Is Mate Choice in Humans MHC-Dependent?
Raphae ¨lle Chaix1,2*, Chen Cao3, Peter Donnelly1,4
1Department of Statistics, University of Oxford, Oxford, United Kingdom, 2Unite ´ d’Eco-Anthropologie, CNRS UMR 5145, Muse ´e de l’Homme, Paris, France, 3CAS-MPG
Partner Institute for Computational Biology, Shanghai, China, 4The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
In several species, including rodents and fish, it has been shown that the Major Histocompatibility Complex (MHC)
influences mating preferences and, in some cases, that this may be mediated by preferences based on body odour. In
humans, the picture has been less clear. Several studies have reported a tendency for humans to prefer MHC-dissimilar
mates, a sexual selection that would favour the production of MHC-heterozygous offspring, who would be more resistant to
pathogens, but these results are unsupported by other studies. Here, we report analyses of genome-wide genotype data
(from the HapMap II dataset) and HLA types in African and European American couples to test whether humans tend to
choose MHC-dissimilar mates. In order to distinguish MHC-specific effects from genome-wide effects, the pattern of
similarity in the MHC region is compared to the pattern in the rest of the genome. African spouses show no significant
pattern of similarity/dissimilarity across the MHC region (relatedness coefficient, R=0.015, p=0.23), whereas across the
genome, they are more similar than random pairs of individuals (genome-wide R=0.00185, p,1023). We discuss several
explanations for these observations, including demographic effects. On the other hand, the sampled European American
couples are significantly more MHC-dissimilar than random pairs of individuals (R=20.043, p=0.015), and this pattern of
dissimilarity is extreme when compared to the rest of the genome, both globally (genome-wide R=20.00016, p=0.739)
and when broken into windows having the same length and recombination rate as the MHC (only nine genomic regions
exhibit a higher level of genetic dissimilarity between spouses than does the MHC). This study thus supports the hypothesis
that the MHC influences mate choice in some human populations.
Citation: Chaix R, Cao C, Donnelly P (2008) Is Mate Choice in Humans MHC-Dependent?. PLoS Genet 4(9): e1000184. doi:10.1371/journal.pgen.1000184
Editor: Molly Przeworski, University of Chicago, United States of America
Received February 25, 2008; Accepted July 30, 2008; Published September 12, 2008
Copyright: ? 2008 Chaix et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: R. Chaix was funded by a postdoctoral fellowhip from EMBO. C. Cao was funded by the Chinese Academy of Sciences and Max Planck Society. P.
Donnelly was supported by the Wellcome Trust and the Wolfson Foundation.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: email@example.com
In vertebrates, several studies have revealed that highly
polymorphic genes within the Major Histocompatibility Complex
(MHC) may have a role in mate choice. In particular, it has been
shown that MHC genes influence individual body odor in mice and
rats [1–7] and that mice prefer MHC-dissimilar mates e.g. [8–11],
and  for a review. Evidence for MHC-disassortative mating was
also found in sand lizards . Studies in fish (and in particular
Arctic charr) have shown their ability to discriminate the odors of
similar and dissimilar MHC siblings , and shown that salmon
prefer MHC dissimilar mates  while female sticklebacks choose
a mate in order to complement their own set of MHC genes and to
optimize the number of different alleles in their offspring .
Complex MHC-based mate choice was also observed in birds
[17,18]. The MHC is the most important part of the genome with
respect to immunity  and such MHC-based mate choice could
increase or optimize the number of non-self antigens that future
offspring can recognize and thus increase their resistance to
pathogens [12,20,21]. It could also have contributed to the
extraordinary polymorphism observed at MHC loci .
On the other hand, in humans, the role of the MHC in mate
choice is very controversial. Ober et al studied classical HLA types
for 400 couples from the Hutterite community and found
significantly fewer HLA matches between husbands and wives
than expected when taking into account the social structure of
Hutterites . On the other hand, no evidence of MHC-based
mate choice was found in a study of 200 couples from South
Amerindian tribes . In a less direct way, other studies have
focused on odor preferences: in ‘‘sweaty T-shirts experiments’’, in
which females were asked to smell T-shirts worn by different
males, it was shown that females significantly prefer the odor of T-
shirts worn by MHC-dissimilar males, although such preference
was not found among females taking the contraceptive pill [24,25].
However, in another sweaty T-shirts experiment, in which males
where chosen from a different ethnicity from the females and
females were not aware of the nature of the smell (contrary to the
two previous studies), females significantly preferred the odor of
males having a small number of HLA alleles matching their
paternal inherited alleles than the odor of males having fewer
matches . Although it has not been established that odor
preference is a key factor in mate choice, such studies support the
hypothesis that humans are able to discriminate MHC types of
potential mates through odor cues and that humans may use such
information when choosing a mate. However, the lack of
congruence between these studies means that there is still
uncertainty as to whether MHC variation influences mate choice
in humans, and to what extent. The availability of genetic
variation data at genomic scales now allows careful assessment of
this question. Crucially, it allows us to distinguish MHC-specific
effects from genome-wide effects.
In this study, we tested the existence of MHC-disassortative
mating in humans by directly measuring the genetic similarity at
the MHC level between spouses. These data were extracted from
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the HapMap II dataset, which includes 30 European American
couples from Utah and 30 African couples from the Yoruba
population in Nigeria . Our analyses are based on HLA types
and on 9,010 Single Nucleotide Polymorphisms (SNPs) densely
distributed across the MHC. Moreover, in order to control for
genome-wide effects, we compared the pattern observed in the
MHC region to patterns assessed in the rest of the genome, using
The genetic similarity at a given genetic variant for a given
couple c was measured using a relatedness coefficient R, defined as
a ratio of probabilities of identity in state R=(Qc2Qm)/(12Qm),
where Qcis the proportion of identical variants between the two
spouses and Qmis the mean proportion of identical variants in the
sample (that is, averaged over all possible pairs of individuals). This
coefficient, combined over the genetic variants in a region or
across the genome, allows an assessment of whether spouses are
more genetically similar or dissimilar than random pairs of
individuals. Significance was assessed by permuting individuals
between couples. All p-values below are two-sided. Positive values
of R indicate genetic similarity between spouses and negative
values indicate genetic dissimilarity between spouses, relative to
random mating in the sample.
Using molecular markers (average relatedness coefficients across
9,010 SNPs), we observed that on average European American
spouses were significantly more MHC-dissimilar from each other
than random pairs of individuals (R=20.043, p=0.015).
Moreover, the distribution of genetic relatedness coefficients
across couples shows no outliers (Figure 1), thus excluding the
possibility that this significantly negative coefficient could result
from only a few couples having extremely low genetic relatedness.
On the other hand, the MHC relatedness coefficient was positive
but not significantly so in African couples (R=0.015, p=0.23). In
addition, our analyses based on HLA types for 6 genes confirmed
this broad pattern: the multilocus relatedness coefficient was
marginally significantly negative in European American couples
(R=20.062, p=0.084) and not significantly positive in Yoruba
couples (R=0.023, p=0.412). (These analyses refer to the 4 digit
classification. Similar patterns were seen with 2 digit classification;
data not shown.) Using SNP data, we observed a higher mean
SNP diversity in the MHC region in the African sample (0.366)
than in the European American sample (0.349).
To control for genome-wide effects, we compared these
observations to the pattern of genetic similarity across the genome
(3,214,339 markers). Genome-wide, European American spouses
were not significantly more or less similar than random pairs of
individuals (genome-wide R=20.00016, p=0.739). On the other
hand, African spouses were more similar genome-wide than
random pairs of individuals (genome-wide R=0.00185, p,1023).
To further control for genome-wide effects, we asked whether
the MHC region was unusual relative to similar regions across the
There has been a longstanding hypothesis that selection
may have led to mating patterns that encourage
(MHC) loci because of improved immune response to
pathogens in the offspring of such matings, and, indeed,
this has been observed in several model systems. However,
in humans, previous studies regarding the role of the MHC
in mate choice or preference, both directly in couples and
also indirectly in ‘‘sweaty T-shirts’’ experiments, have
reported conflicting results. Here, by using genome-wide
genotype data and HLA types in African and European
American couples, we test whether humans tend to
choose MHC-dissimilar mates. This approach allows us to
distinguish MHC-specific effects from genome-wide ef-
fects. In the African sample, the patterns at MHC loci is
confounded by genome-wide effects, possibly resulting
from demographic processes relating to the social
organization of this population, and no tendency to
choose MHC-dissimilar mates is detected. On the other
hand, the sampled European Americans appear to have
favoured MHC-dissimilar mates, supporting the hypothesis
that MHC influences mate choice in some human
populations. Thus, this study suggests that, in some cases,
humans may rely on biological factors, in addition to social
factors, when choosing a mate.
Figure 1. Distribution of relatedness coefficients across the MHC region among couples in the two samples. A) European American
sample. B) African sample.
Is Mate Choice in Humans MHC-Dependent?
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genome with regard to its similarity/dissimilarity between spouses,
by comparing the similarity between spouses at the MHC to that
of all genomic windows having the same length as the MHC
(3.6 Mb). Strikingly, in the European American couples, only
0.4% of the windows, concentrated in 9 genomic regions (listed in
Table 1), exhibited a higher level of genetic dissimilarity between
spouses than the MHC (Figure 2). To account for the particular
linkage disequilibrium structure of the MHC and its low
recombination rate , we compared the MHC region to a
sub-set of windows having the same or lower recombination rate
and still found that only 0.1% of these windows had less genetic
similarity between spouses than did the MHC. In the African
sample, 9% of the windows (and 17% when matching for the
recombination rate) concentrated in 116 regions exhibited more
genetic similarity between spouses than the MHC (Figure 2).
At the molecular level, we found that the European American
couples we studied are significantly more MHC-dissimilar than
random pairs of individuals, and that this pattern of dissimilarity is
extreme when compared to the rest of the genome, both globally
and when broken into windows having the same length and
recombination rate as the MHC. Our analyses based on HLA
types also show a signature of dissimilarity between spouses. Such
dissimilarity, observed from both molecular and serological data,
cannot be explained by demographic processes, since such effects
would affect the whole genome. On the other hand, this MHC
dissimilarity could result from pressure for disassortative mating at
the MHC level. Such a mechanism could be triggered by our
olfactory capacity for discriminating MHC-mediated odour types
[21,29]. Alternatively, this genetic dissimilarity could result from
selection of the spermatozoa by the female oocyte (post-copulatory
sexual selection), a further safeguard favouring the production of
MHC-heterozygous offspring more resistant to pathogens see [29–
31] for reviews. Indeed, all studied couples were selected for
having offspring, and the excess of dissimilarity observed could be
restricted to fertile couples, rather than couples in general.
However, further analysis showed that the offspring of these
couples were not more MHC-diverse than expected by random
selection of parental gametes (results not shown). Moreover, our
results in European American couples reinforce previous evidence
of MHC-disassortative mating among Hutterite couples , in
which all couples were included, regardless of whether they had a
child (C. Ober, personal communication). Like the Ober study, the
sampled couples in our study are from a cultural isolate (in our
case sampled from the Mormon community), so one might
Figure 2. Average relatedness coefficients between spouses across overlapping 3.6 Mb regions throughout the genome, plotted
against their recombination rate. The MHC is plotted in red. A) European American sample. B) African sample.
Table 1. Locations (in build 35 coordinates) of the nine
regions exhibiting a higher level of genetic dissimilarity
between spouses in the European American couples than the
4 27300000 30900000
6 116400000 120000000
12 46800000 51000000
15 40800000 47700000
Is Mate Choice in Humans MHC-Dependent?
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speculate that MHC-based mate choice is stronger or easier to
detect in settings where there is less heterogeneity in other factors
which influence mate choice, but the current absence of detailed
molecular studies of mate choice in other human populations
makes this impossible to assess. The two studies in Swiss males and
females showing a significant preference of females for the odor of
MHC-dissimilar (over MHC-similar) males [24,25] implicate one
possible mechanism by which couples may implement MHC-
dependent mate choice. Taken together, these results strengthen
the hypothesis that MHC genetic variation influences mate choice
in some human populations.
Our analyses of the European American sample also show that
the results based on molecular data weremore significant than those
based on HLA types. Although we cannot rule out power effects in
explaining such a difference, it seems plausible, and consistent with
our data, that the biological mechanisms involved in disassortative
mating would depend on the MHC in ways that are not simply
captured by HLA types. Such biological mechanisms could possibly
result from a summation of effects over multiple genes, and not only
from the six HLA genes studied here.
On the other hand, Yoruba couples exhibited a significant
genome-widesignature ofassortative mating,whichislikelytoresult
from socio-demographic processes specific to this population. The
Yoruba are still organized in paternal lineages, which are
exogamous units  and C. Adebamowo, personal communica-
tion. Although we do not have specific ethnological data collected
with the Yoruba samples to explain our observations, a process in
which matrimonial exchanges between genealogically related
lineages are more frequent than matrimonial exchanges between
genealogically unrelated lineages could have left such a genome-
widesignature. On the contrary, forthe MHCregion, no significant
pattern of similarity/dissimilarity was observed, at either the
molecular level or the serological level. Several hypotheses can be
proposed to explain this observation: firstly, it is possible either that
the MHC is not involved in mate choice in this population, or that
social factors are relatively more important than the MHC and that
the sample size here does not allow detection of MHC effect on
mate choice. Secondly, it is possible that MHC-based mate choice is
aiming for an optimal, rather than maximal, number of MHC
alleles previous theoretical and experimental evidence for this
hypothesis are reviewed in . Such a mechanism would explain
why evidence of disassortative mating was found in the European
Americans, all sampled in the Mormon community exhibiting a
relatively low SNP diversity in the MHC (0.349), as well as in the
genetically isolated Hutterite community , but not in Yoruba.
Indeed, the Yoruba exhibit a relatively higher SNP diversity in the
MHC(0.366) thantheEuropean American,andtheoptimizationof
the number of HLA alleles in Yoruba may involve mating with a
not-so-MHC-dissimilar individual. This hypothesis is also consistent
with the ‘‘sweaty T-shirts’’ experiment performed between females
and males from different ethnicities (thus having a higher range of
MHC dissimilarity than males and females coming from the same
community) and showing that females prefer the odor of males with
little MHC-dissimilarity than the odor of males with more extreme
MHC-dissimilarity . Finally, it is possible that in African
populations, individuals carrying pathogen-resistant alleles are
easier to identify than elsewhere, because of the higher pathogen
pressure. In such conditions, it is possible that mating preferences
for particular pathogen-resistant MHC alleles are stronger than
mating preferences for MHC-dissimilarity per se .
In conclusion, our study, based on a large number of molecular
markers which allow us to control for genome wide effects,
indicates a clear-cut signature of MHC-disassortative mating in a
sample of European American couples. This supports the
existence of MHC-related biological factors contributing to mate
choice in at least some human populations. On the other hand, the
Yoruba exhibit a genome-wide tendency for enhanced similarity
among couples but no significant pattern at the MHC level. This
suggests that socio-demographic factors may be more important
than biological factors for mate choice in this population, although
the existence of MHC-dependent mate choice in Yoruba, aimed at
optimizing (rather than maximizing) the number of HLA alleles in
the offspring, cannot be excluded. Our study indicates that the
relative importance of biological and social factors varies from one
population to another. It also highlights the need for the
exploration of further genome-wide data in larger sample sizes,
including ‘‘just married’’ childless couples, sampled in several
ethnically differentiated groups, in order to build a more robust
view of the biological determinants acting on mate choice in
Materials and Methods
Two datasets were analysed in this study:
a)3,214,339 Single Nucleotide Polymorphism (SNPs) from the
the Hapmap II dataset, typed in 30 European American
couples (60 individuals) from Utah (Centre d’Etude du
Polymorphisme Humain (CEPH) Collection) and 30 African
couples (60 individuals) from the Yoruba population, Ibadan,
Nigeria . We used the phased data files and excluded
SNPs with minor allele frequency below 5%. In this dataset,
9,010 SNPs were located in the MHC region, (positions
29,700,000–33,300,000 on chromosome 6 , in build 35
coordinates). Sex chromosomes were not included in the
b)A set of HLA types for 6 of the main HLA genes (three class I
genes: HLA-A, -B, -C, three class II genes: HLA-DQA, -
DQB, DRB) in 44 European American couples and 30
African couples from the same collections as above . 30
out of the 44 European American couples were shared with
the HapMap II dataset, and all African couples were
common to both datasets. This dataset is available on the
following site: http://www.sanger.ac.uk/HGP/Chr6/.
We estimated the genetic relatedness between spouses using
SNP data and HLA type data. In all cases, the relatedness
coefficient for a given pair of spouses R was defined as
R=(Qc2Qm)/(12Qm), where Qc is the proportion of identical
variants between the two spouses and Qmis the mean proportion of
identical variants in the sample (that is, averaged over all possible
pairs of individuals) . The proportion of identical variants at a
given SNP for a given pair of individuals was 0 if both individuals
were homozygous and carrying a different allele (eg 00 and 11), 1
if both individuals were homozygous and carrying the same allele
(eg 00 and 00), and 0.5 in all others cases. We also considered a
variation of this definition, with pairs of heterozygous individuals
(01 and 01) being attributed a proportion of identical variants of 1
(instead of 0.5). Both definitions gave similar results (we present
here coefficients based on the first definition). We estimated the
average genetic relatedness coefficient between spouses across the
MHC and across the whole genome. We checked that our
estimates were not affected by the heterogeneity of SNP density
and linkage patterns across the genome, by redoing our analyses
on reduced sets of approximately independent SNPs prepared
Is Mate Choice in Humans MHC-Dependent?
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using two different procedures implemented in the software
PLINK (one based on pairwise SNP r2values and the other on the
variance inflation factor) . We also computed the average
genetic relatedness coefficient between spouses for sliding windows
of 3.6 Mb across the genome (in increments of 300 Kb) having at
least 1,000 SNPs and not overlapping a centromere. In the case of
the HLA type data, we defined the proportion of identical variants
as 0 if the two individuals carried different types, 0.5 if one of their
two types was similar, and 1 in all other cases and we computed a
multi-locus relatedness coefficient between spouses based on types
for 6 HLA genes. R was summarized across the MHC region, the
genome or the six HLA genes by averaging Qcand Qmover all
SNPs or over all HLA loci (and then computing the ratio
(Qc2Qm)/(12Qm)). Using molecular data, we also computed the
mean SNP diversity (probability that two randomly chosen
chromosomes are different at a given SNP) in the MHC region
for both samples.
We removed from both datasets two European American and
three African couples, in which one of the spouses had previously
been found to be closely related (relatedness coefficient equal or
higher to 1/32, see supplementary table 15 from ) to another
sample (in each case, we chose at random the couple to be
excluded). The relatedness coefficients before and after these
exclusions were very similar (we present in the paper the estimates
without these couples). In the case of HLA type data, we
considered both the 4 digit and the 2 digit classification, and found
congruent relatedness coefficients (coefficients based on the 4 digit
classification only are reported in this paper). The significance of
the relatedness coefficient was assessed using a permutation
approach: the two-sided p-value is the proportion of permutations
(attributing a new wife randomly to each husband) in which the
permuted couples had the same or more extreme mean relatedness
coefficient than the real couples. 1000 permutations were
We thank D. Davison, G. McVean, and C. Spencer, and several
anonymous reviewers for helpful comments on a previous version of this
manuscript, E. Heyer, P. Khaitovich and M. Somel for helpful discussion,
and G. McVean for access to computational resource.
Conceived and designed the experiments: RC PD. Analyzed the data: RC.
Contributed reagents/materials/analysis tools: CC. Wrote the paper: RC
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