Balancing selection and heterozygote advantage in major histocompatibility complex loci of the bottlenecked Finnish wolf population

Maintaining effective immune response is an essential factor in the survival of small populations. One of the most important immune gene regions is the highly polymorphic major histocompatibility complex (MHC). We investigated how a population bottleneck and recovery have influenced the diversity and selection in three MHC class II loci, DLA‐DRB1, DLA‐DQA1 and DLA‐DQB1, in the Finnish wolf population. We studied the larger Russian Karelian wolf population for comparison and used 17 microsatellite markers as reference loci. The Finnish and Karelian wolf populations did not differ substantially in their MHC diversities ( = 0.047, P = 0.377), but differed in neutral microsatellite diversities ( = 0.148, P = 0.008). MHC allele frequency distributions in the Finnish population were more even than expected under neutrality, implying balancing selection. In addition, an excess of nonsynonymous compared to synonymous polymorphisms indicated historical balancing selection. We also studied association between helminth (Trichinella spp. and Echinococcus canadensis) prevalence and MHC diversity at allele and SNP level. MHC‐heterozygous wolves were less often infected by Trichinella spp. and carriers of specific MHC alleles, SNP haplotypes and SNP alleles had less helminth infections. The associated SNP haplotypes and alleles were shared by different MHC alleles, which emphasizes the necessity of single‐nucleotide‐level association studies also in MHC. Here, we show that strong balancing selection has had similar effect on MHC diversities in the Finnish and Russian Karelian wolf populations despite significant genetic differentiation at neutral markers and small population size in the Finnish population.     

Sequence polymorphism in the bovine major histocompatibility complex DQB loci

Polymorphism in DQB sequences of the bovine major histocompatibility complex was investigated in 22 British Friesian cattle. The first domain exon was amplified, cloned and sequenced. Eight different sequences were identified, six of which had not been identified previously. The high proportion of novel sequences suggests that additional polymorphisms within the DQB loci remain to be discovered in this breed. One sequence was present in at least 21 of the 22 cattle. This sequence, or a closely related sequence, has also been found in American Holstein Friesian, Swedish Red and White and Japanese Black cattle. The remarkably high sequence conservation suggests that the bovine DQB region may contain a locus with a low level of polymorphism and be more similar to the human DQB region than previously supposed. One sequence with three widely spaced frameshift insertions appeared to be a pseudogene.     

Overdispersed molecular clock at the major histocompatibility complex loci.

The extent of amino acid differences of major histocompatibility complex molecules within species is unusually high, consistent with the finding that some pairs of alleles have persisted for more than ten million years and the view that the polymorphism has been maintained by natural selection. The disparity between synonymous and non-synonymous substitutions in the antigen recognition site, however, suggests that some non-synonymous sites have undergone a number of substitutions whereas others have little or none. To describe statistically such an overdispersed underlying process, commonly used Poisson processes are inadequate. An alternative process leads to the surprising conclusion that each non-synonymous site has accumulated as many as 2.6 substitutions, on the average, in the two lineages leading to humans and mice. The standard deviation is also very large (6.6) and the dispersion index (the ratio of the variance to the mean) is at least 17. The substitution process thus inferred qualitatively agrees with the disposition (a boomerang pattern) of substitutions between HLA-A2 and Aw68 alleles, and quantitatively agrees well with that expected where the evolution of major histocompatibility complex molecules has long been driven mostly by balancing selection.     

Polymorphism at the ovine major histocompatibility complex class II loci

Southern hybridization analysis of the ovine major histocompatibility complex (MHC) ( MhcOvar ) class II region, using sheep-specific probes for the DQA1, DQA2, DQB and DRA loci, has revealed extensive polymorphism. DQA1 and DQAP had eight and 16 alleles respectively, DQB had six and DRA had three alleles. Little information was derived from the DRB locus owing to extensive cross-hybridization between the DRB probe and the DQB locus. Differences in allele frequency between breeds were revealed. At the DQA1 locus a null allele (DQA1-N) was observed with a frequency of between 27% and 45%, making this the most common DQA1 allele in all breeds examined. The frequency of DQA1-N homozygotes was between 11% and 18%, raising questions as to the functional significance of the DQA1 gene. Linkage analysis between the DQA1, DQA2, DQB and DRA loci did not reveal any recombination.     

Linkage disequilibrium between two genetic loci of the major histocompatibility complex in rats

The major histocompatibility complex (MHC) in natural populations of rats is composed of genetic phenotypes that are similar, if not identical, to those seen in inbred laboratory strains. Examination of individual wild rats from a single location in the city of Pittsburgh, Pennsylvania, resulted in the identification of seven different RT1.A histocompatibility serotypes and three RT1.B mixed lymphocytes responses. In this population of animals there is a significant association (p < 0.005) between four RT1.A and RT1.B phenotypic pairs: RT1.A⁸B¹, RTl.A^kBⁿ, RTl.A^dB^a and RT1.A¹B^a. The observed values for linkage disequilibrium (0.211,0.076,0.070 and 0.085, respectively) are very high and are close to the maximum expected, given the individual allelic frequencies. Although the animals included in this study were obtained from one location, agreement with Hardy-Weinberg equilibrium is demonstrated for other loci in the same population. The demonstration of equilibrium suggests that significant inbreeding is not affecting this population of rats. Not enough is known about the allelic frequencies in surrounding rat populations to determine how important the effect of migration is on these disequilibrium values. The large linkage disequilibria may indicate that, in the rat, environmental selective forces are operating to ensure the nonrandom association of separate components of the MHC.     

Avian blood parasite richness decreases with major histocompatibility complex class I loci number

Major histocompatibility complex (MHC) genes are among the most polymorphic in the vertebrate genome. The high allele diversity is believed to be maintained primarily by sexual and pathogen-mediated balancing selection. The number of MHC loci also varies greatly across vertebrates, most notably across birds. MHC proteins play key roles in presenting antigens on the cell surface for recognition by T cells, with class I proteins specifically targeting intracellular pathogens. Here, we explore the hypothesis that MHC class I diversity (measured as loci number) coevolves with haemosporidian parasite burden of the host. Using data on 54 bird species, we demonstrate that high-MHC class I diversity is associated with significantly lower richness of Plasmodium, Haemoproteus as well as overall haemosporidian parasite lineages, the former thus indicating more efficient protection against intracellular pathogens. Nonetheless, the latter associations were only detected when MHC diversity was assessed using cloning and not 454 pyrosequencing-based studies, nor across all genotyping methods combined. Our results indicate that high-MHC class I diversity might play a key role in providing qualitative resistance against diverse haemosporidian parasites in birds, but further clarification is needed for the origin of contrasting results when using different genotyping methods for MHC loci quantification.     

Multiple parasites are driving major histocompatibility complex polymorphism in the wild

Parasite mediated selection may result in arms races between host defence and parasite virulence. In particular, simultaneous infections from multiple parasite species should cause diversification (i.e. balancing selection) in resistance genes both at the population and the individual level. Here, we tested these ideas in highly polymorphic major histocompatibility complex (MHC) genes from three-spined sticklebacks (Gasterosteus aculeatus L.). In eight natural populations, parasite diversity (15 different species), and MHC class IIB diversity varied strongly between habitat types (lakes vs. rivers vs. estuaries) with lowest values in rivers. Partial correlation analysis revealed an influence of parasite diversity on MHC class IIB variation whereas general genetic diversity assessed at seven microsatellite loci was not significantly correlated with parasite diversity. Within individual fish, intermediate, rather than maximal allele numbers were associated with minimal parasite load, supporting theoretical models of self-reactive T-cell elimination. The optimal individual diversity matched those values female fish try to achieve in their offspring by mate choice. We thus present correlative evidence supporting the 'allele counting' strategy for optimizing the immunocompetence in stickleback offspring.     

Pulsed field gel electrophoretic analysis of the rat major histocompatibility complex class III region shows extensive inter-species conservation

Using pulsed field gel electrophoresis (PFGE), we have examined the rat major histocompatibility complex (MHC) for the presence of a number of new class III region genes recently identified in the human MHC. We find homologous genes to the human G1, G2, G4, G7a, G9, G9a, G10, G13, G15, and G18 genes, but not the G8 gene in the rat genome, and show that these are linked to the rat TNF- and C4/Slp loci. A long-range restriction map has been constructed on the basis of a PFGE analysis which demonstrates extensive co-linearity in the positions of the homologous sequences in the region between the C4/Slp and TNF loci in the rat MHC when compared with that of the human MHC class III region.Deceased.     

Limited polymorphism at major histocompatibility complex (MHC) loci in the Swedish moose A. alces

The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Both methods revealed limited amounts of polymorphism. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. DNA fingerprinting was used to determine if the unusual pattern of low MHC variability could be explained by a low degree of genome-wide genetic diversity. Hybridizations with two minisatellite probes gave similarity indices somewhat higher than the average for other natural population, but the data suggest that the low MHC variability cannot be explained by a recent population bottleneck. However, since minisatellite sequences evolve more rapidly than MHC sequences, the low levels of MHC diversity may be attributed to a bottleneck of more ancient origin. The selection pressure for MHC variability in moose may also be reduced and we discuss the possibility that its solitary life style may reduce lateral transmission of pathogens in the population.     

Hsp70 genes are linked to the Xenopus major histocompatibility complex

Some of the inducible forms of the heat shock protein 70 (Hsp70) gene family are encoded in the class III region of the major histocompatibility complex (MHC) of mammals. This study was undertaken to determine whether Hsp 70 genes are linked to the MHC of Xenopus, an amphibian last sharing a common ancestor with mammals 300–350 million years ago. Segregation analyses involving seven haplotypes demonstrated the linkage of two or three inducible Hsp70 genes to the frog MHC. Another Hsp70 gene is not closely linked to the MHC. We conclude that the physical association of MHC class I and class II genes with Hsp70 genes is ancient. Correspondence to: M. F. Flajnik.     

Signals of major histocompatibility complex overdominance in a wild salmonid population

The major histocompatibility complex (MHC) contains the most variable genes in vertebrates, but despite extensive research, the mechanisms maintaining this polymorphism are still unresolved. One hypothesis is that MHC polymorphism is a result of balancing selection operating by overdominance, but convincing evidence for overdominant selection in natural populations has been lacking. We present strong evidence consistent with MHC-specific overdominance in a free-living population of Arctic charr (Salvelinus alpinus) in northernmost Europe. In this population, where just two MHC alleles were observed, MHC heterozygous fish had a lower parasite load, were in better condition (as estimated by a fatness indicator) and had higher survival under stress than either of the homozygotes. Conversely, there was no consistent association between these fitness measures and assumedly neutral microsatellite variability, indicating an MHC-specific effect. Our results provide convincing empirical evidence consistent with the notion that overdominance can be an important evolutionary mechanism contributing to MHC polymorphism in wild animal populations. They also support a recent simulation study indicating that the number of alleles expected to be maintained at an MHC loci can be low, even under strong heterozygote advantage.     

Olfactory cues associated with the major histocompatibility complex

Besides its immunological function of self/non‐self discrimination the major histocompatibility complex (MHC) has been recognized as a possible source of individual specific body odors. Dating back to speculations on the role of the extraordinary polymorphism of the MHC as background of an individual chemosensory identity and to early observations of MHC‐dependent mate choice in inbred strains of mice, systematic experimental studies revealed a first evidence for H‐2 related body odors in this species. Meanwhile a large number of animal studies with rodents and a series of field studies and experiments with humans have extended our knowledge of MHC‐related odor signals and substantiated the hypothesis of immunogenetic associated odortypes. These results suggest that the most prominent feature of the MHC, its extraordinary genetic diversity, seems in part to be selectively maintained by behavioral mechanisms which operate in contemporary natural populations. The high degree of heterozygosity found in natural populations of most species seems to be promoted by non‐disease‐based selection such as mating preferences and selective block of pregnancy. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.     

Characterization of six new loci within the swine major histocompatibility complex class III region

A search for new potential coding sequences was conducted within two overlapping cosmid genomic DNA clusters of about 170 and 45 kb from the swine major histocompatibility complex class III region. The sequences were detected with various probes, including pools of swine cDNA, homologous and heterologous genomic sequences, and synthetic oligonucleotides. The 170 kb cluster was centered on the tumor necrosis factor genes (TNF), and the 45 kb cluster contained the heat-shock protein 70 genes (HSP70). The TNF cluster revealed the presence of five new genes: lymphotoxin , BAT1, BAT2, BAT3, and a sequence related to DNA-binding factors. No sequence homologous to B144 was found in the TNF cluster, although other unidentified coding sequences may be present in this cluster. The HSP70 cluster contained a gene identified as BAT6, that is, tRNA-valyl synthetase. These results provide new evidence that the genomic maps of these various genes in the TNF and HSP70 sub-regions are similar in swine and human.     

A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum)

The major histocompatibility complex (MHC) contains genes integral to immune response in vertebrates. MHC genes have been shown to be under selection in a number of vertebrate taxa, making them intriguing for population genetic studies. We have conducted a survey of genetic variation in an MHC class II gene for steelhead trout from 24 sites in coastal California and compared this variation to that observed at 16 presumably neutral microsatellite loci. A high amount of allelic variation was observed at the MHC when compared to previously published studies on other Pacific salmonids. Elevated nonsynonymous substitutions, relative to synonymous substitutions, were detected at the MHC gene, indicating the signature of historical balancing selection. The MHC data were tested for correlations to and deviations from the patterns found with the microsatellite data. Estimates of allelic richness for the MHC gene and for the microsatellites were positively correlated, as were estimates of population differentiation (F(ST)). An analysis for F(ST) outliers indicates that the MHC locus has an elevated F(ST) relative to the neutral expectation, although a significant result was found for only one particular geographical subgroup. Relatively uniform allele frequency distributions were detected in four populations, although this finding may be partially due to recent population bottlenecks. These results indicate that, at the scale studied here, drift and migration play a major role in the observed geographical variability of MHC genes in steelhead, and that contemporary selection is relatively weak and difficult to detect.     

The major histocompatibility complex in the chicken

The chicken B complex is the first non-mammalian MHC characterized at the molecular level. It differs from the human HLA and murine H-2 complexes in the small size of the class I (B-F) and class II (B-L) genes and their close proximity. This proximity accounts for the absence of recombination between B-F and B-L genes and leaves no space for class III genes. Moreover the B-F and B-L genes are tightly linked to unrelated genes absent from mammalian MHCs, such as the polymorphic B-G genes and a member of the G protein beta subunit family. This linkage could form the basis for resistance to viral-induced tumors associated with some B complex haplotypes.     

A three-locus model for the chicken major histocompatibility complex

The major histocompatibility complexes (B complexes) of chickens of various origins have been studied by serological and biochemical methods. TwoB complexes are of particular interest:B ^R1, a recombinant haplotype derived from theB complexes of the inbred CB and CC strains, andB ^G-B1 , theB haplotype of the G-B1 strain. TheB ^R1 haplotype differs detectably from theB ^CB haplotype only at a locus controlling the synthesis of an antigen, B-G, which (in peripheral blood) is present only on red cells. Anti-B-G sera precipitate, from¹²⁵I-labeled red cell lysates, two chains of apparent molecular weights 42,000 and 31,000 (measured under reducing conditions); the smaller is perhaps derived by proteolysis from the larger. TheB ^G-B1 haplotype differs detectably from theB ^CC haplotype only at a locus controlling the synthesis of an antigen whose tissue distribution and biochemical and biological properties are identical to those of B-G. The chicken major histocompatibility complex therefore contains at least three loci—those controlling synthesis of the B-G, and of the previously defined B and B-L antigens.The following abbreviations are used in this paper MHC major histocompatibility complex - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis - MLR mixed leukocyte reaction - GVH graft-versus-host reaction     

Origin and evolution of the major histocompatibility complex class I region in eutherian mammals

Major histocompatibility complex (MHC) genes in vertebrates are vital in defending against pathogenic infections. To gain new insights into the evolution of MHC Class I (MHCI) genes and test competing hypotheses on the origin of the MHCI region in eutherian mammals, we studied available genome assemblies of nine species in Afrotheria, Xenarthra, and Laurasiatheria, and successfully characterized the MHCI region in six species. The following numbers of putatively functional genes were detected: in the elephant, four, one, and eight in the extended class I region, and κ and β duplication blocks, respectively; in the tenrec, one in the κ duplication block; and in the four bat species, one or two in the β duplication block. Our results indicate that MHCI genes in the κ and β duplication blocks may have originated in the common ancestor of eutherian mammals. In the elephant, tenrec, and all four bats, some MHCI genes occurred outside the MHCI region, suggesting that eutherians may have a more complex MHCI genomic organization than previously thought. Bat‐specific three‐ or five‐amino‐acid insertions were detected in the MHCI α1 domain in all four bats studied, suggesting that pathogen defense in bats relies on MHCIs having a wider peptide‐binding groove, as previously assayed by a bat MHCI gene with a three‐amino‐acid insertion showing a larger peptide repertoire than in other mammals. Our study adds to knowledge on the diversity of eutherian MHCI genes, which may have been shaped in a taxon‐specific manner.     

Orientation of the loci encoding RTI.B polypeptides in the major histocompatibility complex of the rat

The major histocompatibility complex of the rat (RTI) contains genes that code for two class II histocompatibility antigens. The r12 rat strain (WRC) was derived from a mating which revealed a genetic recombination that defines the two loci, RTI.B and RT1.D, that code for the class II antigens. The RT1.B and RT1.D antigens of the RT1 complex are protein dimers consisting of an alpha and beta glycoprotein chain and are homologous to I-A and I-E genes, respectively, in the H-2 complex of the mouse. We have performed Southern blot analysis on liver DNA from the r12 and parental strains to examine the precise location of the recombinant event. After digestion with restriction enzymes, the DNA was separated on agarose gels, blotted onto nitrocellulose, and hybridized with mouse H-2 cDNA probes specific for I-A alpha and beta genes. The pattern of restriction fragment polymorphisms demonstrated that the site of recombination is between the RT1.B alpha and the RTI.B beta genes. As a result of these findings, we suggest that the sequence of genes within the RTI complex consists of RT1.A ... RT1.B ... RT1.B ... RT1.D(, ) ... Other class I genes, possibly corresponding to mouse Qa and Tla-like genes, were also apparent in these experiments.     

SNPs in ecological and conservation studies: a test in the Scandinavian wolf population

Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.