Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism

Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought.     

Gene duplication,allelic diversity,selection processes and adaptive value of MHC class II <Emphasis Type="Italic">DRB</Emphasis> genes of the bank vole, <Emphasis Type="Italic">Clethrionomys glareolus</Emphasis>

The generation and maintenance of allelic polymorphism in genes of the major histocompatibility complex (MHC) is a central issue in evolutionary genetics. Recently, the focus has changed from ex situ to in situ populations to understand the mechanisms that determine adaptive MHC polymorphism under natural selection. Birth-and-death evolution and gene conversion events are considered to generate sequence diversity in MHC genes, which subsequently is maintained by balancing selection through parasites. The ongoing arms race between the host and parasites leads to an adaptive selection pressure upon the MHC, evident in high rates of non-synonymous vs synonymous substitution rates. We characterised the MHC class II DRB exon 2 of free living bank voles, Clethrionomys glareolus by single-strand conformation polymorphism and direct sequencing. Unlike other arvicolid species, the DRB locus of the bank vole is at least quadruplicated. No evidence for gene conversion events in the Clgl-DRB sequences was observed. We found not only high allelic polymorphism with 26 alleles in 36 individuals but also high rates of silent polymorphism. Exceptional for MHC class II genes is a purifying selection pressure upon the majority of MHC-DRB sequences. Further, we analysed the association between certain DRB alleles and the parasite burden with gastrointestinal trichostrongyle nematodes Heligmosomum mixtum and Heligmosomoides glareoli and found significant quality differences between specific alleles with respect to infection intensity. Our findings suggest a snapshot in an evolutionary process of ongoing birth-and-death evolution. One allele cluster has lost its function and is already silenced, another is loosing its adaptive value in terms of gastrointestinal nematode resistance, while a third group of alleles indicates all signs of classical functional MHC alleles.     

MHC variability, life-traits and parasite diversity of European cyprinid fish

Potential links between fish life history traits, an immune investment as measured by variability of the MHC genes and parasitism were analysed in 14 species of cyprinid fish. The hypothesis of the diversity of MHC genes being driven by high parasite diversity, i.e. species richness, was tested and a potential relationship between the MHC diversity and fish life-history traits including adult mortality rate, fecundity, longevity and maturity was investigated. Molecular techniques (SSCP and sequencing) were applied to analyse the MHC nucleotide diversity of the exons 2 and 3 of DAB genes belonging to the MHC class IIB. The comparative analyses, using phylogenetic independent contrasts, revealed a negative relationship between parasite species richness and adult fish mortality rate. We also found a positive relationship between nucleotide diversity of the exon 2 and parasite species richness. Our results suggest that fish species, of which populations are exposed to high parasite pressure, in terms of high parasite species richness, maintain a high genetic diversity of the exon 2 of the MHC genes (presenting the peptide binding regions), allowing them to decrease their natural mortality rate.     

Coevolutionary relationship between helminth diversity and MHC class II polymorphism in rodents

Parasite-mediated selection on major histocompatibility complex (MHC) genes has mainly been explored at the intraspecific level, although many molecular studies have revealed trans-species polymorphism. Interspecific patterns of MHC diversity might reveal factors responsible for the long-term evolution of MHC polymorphism. We hypothesize that host taxa harbouring high parasite diversity should exhibit high levels of MHC genetic diversity. We test this assumption using data on rodent species and their helminth parasites compiled from the literature. Controlling for similarity due to common descent, we present evidence indicating that high helminth species richness in rodent species is associated with increased MHC class II polymorphism. Our results are consistent with the idea that parasites sharing a long-term coevolutionary history with their hosts are the agents of selection explaining MHC polymorphism.     

Shared evolutionary origin of major histocompatibility complex polymorphism in sympatric lemurs

Genes of the major histocompatibility complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite‐mediated selective pressures, either favouring the long maintenance of ancestral MHC allelic lineages across successive speciation events by balancing selection (“trans‐species polymorphism”), or alternatively favouring the independent emergence of functionally similar alleles post‐speciation via convergent evolution. Here, we investigate the origins of MHC similarity across several species of dwarf and mouse lemurs (Cheirogaleidae). We examined MHC class II variation in two highly polymorphic loci (DRB, DQB) and evaluated the overlap of gut–parasite communities in four sympatric lemurs. We tested for parasite‐MHC associations across species to determine whether similar parasite pressures may select for similar MHC alleles in different species. Next, we integrated our MHC data with those previously obtained from other Cheirogaleidae to investigate the relative contribution of convergent evolution and co‐ancestry to shared MHC polymorphism by contrasting patterns of codon usage at functional vs. neutral sites. Our results indicate that parasites shared across species may select for functionally similar MHC alleles, implying that the dynamics of MHC‐parasite co‐evolution should be envisaged at the community level. We further show that balancing selection maintaining trans‐species polymorphism, rather than convergent evolution, is the primary mechanism explaining shared MHC sequence motifs between species that diverged up to 30 million years ago.     

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates

Background  

The major histocompatibility complex (MHC) is a key model of genetic polymorphism. Selection pressure by pathogens or other microevolutionary forces may result in a high rate of non-synonymous substitutions at the codons specifying the contact residues of the antigen binding sites (ABS), and the maintenance of extreme MHC allelic variation at the population/species level. Therefore, selection forces favouring MHC variability for any reason should cause a correlated evolution between substitution rates and allelic polymorphism. To investigate this prediction, we characterised nucleotide substitution rates and allelic polymorphism (i.e. the number of alleles detected in relation to the number of animals screened) of several Mhc class II DRB lineages in 46 primate species, and tested for a correlation between them.     

Genetic variation in MHC class II expression and interactions with MHC sequence polymorphism in three-spined sticklebacks

Genes of the major histocompatibility complex (MHC) have been studied for several decades because of their pronounced allelic polymorphism. Structural allelic polymorphism is, however, not the only source of variability subjected to natural selection. Genetic variation may also exist in gene expression patterns. Here, we show that in a natural population of three-spined sticklebacks (Gasterosteus aculeatus) the expression of MHC class IIB genes was positively correlated with parasite load, which indicates increased immune activation of the MHC when infections are frequent. To experimentally study MHC expression, we used laboratory-bred sticklebacks that were exposed to three naturally occurring species of parasite. We found strong differences in MHC class IIB expression patterns among fish families, which were consistent over two generations, thus demonstrating a genetic component. The average number of MHC class IIB sequence variants within families was negatively correlated to the MHC expression level suggesting compensatory up-regulation in fish with a low (i.e. suboptimal) MHC sequence variability. The observed differences among families and the negative correlation with individual sequence diversity imply that MHC expression is evolutionary relevant for the onset and control of the immune response in natural populations.     

Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum.

DNA sequences of alleles at the merozoite surface antigen-1 (MSA-1) gene locus of the malaria parasite Plasmodium falciparum show evidence of repeated past recombination events between alleles. These include both (1) nonreciprocal recombination events that have homogenized certain gene regions among alleles and (2) reciprocal recombination events that have combined allelic segments with divergent evolutionary histories, thereby enhancing allelic diversity. In three different gene regions, the rate of nonsynonymous nucleotide substitution significantly exceeds that of synonymous nucleotide substitution, implying that positive Darwinian selection has acted to diversify alleles at the amino acid level. The MSA-1 polymorphism seems to be quite ancient; the two major allelic types have been maintained for approximately 35 Myr.     

Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest

The adaptive potential of a species to a changing environment and in disease defence is primarily based on genetic variation. Immune genes, such as genes of the major histocompatibility complex (MHC), may thereby be of particular importance. In marsupials, however, there is very little knowledge about natural levels and functional importance of MHC polymorphism, despite their key role in the mammalian evolution. In a previous study, we discovered remarkable differences in the MHC class II diversity between two species of mouse opossums (Gracilinanus microtarsus, Marmosops incanus) from the Brazilian Atlantic forest, which is one of the most endangered hotspots for biodiversity conservation. Since the main forces in generating MHC diversity are assumed to be pathogens, we investigated in this study gastrointestinal parasite burden and functional associations between the individual MHC constitution and parasite load. We tested two contrasting scenarios, which might explain differences in MHC diversity between species. We predicted that a species with low MHC diversity would either be under relaxed selection pressure by low parasite diversity (‘Evolutionary equilibrium’ scenario), or there was a recent loss in MHC diversity leading to a lack of resistance alleles and increased parasite burden (‘Unbalanced situation’ scenario). In both species it became apparent that the MHC class II is functionally important in defence against gastrointestinal helminths, which was shown here for the first time in marsupials. On the population level, parasite diversity did not markedly differ between the two host species. However, we did observe considerable differences in the individual parasite load (parasite prevalence and infection intensity): while M. incanus revealed low MHC DAB diversity and high parasite load, G. microtarsus showed a tenfold higher population wide MHC DAB diversity and lower parasite burden. These results support the second scenario of an unbalanced situation.     

Spatio‐temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow

Climate change will strongly impact aquatic ecosystems particularly in arid and semi‐arid regions. Fish–parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species’ adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio‐temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio‐temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.     

Historical and contemporary selection of teleost MHC genes: did we leave the past behind?

The extreme polymorphism of antigen‐presenting genes of the major histocompatibility complex (MHC) has spurred intense research unparalleled for any other gene family. This applies also to teleosts where sequence information is available for 3559 MHC class I and class II allelic variants from 137 species. This review summarizes current knowledge on the origin and maintenance of diversity at classical MHC loci. Most studies identified positive selection (i.e. elevated rates of non‐synonymous over synonymous substitutions, dN/dS) as a sign of balancing selection. A meta‐analysis on nine species with sufficient numbers of class I and class II sequences revealed that recombination rate and intensity of positive selection were positively correlated, suggesting that recombination and gene conversion played a significant role in shaping the allelic repertoire. Processes that create diversity over long timescales need to be complemented by contemporary balancing selection, either through overdominance or frequency‐dependent selection, in order to explain the high allelic diversity observed today. While some evidence for overdominance exists for a few taxa (mainly salmonids) by correlating parasite infection data or survival to MHC genotypes, field or experimental data on negative frequency‐dependent selection are lacking altogether, even though some fish species are particularly suitable as model systems. Theoretical predictions suggest that negative frequency‐dependent selection is necessary to maintain the existing polymorphism. Hence, future empirical studies should focus on detecting signals that differentiate between mechanisms of contemporary selection rather than repeatedly showing historical selection events.     

Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus

The MHC class II loci encoding cell surface antigens exhibit extremely high allelic polymorphism. There is considerable uncertainty in the literature over the relative roles of recombination and de novo mutation in generating this diversity. We studied class II sequence diversity and allelic polymorphism in two populations of Peromyscus maniculatus, which are among the most widespread and abundant mammals of North America. We find that intragenic recombination (or gene conversion) has been the predominant mode for the generation of allelic polymorphism in this species, with the amount of population recombination per base pair exceeding mutation by at least an order of magnitude during the history of the sample. Despite this, patchwork motifs of sites with high linkage disequilibrium are observed. This does not appear to be consistent with the much larger amount of recombination versus mutation in the history of the sample, unless the recombination rate is highly non-uniform over the sequence or selection maintains certain sites in linkage disequilibrium. We conclude that selection is most likely to be responsible for preserving sequence motifs in the presence of abundant recombination.     

Insights into the complex associations between MHC class II DRB polymorphism and multiple gastrointestinal parasite infestations in the striped mouse

Differences in host susceptibility to different parasite types are largely based on the degree of matching between immune genes and parasite antigens. Specifically the variable genes of the major histocompatibility complex (MHC) play a major role in the defence of parasites. However, underlying genetic mechanisms in wild populations are still not well understood because there is a lack of studies which deal with multiple parasite infections and their competition within. To gain insights into these complex associations, we implemented the full record of gastrointestinal nematodes from 439 genotyped individuals of the striped mouse, Rhabdomys pumilio. We used two different multivariate approaches to test for associations between MHC class II DRB genotype and multiple nematodes with regard to the main pathogen-driven selection hypotheses maintaining MHC diversity and parasite species-specific co-evolutionary effects. The former includes investigations of a 'heterozygote advantage', or its specific form a 'divergent-allele advantage' caused by highly dissimilar alleles as well as possible effects of specific MHC-alleles selected by a 'rare allele advantage' (= negative 'frequency-dependent selection'). A combination of generalized linear mixed models (GLMMs) and co-inertia (COIA) analyses made it possible to consider multiple parasite species despite the risk of type I errors on the population and on the individual level. We could not find any evidence for a 'heterozygote' advantage but support for 'divergent-allele' advantage and infection intensity. In addition, both approaches demonstrated high concordance of positive as well as negative associations between specific MHC alleles and certain parasite species. Furthermore, certain MHC alleles were associated with more than one parasite species, suggesting a many-to-many gene-parasite co-evolution. The most frequent allele Rhpu-DRB*38 revealed a pleiotropic effect, involving three nematode species. Our study demonstrates the co-existence of specialist and generalist MHC alleles in terms of parasite detection which may be an important feature in the maintenance of MHC polymorphism.     

Wild cyclic voles maintain high neutral and MHC diversity without strong evidence for parasite-mediated selection

The major histocompatibility complex (MHC) is an important component of vertebrate immune defense involved with self/nonself recognition and disease susceptibility. The high variability of genes of the MHC is thought to arise from both parasite-mediated and sexual selection. An outstanding question involves the degree to which balancing selection can oppose genetic drift to maintain high MHC diversity in the face of population bottlenecks. To address this question we examined genetic diversity and population structure at neutral (microsatellite) and MHC genes in montane voles [Microtus montanus (Peale, 1848)] subject to high amplitude population fluctuations, and compared these to measures of infection by common gastrointestinal parasites. We found high neutral and MHC allelic variability, indicating low impacts of genetic drift despite large fluctuations in population size. Greater MHC diversity did not predict lower parasite richness or infection by the two most common endoparasites (cestodes and coccidian protozoa), as might be expected if genotypic composition confers resistance to infection. One specific MHC allele predicted lower cestode intensity, but we found no other associations between MHC and infection measures. Neutral heterozygosity was positively associated with total parasite richness, possibly owing to greater parasite tolerance among heterozygous relative to more inbred hosts. Overall, these results suggest that factors beyond the parasites examined here, such as high inter-patch migration, mate choice, gene conversion or other infectious agents, are likely maintaining the high levels of MHC diversity observed in wild montane voles.     

Parasite infection reflects host genetic diversity among non-native populations of pumpkinseed sunfish in Europe

Species introductions often coincide with loss of genetic diversity and natural enemies. Anthropogenic translocation of the North-American pumpkinseed Lepomis gibbosus (L., 1758) (Centrarchidae) and its further spread have resulted in recent species establishment in most European countries. This study determines genetic differentiation of non-native European pumpkinseed populations and identifies how their genetic structure relates to the distribution and abundance of parasite species. Microsatellite analysis indicated presence of three genetic lineages, which were well supported by discriminant analysis based on parasite abundance data. The first lineage clustered pumpkinseed populations from northern and southern France and showed high allelic richness, heterozygosity and parasite richness. The second included populations along the “Southern invasion corridor” connecting the rivers Rhine, Main and Danube. The fish exhibited low to high genetic and parasite diversity and generally high parasite abundance. The third lineage clustered populations with low genetic and parasite diversity, located in Portuguese reservoirs and water bodies along the upper Elbe. Parasite species richness was significantly associated with host microsatellite heterozygosity and allelic richness, a trend partially affected by richness of North-American parasites. Furthermore, our results indicate that parasite community composition may serve as a useful biological tool to discriminate non-native fish populations and their inter-relationships.

     

The role of major histocompatibility complex diversity in vigour of fish males (Abramis brama L.) and parasite selection

The major histocompatibility complex (MHC) presents a group of genes with highly polymorphic loci involved in specific immune responses. The factors maintaining extensive MHC polymorphism have been questioned, considering three possible hypotheses of parasite‐mediated selection driving an extensive MHC diversity (i.e. heterozygote advantage, rare‐allele advantage, and favouring optimal MHC diversity). The patterns of MHC diversity of class IIB genes were investigated following two noncontradicting hypotheses, parasite‐driven selection and MHC‐based mating preferences, using males of common bream collected in the spawning period. Two allelic groups DAB1 and DAB3 were recognized from the phylogenetic analyses. Individuals expressed one or two alleles of the same or different allelic groups. Several individuals shared identical alleles; however, the presence of parasite species was not associated with the occurrence of a particular allele. The presence of different allelic groups (only DAB1, only DAB3, or both DAB1 and DAB3) in individuals was not associated with parasite presence or diversity. The expression of two DAB1 alleles was associated with higher endoparasite abundance. Moreover, nucleotide diversity in individuals expressing a single type of alleles (DAB1 or DAB3) increased with the abundance of ectoparasitic Dactylogyrus spp. (Monogenea) and Ergasilus sp. (Crustacea). This suggests that the expression of two alleles of a single allelic type is related to high metazoan parasite infection whereas no significant influence of parasitism on the combined allelic form (the presence of both DAB1 and DAB3 alleles) was found. Moreover, the expression of two alleles of a single allelic type was related to decreased immunocompetence measured by spleen size. The condition factor was higher in fish expressing the combined allelic type. Thus, the presence of alleles of different lineages in individuals appears to be advantageous for individual male fitness. The expression of a single allelic type was related to higher sexual ornamentation, which could support the role of MHC in the hypothesis of the sexual selection of ‘good genes’. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 525–538.     

Sexual selection and the evolutionary dynamics of the major histocompatibility complex

The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host–pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host–parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.     

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high‐amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model‐averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC.     

Parasite load and MHC diversity in undisturbed and agriculturally modified habitats of the ornate dragon lizard

Major histocompatibility complex (MHC) gene polymorphism is thought to be driven by host–parasite co‐evolution, but the evidence for an association between the selective pressure from parasites and the number of MHC alleles segregating in a population is scarce and inconsistent. Here, we characterized MHC class I polymorphism in a lizard whose habitat preferences (rock outcrops) lead to the formation of well‐defined and stable populations. We investigated the association between the load of ticks, which were used as a proxy for the load of pathogens they transmit, and MHC class I polymorphism across populations in two types of habitat: undisturbed reserves and agricultural land. We hypothesized that the association would be positive across undisturbed reserve populations, but across fragmented agricultural land populations, the relationship would be distorted by the loss of MHC variation due to drift. After controlling for habitat, MHC diversity was not associated with tick number, and the habitats did not differ in this respect. Neither did we detect a difference between habitats in the relationship between MHC and neutral diversity, which was positive across all populations. However, there was extensive variation in the number of MHC alleles per individual, and we found that tick number was positively associated with the average number of alleles carried by lizards across reserve populations, but not across populations from disturbed agricultural land. Our results thus indicate that local differences in selection from parasites may contribute to MHC copy number variation within species, but habitat degradation can distort this relationship.