetic
variation is maintained in natural populations (Dobzhansky, 1982),
either invoking selection or neutral processes. One of the most dramatic
cases of genetic variation concerns polymorphism at Major
Histocompatibility Complex (MHC) genes, which are commonly the most
variable genes in vertebrate genomes (Sommer, 2005). Surprisingly,
despite decades of research on MHC evolution, the evolutionary processes
sustaining MHC polymorphism remain unclear, with inconsistent and often
ambiguous support for competing hypotheses (Radwan, Babik, Kaufman,
Lenz, & Winternitz, 2020). Here, we evaluate predictions of multiple
competing MHC evolution models (adaptive and neutral), using an
exceptionally large dataset of genetic variation and macroparasite
infection in a metapopulation of threespine stickleback
(Gasterosteus aculeatus ) inhabiting lakes on Vancouver Island.
MHC genes play a key role in the adaptive immune system of vertebrates.
The main function of these genes is to encode for cell surface proteins,
which are used to detect foreign molecules. These molecules are then
presented to T cells to initiate appropriate immune responses. The MHC
gene family consists of two classes of genes, MHC I and MHC II, each of
which can be represented by multiple paralog copies. MHC class I genes
are expressed in all nucleated cells and typically bind to peptides
derived from intracellular molecules, such as virus protein (Jensen,
2007). MHC class II genes (our focus here) are expressed only in antigen
presenting cells, such as macrophages, dendritic cells, and B cells.
These cells phagocytize extracellular material, digest the proteins, and
if the MHC II proteins bind to the resulting fragments, these are
presented on the cell surface to T cells, to possibly initiate an
adaptive immune response (Jensen, 2007). The second exon of MHC II gene
is often used to characterize the variability of MHC II genes, because
it contains the antigen-binding domain (Sommer, 2005).
The maintenance of MHC diversity is often attributed to
pathogen-mediated selection, although intraspecific processes, such as
mate choice (Penn & Potts, 1999), are also potential sources of
selection. As reviewed in Spurgin & Richardson (2010), there are three
non-mutually exclusive pathogen-mediated selection mechanisms to explain
MHC diversity: (1). Heterozygote advantage . Individuals with more
MHC alleles might be able to recognize a more diverse set of parasite
species, thus have fewer parasites. This advantage may lead to
directional selection for ever-increasing diversity, but some
widely-cited studies have presented evidence for intermediate optima (K.
Mathias Wegner, Kalbe, Kurtz, Reusch, & Milinski, 2003). (2).Negative frequency-dependent selection . In a given population,
common MHC alleles that protect against parasites impose selection on
those parasites to change their antigens and evade recognition. Once
parasites evolve strategies to evade these common alleles, individuals
carrying the common alleles may be at a selective disadvantage. By
contrast, a rare MHC allele imposes little selection on the parasites it
recognizes (because it is rare), and so may tend to be more protective.
For this negative frequency-dependence to work in the long run, it must
on average hold that rare alleles are more protective (and hence more
fit) than common alleles. (3) Fluctuating selection . Parasite
community and parasite genotypes may vary in space and time. Given this,
different host MHC alleles may be selectively favored in different
locations and at different times. Gene flow between locations subject to
divergent selection can sustain MHC diversity, as can temporally
fluctuating selection.
Although many studies have examined the roles of the above-mentioned
mechanisms in maintaining MHC diversity, the results are often mixed or
even contradictory. For example, heterozygote advantage was supported in
one experimental infection study with inbred mice (Penn, Damjanovich, &
Potts, 2002), but the effect was not found in another study with outbred
mice (Ilmonen et al., 2007). Theoretically, negative frequency dependent
selection is more likely to explain the extraordinary diversity in MHC
genes than heterozygote advantage (Borghans, Beltman, & De Boer, 2004).
However, empirically demonstrating negative frequency dependent
selection is more challenging, as the pattern is often also consistent
with other mechanisms. For example, in house sparrows,
population-specific MHC alleles were linked to host resistance or
susceptibility to malaria (Bonneaud, Pérez‐Tris, Federici, Chastel, &
Sorci, 2006), but this pattern could be explained either by negative
frequency dependent selection or spatially varying selection. A previous
study of stickleback from three lake-stream population pairs (Stutz &
Bolnick, 2017) tried to distinguish between negative frequency dependent
selection or spatially varying selection. The study took advantage of
migration between parapatric populations with different parasite
communities, which in principle would allow them to partition benefits
of rarity within populations, from costs of being a (rare) immigrant to
a foreign habitat. Yet, no overall trend was found to support either
mechanism. Such inconsistent or ambiguous results are typical in the MHC
evolution literature. Therefore, a consensus regarding the relative
importance of these mechanisms in maintaining MHC diversity has not been
reached (Radwan et al., 2020).
In contrast to these adaptive hypotheses, whether and how MHC diversity
is shaped by neutral processes is less studied. In small and/or isolated
populations, MHC diversity is often heavily influenced by genetic drift,
rather than balancing selection (Hedrick, Parker, & Lee, 2001; Miller
& Lambert, 2004; Seddon & Ellegren, 2004). In large metapopulations,
it is unclear what role neutral processes play in shaping MHC diversity.
MHC studies in threespine stickleback have generated some unique
insights in the past (Eizaguirre, Lenz, Kalbe, & Milinski, 2012;
Matthews, Harmon, M’Gonigle, Marchinko, & Schaschl, 2010; Mccairns,
Bourget, & Bernatchez, 2011; Milinski et al., 2005; K. Mathias Wegner
et al., 2003). For example, Wegner et al. (2003) conducted a study on 8
stickleback populations to examine the association between MHC diversity
and 15 parasite species. They found populations exposed to a wider range
of parasites had higher MHC allelic diversity, though MHC diversity also
positively, albeit weakly, correlated with neutral diversity. Moreover,
at the individual level, parasite burden was minimized in fish with an
intermediate, rather than maximal, number of MHCIIβ alleles. This result
supports the theoretical model of stabilizing selection on MHC
heterogeneity (Nowak, Tarczy-Hornoch, & Austyn, 1992). The logic is
that low MHC-diversity individuals do not have the capacity to recognize
diverse parasites, but high MHC-diversity individuals deplete their T
cells via negative selection on self-reactive T cells. The resulting
paucity of T cell receptor diversity also limits their ability to
recognize diverse parasites. However, this intermediate-advantage
hypothesis, while widely cited, has not been replicated in many systems
and remains controversial (Borghans, Noest, & De Boer, 2003). Another
example of interesting insights from stickleback is the involvement of
MHC alleles in mate recognition. It was found that female stickleback
could choose their mate based on odor to optimize the number of MHC
alleles in their offspring, though the molecular mechanism is unknown
(Milinski et al, 2005).
In this study, we set out to test predictions associated with three main
models of MHC polymorphism invoking parasite-mediated selection, using
an extensive field survey of parasites in a metapopulation of threespine
stickleback. We did not find evidence for stabilizing or positive
selection for MHC heterozygosity, contrary to Wegner et al. (2003). Nor
did we observe fluctuating selection across populations. Although we
found significant associations between specific MHC alleles and parasite
species both within and across populations, neutral processes in our
dataset best explained within- and between-population MHC diversity in
our data set.