The evolutionary ecology of the major
SB Piertney and MK Oliver
School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
The major histocompatibility complex (MHC) has become a
paradigm for how selection can act to maintain adaptively
important genetic diversity in natural populations. Here, we
review the contribution of studies on the MHC in non-model
species to our understanding of how selection affects MHC
diversity, emphasising how ecological and ethological pro-
cesses influence the tempo and mode of evolution at the
MHC, and conversely, how variability at the MHC affects
individual fitness, population dynamics and viability. We
focus on three main areas: the types of information that have
been used to detect the action of selection on MHC genes;
the relative contributions of parasite-mediated and sexual
selection on the maintenance of MHC diversity; and possible
future lines of research that may help resolve some of the
unanswered issues associated with MHC evolution.
published online 10 August 2005
Keywords: balancing selection; mate choice; MHC; parasites; sexual selection
Determining the relative contributions of different
stochastic and deterministic microevolutionary processes
in the maintenance of genetic diversity in natural
populations has been a major focus in evolutionary
biology for several decades. The advent of allozyme
electrophoresis in the 1960s (Harris, 1966; Lewontin and
Hubby, 1966) prompted a proliferation of studies that
examined genetic diversity across a broad taxonomic
spectrum, and fuelled the neutralism vs selectionism
debate that is still ongoing (Hey, 1999). Latterly, a
burgeoning amount of DNA sequence information has
facilitated efforts to identify the effects of selection on
different gene regions and estimate the distribution of
selective effects across the genome (Ford, 2002). Such
data, however, does not necessarily help clarify what
processes underpin selection, as DNA sequence informa-
tion may not help to determine a gene’s function.
Our understanding of how selection can act to
maintain adaptive polymorphism in natural populations
remains based on a small number of key gene regions,
such as the major histocompatibility complex (MHC).
The MHC has been characterised at the molecular
level for a considerable number of years, and research
describing MHC diversity has been extensive. Notwith-
standing, the MHC remains a potent model on which
competing hypotheses on the causes and consequences
of selection can be tested.
The MHC is central to the vertebrate immune system.
It is a multigene family that encodes key receptor
molecules that recognise and bind foreign peptides for
presentation to specialist immune cells and subsequent
initiation of an immune response (Klein, 1986). From an
evolutionary perspective, the pre-eminent feature of the
MHC is the extreme diversity that is observed at
expressed loci. The MHC contains the most variable
functional genes described in vertebrates. At three of the
more variable human MHC loci, HLA-A, HLA-B and
HLA-DRB1, 243, 499 and 321 alleles have been resolved
worldwide, respectively, and nucleotide diversity in the
human MHC is up to two orders of magnitude higher
than the genomic average (Gaudieri et al, 2000; Garrigan
and Hedrick, 2003). As more MHC genes are examined
from an increasing number of species across a broad
taxonomic range, it is apparent that such high diversity is
a characteristic feature of MHC loci.
A pressure to maintain high allelic diversity at MHC
loci might appear intuitively obvious, given that indivi-
duals or populations with higher sequence variation at
MHC loci can identify and process a larger number of
pathogenic antigens, and as such combat a wider range
of immune insults. However, despite sustained effort we
are still far from properly understanding what evolu-
tionary, ecological and ethological processes generate,
and more importantly maintain, MHC diversity in
natural populations (Potts and Slev, 1995; Edwards and
The critical role in the immune recognition of parasites
and pathogens means that the MHC might also be
associated with a number of quantitative traits linked to
the fitness and behaviour of individuals in natural
populations. As such, the evolutionary dynamics of the
MHC has become of relevance in ecology, population
biology and conservation, and a paradigm for adaptively
important genetic diversity. The potential ecological
significance of the MHC was mooted while there was
still a paucity of data on MHC variation from non-model
Received 1 March 2005; accepted 27 June 2005; published online
10 August 2005
Correspondence: SB Piertney, School of Biological Sciences, University
of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ,
UK. E-mail: email@example.com
Heredity (2006) 96, 7–21
& 2006 Nature Publishing Group All rights reserved 0018-067X/06 $30.00
species in natural populations, but it was predicted that
despite the potentially intimidating pre-requisite barrier
of characterising MHC homologues in non-model spe-
cies, there would be a rapid proliferation of studies
across a range of vertebrate species (Potts and Wakeland,
1990, 1993; Hedrick, 1994; Lenington, 1994; Edwards et al,
1995; Edwards and Hedrick, 1998). It was also suggested
that widespread characterisation of MHC diversity in
natural populations would add considerably to our
understanding of the tempo and mode of MHC evolu-
tion by explicitly examining relationships with ecological
processes that had been deemed to drive the evolu-
tionary dynamics (Edwards et al, 1995).
This review is not directed at providing an exhaustive
synthesis of the literature on levels, causes and con-
sequences of MHC diversity. Instead, we highlight
key studies on classical laboratory model species, and
more recent studies from non-model species in natural
populations that have added to our understanding of
MHC evolution. Other reviews have followed a similar
thread (Apanius et al, 1997; Bernatchez and Landry, 2003;
Garrigan and Hedrick, 2003), but such is the degree of
dynamism in this field that even in the few years since
their publication, the number of studies on non-model
species has increased dramatically, as has our overall
understanding of the ecological significance of MHC
The structure and function of the MHC
The primary role of the MHC is to recognise foreign
proteins, present them to specialist immune cells and
initiate an immune response (Klein, 1986). In general,
foreign proteins enter cells either by infection or by
phagocytosis into antigen-presenting cells such as
macrophages. These foreign proteins are broken down
into small peptides and loaded onto specific MHC
molecules. A subset of these protein/MHC complexes
are then transported to the cell surface and presented for
interrogation by the circulating T-cell population. A
complex cascade of immune responses is triggered when
the T cell binds to the presented peptide.
The MHC gene family encompasses two main sub-
groups of immunologically active molecules. Class I
molecules are expressed on the surface of all nucleated
cells except sperm cells and some neurons. They present
endogenously derived peptides to CD8þ
T-cells, so are primarily associated with defense against
intracellular pathogens such as viruses. Class II mole-
cules are present on antigen-presenting cells like macro-
phages, lymphocytes and dendritic cells, and present
processed exogenous antigens to CD4þ T-helper cells.
As such, class II molecules are associated with immune
insults derived from extracellular parasites and patho-
The MHC molecule comprises an immunoglobulin
‘stalk’, which anchors the molecule to the cell surface,
and a ‘basket’ receptor called the peptide-binding region
(PBR; also called the peptide-binding groove, peptide-
binding site, antigen recognition site or antigen pre-
sentation site). It is the PBR that is responsible for antigen
recognition, and a match between PBR, antigenic peptide
and T-cell receptor is required to produce an immune
cascade. Although PBRs do show a degree of specificity,
a single MHC molecule can bind multiple peptides that
have common amino acids at particular anchor positions
(Altuvia and Margalit, 2004).
Class I MHC molecules are heterodimers, comprising
a transmembrane peptide (class I heavy chain), and three
extracellular domains (a1, a2, a3) each of which is
encoded by a different exon from a single gene. The
Class I PBR consists of two a-helices next to a b-pleated
sheet, formed by the a1 and a2 domains of the class I
heavy chain (Jeffrey and Bangham, 2000). The MHC class
II molecule is a heterodimer that consists of two
transmembrane proteins, an a and a b chain, which are
encoded by two separate genes. Specific sites within both
chains form the Class II PBR.
The genetic architecture of the MHC has been detailed
for several model vertebrate species, most notably in
humans (termed HLA; MHC Sequencing Consortium,
1999), mouse (H-2; Younger et al, 2000), rat (RT-1;
Gunther and Walter, 2001; Hurt et al, 2004) and chicken
(B-locus; Kaufman et al, 1999). There are similarities
across these model systems in MHC structure, in that the
class I and class II genes are linked together in a single
gene complex in each case (Hughes and Yeager, 1998;
Hess and Edwards, 2002). There are also, however, some
striking differences. For example, the mammalian MHC
encodes multiple loci for both class I and class II
molecules, whereas in chicken the B-complex codes for
two class I and two class II genes, and only one in each
class is polymorphic and expressed at high levels
(Guillemot et al, 1989; Kaufman and Salomonsen, 1997).
An increasing number of MHC genes from non-model
species are being characterised for comparison (Shiina
et al, 2002; Kelley et al, 2005), and are highlighting
considerably more variation in architecture. Large
differences in the number of MHC loci are apparent
across species, and some groups have silenced particular
loci or have them arranged in unlinked gene clusters
(Flajnik et al, 1993; Hansen et al, 1999; Kuroda et al, 2002).
What is clear is that despite the conserved proximate
function of MHC in immune recognition, the architecture
of MHC genes varies sufficiently that a small number of
model species is insufficient to describe the complex
processes of antigen binding and recognition.
Several lines of evidence from a large body of empirical
data indicate that positive selection operates on MHC
loci to maintain MHC variation. A number of different
statistical tests can be used to test for selection on DNA
sequences (reviewed in Kreitman and Akashi, 1995;
Hughes, 1999; Kreitman, 2000; Ford, 2002; Garrigan and
Hedrick, 2003). Here, we highlight those that have been
frequently used in studies on MHC. These can be
categorised as detecting selection in contemporary
populations and the current generation, over the history
of populations, and over the evolutionary history of
Detecting selection in contemporary populations
Selection acting in contemporary populations is expected
to have a detectable effect on genotypic frequencies
within that population (Hedrick et al, 2000). Over-
dominance models of selection predict that heterozygote
genotypes will be fitter than homozygote genotypes
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
(Doherty and Zinkernagel, 1975) given that two variant
alleles will identify a broader range of pathogens. As
such, if the intensity of selection is sufficient, there can be
detectable deviations from Hardy–Weinberg proportions
in adult populations, and/or deviations from Mendelian
proportions in offspring, with an over-representation of
heterozygote genotypes in both cases. Potts et al (1991)
showed consistent deficiencies in the number of MHC
homozygotes in the progeny of mice. However, other
studies have detected little or no deviation from Hardy–
Weinberg expectations (Paterson et al, 1998; Gutierrez-
Espeleta et al, 2001; Seddon and Ellegren, 2004), perhaps
suggesting that selection is spatially or temporally
variable, that it cannot be detected in a single generation,
or does not conform to a simple overdominance
mechanism. It is also possible that studies lack sufficient
sample size or allelic diversity at the MHC to have the
statistical power to detect any effects, or that demo-
graphic processes acting on small or fluctuating popula-
tions mask any observable bias (Seddon and Ellegren,
Detecting selection over the history of a population
The effects of selection acting through the course of the
history of a population can be detected from information
on the frequency of alleles and the distribution of
mutations within and between populations. Ewens
(1972) highlighted that under neutral theory there is a
low probability of an even frequency distribution for all
alleles within a population. As such, there is an
equilibrium distribution for heterozygosity for a given
number of alleles and a known sample size when only
mutation and drift are operating. Watterson (1978)
proposed that deviation from such an equilibrium is an
indicator of departures from neutrality and hence
selection. The so-called Ewens–Watterson test of neu-
trality has been used to confirm the effects of balancing
selection acting on the MHC in both non-model species
(Paterson, 1998; Landry and Bernatchez, 2001; Miller
et al, 2001; Hambuch and Lacey, 2002) and humans
(Mack et al, 2000; Begovich et al, 2001).
A number of studies that have utilised the Ewens–
Watterson test in multiple local populations have found
variation in the level of decreased homozygosity among
the different populations. In wild Atlantic salmon (Salmo
salar), evidence for class IIb MHC diversity maintained
by balancing selection was found in only six out of 14
populations (Landry and Bernatchez, 2001). Similarly, in
sockeye salmon (Oncorhynchus nerka), a deficit of homo-
zygosity at the MHC class II DAB-b1 locus was observed
in 13 of 31 populations (Miller et al, 2001). Such
observations were attributed to variation in the strength
and nature of selection across populations. However, the
Ewens–Watterson test assumes that the populations
examined are at equilibrium and have remained at
constant size through evolutionary time (Nei, 1987).
Given that the demographic history of the vast majority
of natural populations involves fluctuations in size, it is
unclear whether these patterns reflect a violation of the
assumptions of the Ewens–Watterson test, or actual
spatio-temporal variation in selection.
In an attempt to obviate this problem, patterns of MHC
variation are frequently compared with those expected
from neutral expectations, which are empirically derived
from markers such as microsatellites or mitochondrial
DNA sequences. Studies have generally taken one of two
approaches. Firstly, by contrasting levels of MHC and
neutral diversity within populations. Given that demo-
graphic processes are predicted to affect all loci, whereas
selection will not influence the allele frequency distribu-
tion of neutral markers, the effects of variation in
population size and other historical processes can be
detected and controlled for. Secondly, by comparing
levels of population divergence derived from both MHC
and neutral markers. If selection is operating, and is
relatively constant across populations, then it is expected
that measures of population divergence should be lower
for MHC alleles than neutral microsatellites as balancing
selection will create a more even spatial distribution of
alleles, or may favour new or rare alleles, and hence
dispersers with novel genotypes enjoy a higher effective
migration rate. Conversely, if selection varies, then MHC
divergence is expected to be higher than estimated from
Several studies have used either or both of these
approaches to examine the effects of selection acting on
MHC diversity in populations. However, few studies
have actually found an among-population effect consis-
tent with balancing selection. Instead, studies have
identified that either the strength of selection on MHC
genes is weak relative to other microevolutionary forces
acting in subdivided populations, or that selection
pressures vary across populations, potentially as a result
of heterogeneity in parasite load or diversity.
Westerdahl et al (2004) observed that the frequency of
two (out of 23) specific MHC class I alleles varied more
between cohorts of great reed warblers (Acrocephalus
arundinaceus) than expected from random, whereas
microsatellite markers showed fluctuations consistent
with stochastic variation. This was used as evidence of
the effects of selection rather than demographic factors in
driving MHC variation.
Sommer (2003) found that genetic divergence esti-
mates for both MHC DQA and DRB genes between two
remnant populations of Malagasy giant jumping rat
(Hypogeomys antimena) were much lower than those
derived from mitochondrial control region DNA se-
quences. This could be explained by balancing selection
producing a more even allele frequency distribution over
the two subpopulations. However, this could also be
influenced by sex-biased dispersal with a high level of
female philopatry. Sequence analysis of the DRB PBR
revealed a pattern consistent with the effects of selection
at some time during evolutionary history, but such
effects are probably now outweighed by contemporary
Similarly, Boyce et al (1997) compared patterns of
diversity for MHC and microsatellite loci in 11 popula-
tions of bighorn sheep (Ovis canadensis). A high incidence
of mortality attributed to infectious disease in these
populations (Buechner, 1960) implies the potential for
pathogen-mediated selection on MHC loci (Boyce et al,
1997). However, neither MHC nor microsatellite deviated
significantly from the Hardy–Weinberg expectations and
mean overall heterozygosity was higher for microsatel-
lites than for MHC loci. It was concluded that if
balancing selection was operating, then its effect is
sufficiently weak to be masked by other microevolu-
tionary forces. Similar conclusions were reached by
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
Miller et al (2004) from bottlenecked populations of New
Zealand robins Petroicidae, and Huang and Yu (2003)
from 19 populations of the Southeast Asian house mouse
Mus musculus castaneus in Taiwan.
Miller et al (2001) examined variation at the MHC class
II DAB-b1 locus for 31 populations of sockeye salmon
Oncorhynchus nerka within the Fraser River drainage.
They reported that 25% of variation at the b1 locus was
apportioned between populations compared to 5% at
neutral markers. Similar patterns of increased MHC
population differentiation relative to neutral loci have
also been observed in Atlantic salmon (Salmo salar)
(Landry and Bernatchez, 2001). Both of these studies
emphasise the potential for opposing directional selec-
tion working at different geographic scales to increase
between-population differences in MHC variation.
The major concern with studies that compare micro-
satellites and MHC markers in this way is that there is
little consistent theory to derive predictions on the
comparative patterns or between-population divergence
for neutral loci and genes under selection in a sub-
divided population (Schierup, 1998; Schierup et al, 2000;
Muirhead, 2001). Certainly, the effects of demographic
history or social structure could confound any compara-
Detecting selection over the evolutionary history
of a species
Selection is expected to both increase the apparent rate of
nucleotide substitution relative to neutral expectations,
and also retain mutations longer than would normally be
expected under a neutral model. The detection of these
sorts of effects is used by several approaches aimed at
detecting positive selection in MHC genes.
The ratio of nonsynonymous (amino-acid altering) to
synonymous (silent) nucleotide substitutions per non-
synonymous and synonymous site (dN:dS) can be used
to test for balancing selection at any gene region (Hill
and Hastie, 1987; Hughes and Nei, 1988). Synonymous
mutations do not affect amino-acid composition and
are therefore effectively neutral. As such, the rate of
synonymous substitution should equal the mutation rate
(Kimura, 1983). Nonsynonymous mutations, however,
that do alter amino-acid composition, are more likely to
be under selection. Deleterious nonsynonymous muta-
tions are generally removed by purifying selection,
making the rate of nonsynonymous evolution lower
than the neutral rate, resulting in dN:dS o1. Conversely,
beneficial nonsynonymous mutations will be retained by
selection, increasing the rate of evolution relative to the
neutral rate, resulting in dN:dS 41. Therefore, if
balancing selection favours diversity at the PBR of
MHC genes, advantageous nonsynonymous mutations
will be retained and a high ratio of nonsynonymous to
synonymous substitutions will be observed. Tests of
deviation of dN:dS from parity are becoming increas-
ingly sophisticated (Nielsen, 1997; Yang and Nielsen,
2000; Bierne and Eyre-Walker, 2003), and can now
explicitly examine which amino-acid sites show the most
potent signatures of selection (Nielsen and Yang, 1998;
Yang et al, 2000; Suzuki, 2004; Massingham and Gold-
man, 2005). Such approaches will prove useful in studies
of the MHC, as the effects of selection on specific
peptide-binding codons can be ascertained.
Application of dN:dS tests across a range of vertebrate
species confirms the actions of balancing selection at
MHC regions (Hughes and Nei, 1988, 1989; Slade and
McCallum, 1992). Indeed, Bernatchez and Landry (2003)
reported a meta-analysis including 48 studies of which
only one did not have an excess of nonsynonymous to
synonymous substitutions. One disadvantage of using
dN:dS is that the accumulation of high ratios may occur
over large timescales (10000–100000 generations), and if
selection is relaxed, the time for the ratio to return to
equivalence can be even longer (Garrigan and Hedrick,
2003). As such, elevated dN:dS can provide powerful
evidence that balancing selection has operated on a gene
extensively at some period in its evolutionary history, but
provides little insight as to the timing or cause of
selection. dN:dS may thus have limited applicable value
when attempting to understand the nature of selection
acting in contemporary populations.
A second approach used to detect the effects of
selection acting through evolutionary history of a species
is the occurrence of extensive trans-species allelism (also
called trans-species polymorphism and originally trans-
species evolution; Klein, 1980). This is the non-neutral
retention of alleles among species such that gene trees
fail to provide an accurate representation of the species
relationships. Coalescent and neutral theories predict
that immediately following divergence from their ances-
tral form, two species will share a proportion of alleles at
any given locus. Over time, this proportion is reduced by
stochastic and/or deterministic microevolutionary forces
until each sister species has a distinct set of alleles. From
a phylogenetic perspective, this process will see a
gradual progression from polyphyly, through paraphyly,
to reciprocal monophyly, and this end point should be
reached in o4N generations for neutral alleles (where N
is the population size). Balancing selection can act to
retain alleles among species for considerably longer
periods of time (Takahata and Nei, 1990), increasing the
time over which there is incomplete lineage sorting and
delaying the time to monophyly. As a result, MHC gene
phylogenies can pre-date the species phylogenies from
which they were derived. Such trans-species allelism has
been identified in a wide range of taxa including
salmonids (Miller and Withler, 1997; Garrigan and
Hedrick, 2001), ungulates (Van Den Bussche et al, 2002),
pinnipeds (Hoelzel et al, 1999), rodents (Musolf et al,
2004), geckos (Radtkey et al, 1996) and warblers
(Richardson and Westerdahl, 2003). However, trans-
species polymorphism is apparently not ubiquitous for
MHC genes. Pfau et al (2001) found concordance between
species and gene trees for an MHC DQA locus when
comparing alleles from the cotton rat (Sigmondon
hisipidus) with other rodents. Moreover, mutational
processes such as gene conversion and interlocus
recombination can bias analysis by affecting divergence
and retention times (Martinsohn et al, 1999). As such,
some MHC alleles may be considerably younger than
they would appear from an MHC-based phylogeny.
Some studies have managed to provide a functional
validation that alleles have been retained over evolu-
tionary time scales. Phylogenetic analysis indicated that
related MHC-DRB alleles are present in humans,
chimpanzee and other primates (Geluk et al, 1993). The
binding and antigen presentation capacity of these trans-
specific alleles for a mycobacterial antigen was similar
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
and the homologous MHC proteins were also competent
for presentation to a human T-cell line. This emphasises
that the MHC allele members must have been present in
a common ancestor of these primate species that lived
about 30 million years ago, and that function has been
conserved across speciation events.
What underpins selection at the MHC?
Garrigan and Hedrick (2003) highlighted that some
signals of selection may be detectable after only a short
period of selective pressure, but that this signal can
remain for considerable periods of time, certainly well
after selection has been relaxed. As such, little informa-
tion on the timing of selection is achieved. Perhaps more
importantly though is that this can prevent inference
about those processes that might underpin selection.
This has been a major issue in studies on MHC evolution
(Apanius et al, 1997). It has been proposed that the
mechanisms are associated with either parasite-mediated
or sexual selection, although these two paradigms are
not necessarily mutually exclusive. Evidence in favour of
both of these forces is outlined below. One strength of
examining non-model systems in natural populations is
that it allows examination of selection acting in an
ecological context over short time scales which enhances
the potential for identifying sources of selective pressure.
Parasite-mediated selection and MHC
The fundamental role of the MHC in combating immune
insults from parasites and pathogens underpins the
concept that MHC polymorphism is maintained through
some form of pathogen-driven selection (Doherty and
Zinkernagel, 1975; Hedrick and Kim, 1998). Initially, it
was considered that this might not be the case, given that
the human MHC is intimately linked with autoimmune
disease, such as insulin-dependent diabetes and multiple
sclerosis, rather than with infectious pathogens (Kauf-
man et al, 1995). However, relationships between certain
human diseases, such as malaria, and specific HLA class
I and class II DRB haplotypes are now well established
(Hill et al, 1991, 1992, 1994; Hill, 1998, 1999). Similarly, in
chickens, an extremely strong association exists between
the class II B21 allele with resistance, and the class II B19
allele with susceptibility, to Marek’s disease, a potentially
lethal T lymphoma induced by a herpes virus (Briles
et al, 1977). Experimental studies in mice have demon-
strated the influence of MHC genes in both resistance
and susceptibility to a variety of disease ranging from
gastrointestinal helminths to viruses (for a comprehen-
sive overview, see Apanius et al (1997)).
Once a link between MHC type and disease resistance
was established, emphasis shifted to understanding the
mechanistic processes most likely to explain the high
observed MHC diversity. Two primary theories were
proposed – the negative frequency-dependent selection
hypothesis and the overdominance hypothesis (Takahata
and Nei, 1990; Slade and McCallum, 1992).
The negative frequency-dependent selection (or rare
allele advantage) hypothesis proposes that new or rare
alleles may incur a selective advantage when a novel
pathogen strain arises. If the rare allele confers an
advantage over a common allele, then it would subse-
quently increase in frequency. As the advantageous allele
becomes more common, selection will favour novel
pathogenic strains that are not recognised by this allele.
If the pathogen is unrecognised, it will increase in
frequency and selection will favour a different MHC
allele that can recognise and process that pathogen
(Slade and McCallum, 1992). Mechanistic models have
shown that negative frequency-dependent selection can
retain a large number of MHC alleles in flux (Borghans
et al, 2004). Apanius et al (1997) estimated that it would
take almost 1000 host generations for a deleterious MHC
allele that does not recognise the dominant pathogen
to deplete in frequency from 1 to 0.1%. Empirically,
frequency-dependent selection is hard to detect, given
the temporal aspects implicit in the relationship among
alleles. Inference can be made from the spatial variation
in the relationship between resistance and MHC type
(Hedrick et al, 1976; Gillespie, 1978; Hill et al, 1994), or
from changes in MHC allele frequency over short time
scales (Westerdahl et al, 2004). This, however, can be
problematic as it provides little scope for differentiating
between frequency-dependent selection and directional
selection for an individual allele that may go to fixation.
The overdominance hypothesis was first suggested by
Doherty and Zinkernagel (1975), who proposed that
immune competence, in terms of the recognition and
elimination of pathogens, could be substantially en-
hanced by heterozygosity at MHC loci, as heterozygotes
recognise a wider variety of antigens derived from
multiple pathogens and so have a higher relative fitness
than either homozygote. This supposition depends some-
what on the degree of divergence in the structure of
peptide groups bound by different alleles, and as such,
individuals with haplotypes showing less overlap in
binding specificity would be favoured. From an empirical
perspective, the overdominance hypothesis predicts a
stable polymorphism, and can only be tested fully in
systems with multiple pathogen strains. Some models,
however, have demonstrated that overdominance can
only retain high levels of MHC diversity in natural
populations if all heterozygote genotypes have equivalent
fitness (De Boer et al, 2004), which is arguably unrealistic.
It should be emphasised that there are several
potentially confounding problems trying to separate
the effects of dominant vs overdominant processes as
the primary driver of selection, and these problems may
be exacerbated in natural populations that examine
relatively small sample sizes and where populations
are exposed to a generally unknown range of parasite
and pathogen insults. Firstly, Apanius et al (1997)
highlighted an implicit frequency-dependent component
to the heterozygote advantage hypothesis in that rare
alleles occur disproportionately in heterozygous geno-
types, whereas common alleles occur disproportionately
in homozygous genotypes. In this case, rare alleles
would always seem to have an advantage, but the
relative contributions of overdominance or frequency-
dependent selection cannot be separated. Secondly, in
the strictest sense, overdominance can only be inferred
when the fitness of the heterozygote genotype is
significantly greater than both homozygotes. Frequently,
the fitness of the heterozygote is greater than the average
of the two homozygotes, but not significantly greater
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
than the fittest homozygote, as fitness is a consequence of
the presence of a dominant resistant allele that both the
heterozygote and homozygote genotypes carry. In this
case, there is a heterozygote advantage in the broadest
sense, but this is not synonymous with overdominance.
The two processes are predicted to be considerably
different in their efficacy for retaining diversity in natural
populations (Penn et al, 2002; McClelland et al, 2003).
Experimental studies have been used to explicitly test
the overdominance hypothesis, by infecting laboratory
populations with multiple pathogens. Penn et al (2002)
showed that MHC heterozygote mice had greater
survival and clearance capacity to avirulent Salmonella
infections than homozygote mice. However, the hetero-
zygote genotypes were not significantly more resistant
than the most resistant homozygote, inferring that
resistance was dominant rather than overdominant.
McClelland et al (2003) have shown a true overdominant
effect in mice coinfected with Salmonella and Theiler’s
murine encephalomyelitis virus. When the two hetero-
zygote haplotypes had opposite susceptibility profiles to
the two pathogens (ie haplotype 1 is resistant to one and
susceptibility to the other, and vice versa for haplotype 2),
heterozygote genotypes were fitter than both homozy-
Studies on non-model species from natural popula-
tions have added to our understanding of the signifi-
cance of disease association in MHC evolution, both by
clarifying the intimate relationship between MHC type
and resistance to specific parasites and pathogens, and
also determining the relative contributions of dominant
vs overdominant selection in maintaining MHC diversity.
A large number of studies have highlighted significant
relationships between MHC type and parasite burden.
These studies vary in their degree of complexity and
sophistication, ranging from moderately simple indirect
correlative studies, to large-scale, replicated experimen-
In subterranean mole rats Spalax ehrenbergi, MHC
heterozygosity was highest in the most humid/warm
areas where infectivity of gamasid mites and endopar-
asitic helminths was also highest (Nevo and Beiles, 1992).
This suggested that selective pressures arising from
macroparasite burdens help to maintain differential
levels of MHC diversity across geographical areas with
varying environmental characteristics.
In Scottish Blackface sheep, Schwaiger et al (1995) and
Buitkamp et al (1996) detected a significant influence of
MHC genes in regulating faecal egg burdens of the
gastrointestinal helminth Ostertagia circumcincta, with 58-
fold, eight-fold and 218-fold reductions in faecal egg
counts in 6-month old lambs carrying particular alleles at
DRB-1, class I and class IIb (DY) genes, respectively,
relative to lambs carrying the most common allele in
Paterson et al (1998) showed that specific MHC alleles
affected both resistance and susceptibility to gastro-
intestinal nematodes in a natural population of Soay
sheep (Ovis aries), as did Meyer-Lucht and Sommer
(2005) in yellow-necked mouse (Apodemus flavicollis) and
Schad et al (2005) in Malagasy mouse lemurs (Microcebus
murinus). In striped mice (Rhabdomys pumilio), MHC DRB
heterozygosity influenced infection status to parasites,
and particular alleles occurred more frequently than
expected in both high and low parasitised individuals
(Froeschke and Sommer, 2005). This study provides
evidence that both overdominant and frequency-depen-
dent selection may operate simultaneously.
A corollary of heterozygote advantage models that
indicate that individuals with two alleles have increased
fitness relative to those with one, is that across multiple
paralogous genes, an increasing number of alleles should
confer a greater ability to respond to a broad range of
pathogens and hence maximise immunocompetence to
multiple simultaneous infections. This hypothesis was
tested in three-spined sticklebacks (Wegner et al, 2003a,b)
exposed to a range of parasite species across lake and
river populations. Between 13 and 28 class IIb MHC
alleles were resolved within populations, and between
two and nine alleles across duplicated genes within
individuals. The lowest parasite burdens, however, were
found in those individuals with an intermediate number
of alleles (ca. 5). It was proposed that high intraindivi-
dual diversity might reduce fitness by overdepletion of
the T-cell repertoire during self-tolerance induction in
the thymus. This in turn would reduce the potential that
an immune response could be mounted against any
given foreign antigen (Nowak et al, 1992). However,
selection for intermediate numbers of alleles was not
observed in hairy-footed gerbils (Gerbillus paeba; Harf
and Sommer, 2005). Individuals with an intermediate
number of alleles across duplicated loci were more
intensively infected with intestinal helminth parasites
than individuals with more or fewer alleles. Moreover,
Hedrick (2004a) examined whether selection for inter-
mediate numbers of alleles could retain high levels of
diversity over time in natural populations, and con-
cluded this was only possible with unrealistically high
rates of mutation. Wegner et al (2004) responded by
highlighting that processes other than mutation, such as
recombination, may be operating.
One potential problem with attempting to link any
aspect of the MHC to parasite resistance in natural
populations is that studies typically resolve high
numbers of MHC alleles at low frequencies, which
combined with relatively low sample sizes, makes it
difficult to harness adequate statistical power (Hill,
1998). Although the selection advantage of MHC hetero-
zygosity may be considerable over evolutionary time-
scales, it is relatively weak and hard to detect in
contemporary populations, especially those of the size
typically sampled in most studies. Apanius et al (1997)
highlighted that to demonstrate a 0.05 difference in
fitness between heterozygotes and homozygotes would
require a sample size of over 6000. If multiple pathogens
define the selection pressure, then the cumulative value
of 0.05 would have to be divided per pathogen. More-
over, if different selection mechanisms such as resistance
to infectious, autoimmune and malignant disease vary in
the way in which they act upon MHC polymorphism,
then selection operating through one mechanism may be
obscured by other mechanisms acting in other ways
(Apanius et al, 1997).
While such issues might foster a perception that
studies on natural populations that attempt to correlate
parasite load or disease resistance to particular MHC
alleles or heterozygosity are fatally compromised by
power, two alternative approaches have been utilised:
the use of experimental challenges, and examination of
MHC against lifetime reproductive success.
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
Challenge experiments on individuals taken from
natural populations offer a powerful alternative ap-
proach to correlative association for examining the
efficacy of particular MHC haplotypes against disease
or parasites. They are better suited for replication and
large sample size, and hence abrogate many of the
problems associated with obtaining sufficient statistical
power to detect associations.
Langefors et al (2001) found an association between
certain MHC class IIb alleles and resistance to the
bacterial pathogen Aeromonas salmonicida in experimen-
tally challenged Atlantic salmon (Salmo salar). Lohm et al
(2002) subsequently selectively mated the uninfected
siblings of these fish, combining high- and low-resistance
alleles within full-sibling families, thereby controlling for
the potentially confounding effects of family. This study
revealed a codominant pattern of resistance/suscept-
ibility to A. salmonicida infection. Neither study found
any evidence to support MHC heterozygote advantage,
and in the former case it was suggested that the results
were more consistent with the frequency-dependent
hypothesis (Langefors et al, 2001).
Further experimental challenges of Atlantic salmon
with infectious salmon anaemia virus as well as A.
salmonicida employed very large sample sizes and found
highly significant associations between independently
segregated MHC loci and disease resistance (Grimholt
et al, 2003). MHC heterozygosity (Arkush et al, 2002) and
specific MHC alleles (Miller et al, 2004) have also been
associated with resistance to infectious hematopoietic
necrosis virus (IHNV) in Chinook salmon (Oncorhynchus
tshawytscha) and Atlantic salmon (S. salar), respectively.
Experimental infection in other fish species compli-
ments the work carried out on salmon. In Gila
topminnows (Poeciliopsis o. occidentalis), MHC hetero-
zygotes enjoyed a 15.5% higher survival relative to
homozygotes following infection with an exotic fluke
(Hedrick et al, 2001). Wedekind et al (2004) showed that
certain MHC class II genotypes increased embryo
survival in whitefish (Coregonus sp.) after infection by
the bacterium Pseudomonas fluorescens.
While Apanius et al (1997) underlined potential power
issues associated with correlative studies examining
MHC type and parasite load, it was also highlighted
that measuring alternative variables such as productivity
and reproductive success might be considerably more
powerful. Each small MHC-dependent effect may con-
tribute additively to a more detectable relationship
across a variety of fitness influencing parameters over
an individual’s lifetime. This approach was applied in a
study of free-ranging rhesus macaques (Sauermann et al,
2001; Widdig et al, 2004), and provides strong indirect
evidence for overdominant selection promoting MHC
diversity in primates. Among male macaques, MHC
class II heterozygotes sired significantly more offspring
than homozygotes. No evidence of disassortative mating
preference was found in the study population and the
authors suggest increased resistance to parasites and
reduced debilitative effects of injury-related infection as
the most plausible explanation of increased reproductive
success in MHC heterozygous males. Parasites such as
helminths, although unlikely to lead to mortality, may
cause lethargy, thereby reducing the ability of a male to
gain access to a female and reducing reproductive
success over time (Sauermann et al, 2001). Anti-helminth
treatment improved the reproductive success of males,
supporting suggested links between parasite burden and
MHC-dependent sexual selection, mate
choice and the MHC
The second major paradigm for how MHC diversity can
be maintained at high levels in natural populations
invokes MHC-dependent sexual selection (Brown and
Eklund, 1994; Jordan and Bruford, 1998; Penn and Potts,
1999). A number of adaptive hypotheses, which are not
necessarily mutually exclusive, have been proposed to
explain how MHC could influence mating behaviour and
reproductive success. Those that have received most
attention are: (1) MHC-related selective fertilisation
(Wedekind et al, 1996; Rulicke et al, 1998; Wedekind
et al, 2004); (2) MHC-dependent selective abortion
(Alberts and Ober, 1993); (3) disassortative matings
based on MHC genotype (Penn and Potts, 1999). Here,
we focus on the latter, as this has been the primary focus
for studies in non-model vertebrates. Furthermore,
processes such as maternal–foetal interaction cannot be
a mechanism that accounts for high MHC diversity in
From an individual’s perspective, MHC-based mate
choice would facilitate inbreeding avoidance between
close relatives, enriching genome-wide variation in
offspring. Also, since MHC heterozygotes can potentially
combat a wider range of immune insults than homo-
zygotes, individuals producing heterozygote offspring
enhance progeny fitness by maximising immunological
capability. These processes will maintain high levels of
polymorphism and generate the heterozygote excesses
and linkage disequilibrium characteristic of the MHC in
natural populations (Klein, 1986; Hedrick, 1992; Apanius
et al, 1997).
The concept that MHC genes could be intimately
linked with sexual behaviour and mate choice has been
intuitively attractive given that the primary function of
the MHC is to distinguish self from non-self at the
cellular level, and so could also underpin a mechanism
that distinguishes relatives from non-relatives at an
organismal level. Moreover, the complex architecture
and high polymorphism inherent in the MHC provides
the variability necessary for a genetically based recogni-
tion system (Grafen, 1990).
However, studies that have rigorously examined the
role of MHC in mate choice have drawn mixed
conclusions, and empirical data from non-model species
in natural populations are few. Studies have generally
taken one of two approaches: Firstly, determined
whether there is direct evidence of MHC-based sexual
selection from the types and frequency of MHC
genotypes observed at the population level, family level
or between mates. Secondly, examined whether there
are any phenotypic correlates that allow an individual
to assess the genotypic status of the MHC in another
The most work on MHC-based mate choice has been
undertaken on the mouse, and indeed it was the
serendipitous observation of MHC-biased mate prefer-
ence in crosses established to produce MHC-congenic
mouse strains that initially suggested MHC-based sexual
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
selection could occur (Yamazaki et al, 1976). Jordan and
Bruford (1998) and Acaro and Eklund (1999) provide
thorough summaries of the important studies on mating
preferences among inbred, congenic and seminatural
populations of mice. Initial experiments by Yamazaki
et al (1976) showed that in four of six congenic mouse
strains, males preferred to mate with MHC-dissimilar
females. Subsequently, female mice were also shown
to prefer MHC-dissimilar mates, and oestrus females
preferred MHC-dissimilar odours (Egid and Brown,
1989). This overall picture of MHC-dissimilar preference
is somewhat confused however because different genetic
backgrounds influence the strength and direction of mate
preference, with homozygotes displaying the strongest
responses (Yamazaki et al, 1976).
Potts et al (1991) showed similar patterns for wild mice
held in seminatural conditions. Consistent deficiencies in
the number of MHC homozygotes (27% across popula-
tions) were found in progeny relative to that expected
under random mating. After controlling for other
processes that could generate heterozygote excess, the
authors concluded that MHC based mating patterns
Following the initial work on mice, considerable effort
was invested in examining MHC-based mate choice in
humans. Mixed results were obtained. Hedrick and
Black (1997) found no evidence for HLA-dissimilar mate
choice in 11 south Amerindian tribes, whereas Ober et al
(1997) did find evidence for negative assortative mating
according to HLA type among 411 Hutterite couples, an
isolated caucasian group in north America derived from
400 founders in the 19th century.
Several studies have implicated olfaction as a mechan-
ism by which an individual can assess the MHC type of
another congener (Brown and Eklund, 1994). Although
the process is not fully understood, MHC genes can
affect the concentration of volatile acids that produce
odour in sweat or urine (Yamazaki et al, 1979; Singh et al,
1987; Wedekind et al, 1995; Wedekind and Furi, 1997;
Hurst et al, 2001; Beauchamp and Yamazaki, 2003; Santos
et al, 2004). This could be used as a direct cue to avoid
inbreeding, choose particular MHC genotypes or may
provide an indication of infection status. Female mice
have been found to be less attracted to a male’s urine
during infection with influenza, than before or after
infection (Penn and Potts, 1998). It is also apparent that
an individual’s own mate choice decisions will be based
on those that are experienced during early life, inferring
some form of familial imprinting. Yamazaki et al (1988)
showed through cross fostering experiments that an
individual will choose MHC-similar mates if cross-
fostered to MHC-dissimilar parents. This issue was
confused somewhat by subsequent studies that pro-
duced conflicting results (Acaro and Eklund, 1999).
Studies on MHC-based mate choice in humans and
mice have courted both considerable controversy and
criticism. The validity of experimental studies on mice
has been questioned given that the use of inbred lines
may selectively affect the very behaviours, especially
female mate choice, that the experiments are attempting
to examine (Manning et al, 1992). Also, MHC-congenic
lines will differ across a large swathe of MHC region, not
just the specific class I or class II loci that are supposedly
the focus of selection. As such, MHC-based mate choice
cannot be unambiguously separated from MHC-asso-
ciated mate choice (Hughes and Hughes, 1995). A lack of
repeatability of several studies, and an apparent plasti-
city in response across experiments, further questioned
the robustness of the data, and the general relevance of
mate choice as a primary driver of MHC diversity
(Jordan and Bruford, 1998).
Irrespective of such criticism, an increasing number of
studies are examining MHC-based mating preference in
non-model systems. In wild ring-necked pheasants,
Phasianus colchicus, male spur length is positively
correlated with age, body size and viability. Females
prefer to mate with males with longer spurs, and by
doing so they improve chick survival rate (von Schantz
et al, 1989). It was subsequently shown that male MHC
haplotypes for both class I and class IIb correlate with
spur length and male viability, indicating that females
discriminate among males based on secondary sexual
characters in order to pass on ‘good genes’ for disease
resistance and improve fitness of offspring (von Schantz
et al, 1996, 1997).
Similar inference was made by Ditchkoff et al (2001) for
white tailed deer (Odocoileus virginianus). Associations
were detected between certain MHC DRB genotypes,
rates of antler development and body size, and also a
negative relationship between antler size and abundance
of abomasal helminths. As such, antlers represent an
honest advertisement of parasite resistance, and a way
females can choose males that provide offspring with
superior disease resistance.
Olsen et al (1998) performed a series of fluvarium-
based experiments to examine whether juvenile arctic
charr (Salvelinus alpinus) could discriminate between
individuals of different class IIb MHC genotypes.
Individuals preferred water scented by an MHC-iden-
tical sibling over that scented by an MHC-different
sibling over that scented by an MHC-different nonsi-
bling. No preference was observed over a nonsibling that
shared an MHC allele to a sibling that shared no MHC
alleles, suggesting that some form of self-matching
comparison of MHC may occur. A follow-up study
(Olsen et al, 2002) showed that siblings isolated at
fertilisation failed to show any kin-biased preferences
for MHC genotype, which, as with other model species,
implicates some form of familial imprinting requirement
for effective MHC-based discrimination.
While the studies of Olsen and co-workers on charr
highlighted a degree of kin discrimination, their data
cannot be interpreted to conclude that individuals
choose MHC-dissimilar mates to maximize the fitness
of offspring. Landry et al (2001) have subsequently
shown this does occur in natural populations of Atlantic
salmon (Salmo salar). They highlighted that individuals
prefer to mate with fish with functionally different MHC
alleles to enhance MHC heterozygosity in offspring.
Mating to minimize inbreeding was discounted given
that the genetic relatedness of mates estimated from five
microsatellite loci did not differ from expectations based
on random mating.
Several other studies not detailed here have also
demonstrated MHC-dissimilar mating behaviour, in-
cluding in Savannah sparrows Passerculus sandwichensis
(Freeman-Gallant et al, 2003) and female sand lizards
Lacerta agilis (Olsson et al, 2003, 2004).
Despite some persuasive evidence of the role of MHC
in mate choice, several studies have also found no effect.
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
Moreover, the number of studies highlighting no
relationship between MHC and mate choice is likely to
be conservative given the bias caused by an under-
reporting of negative results. Paterson and Pemberton
(1997) found no evidence for MHC-dependent mate
choice in Soay sheep (Ovis aries) and suggested that the
strength of male–male competition is more important for
determining mating success than intersexual mate
choice. Similarly mate choice was determined to be
independent of MHC type in female great reed warblers
(Acrocephalus arundinaceus) (Westerdahl, 2004), rhesus
macaques (Macaca mulatta) (Sauermann et al, 2001) and
great snipes (Gallinago media) (Ekblom et al, 2004).
The gradual increase in studies examining MHC-
related mate choice has emphasised that choice can be
based on different criteria, be that for specific alleles,
genotypic dissimilarity or overall diversity (Tregenza
and Wedell, 2000; Mays and Hill, 2004). Early studies
such as that of von Schantz et al (1997) and von Schantz
et al (1996) emphasised that specific MHC alleles can be
advertised by extravagant secondary sexual characters.
However, overall immunocompetence might not be
based on the presence or absence of specific haplotypes,
but by the combination of paternal and maternal genes.
Indeed in bluethroats (Luscinia svecica), extra pair half-
sibs have greater immunocompetence relative to their
maternal and paternal half sibs, suggesting that parti-
cular combinations of alleles improve quality of offspring
(Johnsen et al, 2000). As such, individuals must not only
assess their potential mates quality but also how well
they complement their own genes.
If individuals choose mates to maximise the immuno-
competence of offspring, and resistance to parasites and
pathogens is underpinned by several MHC loci, then
individuals should choose based on the number of alleles
across multiple loci, or the compatibility of these alleles
to their own alleles at homologous loci. The potential for
such ‘allele counting’ has been shown in wild three-
spined sticklebacks (Gasterosteus aculeatus). Reusch et al
(2001) characterised MHC class IIb diversity at an
estimated six loci simultaneously. It was shown that
females prefer males that displayed ‘many’ alleles (6–8)
rather than ‘few’ alleles (3–6). Females did not prefer
MHC-dissimilar males, suggesting that allele counting is
a more important process than disassortative mating.
Given it has also been shown that individuals with an
intermediate number of alleles had the lowest parasite
burdens (Wegner et al, 2003a,b), mate choice in this case
appears to be directed towards maximising immuno-
competence across several paralogous loci.
Summary and future directions
The earliest reviews of MHC evolution were inevitably
focused on studies from a small number of laboratory
model species. It was suggested that expanding studies
to include non-model species in natural populations
would clarify the ubiquity of high diversity at MHC
genes, the ecological and ethological processes respon-
sible for underpinning selection, and the significance of
MHC diversity in individual fitness and the viability
of natural population (Edwards et al, 1995). The only
perceived problem was that the requirement to clone
and characterise MHC genes in non-model species might
represent an impediment to studies in natural popula-
tions (Edwards and Hedrick, 1998).
This concern was clearly misplaced. The development
of conserved PCR primers that amplify across diverse
vertebrate taxa (eg Edwards et al, 1995) and an increasing
amount of sequencing information from which to design
degenerate PCR primers for specific taxonomic groups
means that it is now relatively straightforward to target
MHC loci (Potts, 1996; Edwards et al, 2000). Moreover,
the development of rapid, high throughput screening
techniques such as single-stranded conformational poly-
morphism (SSCP) and denaturing gradient gel electro-
phoresis (DGGE) means large numbers of individuals
can be screened for MHC variation both rapidly and
economically (Potts, 1996). As a consequence, a relatively
large, and growing, body of empirical data now exists
in non-model species examining levels of diversity at
both class I and class II MHC genes, the evolutionary
relationships among MHC alleles, and causative links
between MHC diversity and parasite load, mate choice,
individual fitness and lifetime reproductive success.
Indeed, levels of MHC diversity in populations are
increasingly being used in a conservation context to
identify those populations that are relatively depaurpe-
rate in diversity. MHC variation is viewed as being a
better marker for conservation not because it is a better
proxy than any neutral marker for determining genome
wide diversity, but because it is intimately associated
with factors likely to impinge on individual fitness,
population viability and evolutionary potential in a
changing environment (Edwards and Potts, 1996; He-
drick, 1999; Arkush et al, 2002; Aguilar et al, 2004;
Hedrick, 2004b; Seddon and Ellegren, 2004).
A major finding of work on non-model vertebrates is
that it has, with rare exception, confirmed that MHC
variation is strongly influenced by selection. The
majority of studies, however, have identified that
selection has operated at some point through evolu-
tionary time rather than necessarily acting in the extant
generation. It is also clear that data from non-model
species is inconsistent with traditional models that
explain high MHC diversity as a consequence of over-
dominant balancing selection with equivalence between
different heterozygotes. Indeed, consistent associations
between particular alleles and resistance to parasites,
and variation in the difference in estimates of genetic
divergence measured from MHC and neutral markers,
would indicate that fitness is based on dominant, and not
overdominant, associations. Even those studies that have
inferred overdominance may in fact have detected
heterozygote advantage through the effect of a dominant
resistant allele rather than heterozygote superiority
caused by true overdominance.
This large body of data obtained from non-model
species in natural populations also has not identified
which process(es) underpin selection at MHC genes.
Evidence has accrued both in favour of the effects of
parasites and mate choice in maintaining MHC diversity.
Moreover, data can be selectively used to infer that
individuals are choosing mates to maximise MHC
heterozygosity, to minimise inbreeding, or selecting for
a optimal number of alleles across several loci.
So where might future studies focus to clarify how
MHC diversity is retained in natural populations, and its
significance as ecologically meaningful genetic diversity
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
likely to define individual fitness and population
It is our view that first-and-foremost, studies must
more rigorously characterise the diversity that is being
detected. The ease with which MHC variation can now
be resolved could paradoxically impede progress with
our understanding of MHC dynamics. A large number of
studies are characterising MHC variation from genomic
DNA extracts with little or incomplete knowledge of (1)
the number of loci that are actually being simultaneously
PCR amplified; (2) whether any or all of these genes are
actually expressed and (3) whether the variation that is
resolved reflects sequence differences at structurally
important regions such as the peptide-binding amino
acids. Ultimately, an inability to determine the actual
number of expressed loci, identify alleles as being
structural MHC variants, assign alleles to loci and
determine whether an individual is heterozygous or
homozygous for a particular locus compromises rigorous
statistical testing of association between MHC and
parasite load or mating behaviour, either by introducing
variation that is not directly under selection, or preclud-
ing detection of overdominant selection. It will be
problematic, bordering on impossible, to be able to
completely validate studies from mRNA extracts, espe-
cially from natural populations, and certainly if the
species is of conservation concern (though see Miller and
Lambert, 2003). However, every effort should be made to
initially ensure that PCR primers do actually amplify
single expressed products to clarify that subsequent
analysis based on genomic DNA is appropriate (Piertney,
A further concern is that an increasing trend towards
using noninvasive or nondestructive samples for char-
acterising genetic diversity may introduce more geno-
typing errors, as proficient characterisation of MHC
alleles from minute amounts of potentially damaged
DNA will be problematic (see Knapp, 2005 and reply
from Lukas and Vigilant, 2005).
One area where there will be continued emphasis in
studies of natural populations is in the comparison of
how neutral and MHC diversity is apportioned within
and among populations to measure the effects of
selection and infer how it varies across populations
(Landry and Bernatchez, 2001; Miller et al, 2001; Sommer,
2003). However, there is a need to develop a more
rigorous conceptual and theoretical framework that
predicts how selection and drift will interact in naturally
fragmented populations (Muirhead, 2001). Such models
need to incorporate not only variation in population size
and levels of dispersal but also variation in social
structure within populations. In the broader field of
population genetics, there is increasing emphasis on
determining the extent of social affiliation within
populations (Dobson et al, 1997, 1998; Girman et al,
1997; Dobson, 1998; Piertney et al, 1999) and on
developing a framework to model neutral gene dy-
namics in socially structured populations (Chesser,
1991a,b; Sugg and Chesser, 1994; Sugg et al, 1996).
Understanding how social structure affects MHC dy-
namics may be especially important given that social
structure will influence the transmission of parasites and
disease at a local scale, and also the potential for mate
choice decisions will vary in response to levels of local
inbreeding. Such processes do appear to be pertinent –
Hambuch and Lacey (2002) compared the strength of
balancing selection between a social and a solitary
species of tuco-tuco (Ctenomys sociabilis and C. haigi,
respectively), testing the hypothesis that sociality affects
parasite transmission that will influence selection. Selec-
tion coefficients were more than 50 times greater in the
Studies that have compared genetic divergence from
neutral and MHC markers infer spatial heterogeneity in
parasite load as the main process explaining the
observed patterns. However, such inference is often
made without direct examination of how parasite load or
diversity changes spatially, and hence patterns may
simply reflect variation in demographic processes.
Characterising variation in parasite intensity and diver-
sity across populations is daunting, but will shed
considerable light on our understanding of what main-
tains MHC diversity. Better still would be analysis of
spatio-temporal variation in parasite pressure, and
neutral and MHC variation. This allows more rigorous
testing of frequency-dependent, antagonistic coevolution
between parasites and host, but is logistically consider-
ably more difficult. The ability to extract DNA from
archived material facilitates the examination of temporal
MHC dynamics, but ultimately studies may need to be
designed that incorporate a temporal component.
In the context of understanding how mate choice
affects MHC dynamics, it is still unclear whether
individuals aim to reduce inbreeding, select for specific
MHC alleles, ensure offspring are heterozygous at an
MHC locus or maximise MHC diversity across several
loci. It is probable that different species employ different
strategies, and these may be context dependent, or vary
over time. Certainly, mate choice for compatibility differs
from other forms of sexual selection, such as good genes,
as individuals will differ in their choice of mates,
changing the evolutionary dynamics of sexual selection
(Tregenza and Wedell, 2000). One obvious paradox that
needs to be examined explicitly is whether there is a
fitness benefit to increased genetic diversity and a
tendency for females to use genetical dissimilarity as a
criterion for mate choice, how can they use an absolute
criterion such as ornamentation to assess a relative
criterion such as compatibility?
The continuing emphasis on whole-genome sequen-
cing, and the concomitant development of ‘post-geno-
mics’ approaches such as microarrays will impinge on
studies on MHC evolution in several ways.
Firstly, by highlighting the importance of variation in
MHC gene expression as well as in genotype for defining
the fitness and adaptive potential of individuals. There is
a growing understanding of how gene expression can
play an important role in determining phenotypic
variation (Oleksiak et al, 2002; Darvasi, 2003; Abzhanov
et al, 2004), and allelic variation in promoter regions
controlling HLA expression (Cowell et al, 1998) implies
that this may also be true for MHC. However, just as
characterising MHC genes in non-model species was
perceived as a potential stumbling block to the study of
MHC variation in non-model species, so might the
identification and analysis of MHC regulatory regions
in this case.
Secondly, technologies such as microarrays will iden-
tify genes with expression patterns that covary with
MHC to particular selection pressures. These represent
Evolutionary ecology of the MHC
SB Piertney and MK Oliver
potential candidates for genes that show evolutionary
patterns consistent with the effects of positive selection,
and impact on individual fitness (Fitzpatrick et al, 2005).
Paterson et al (1998) showed that specific MHC alleles
explained variation in gastro-intestinal nematode para-
site burden in free-living Soay Sheep. A subsequent
study showed that individuals carrying specific micro-
satellite alleles at a locus closely linked to the interferon-g
gene also had reduced levels of the same parasite and
increased titre of circulating parasite-specific antibodies
(Coltman et al, 2001). Several other potential candidate
genes that play an important role in defining an
individual’s defense against immune insult have been
identified (Behnke et al, 2003), and more can be readily
identified in array-based analyses.
Clearly, while examination of MHC in non-model
systems has increased our understanding of how genes
can be influenced by selection, and themselves influence
ecological processes, there are sufficient unanswered
questions and new avenues of research to suggest that
MHC will remain a major focus, and the number of
studies examining MHC diversity will continue to
increase at a rate similar to the past decade.
We thank the Natural Environment Research Council for
Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ (2004).
Bmp4 and morphological variation of beaks in Darwin’s
Finches. Science 305: 1462–1465.
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