Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

This is the first study to quantify genomic sequence variation of the major histocompatibility complex (MHC) in wild and ornamental guppies, Poecilia reticulata. We sequenced 196-219 bp of exon 2 MHC class IIB (DAB) in 56 wild Trinidadian guppies and 14 ornamental strain guppies. Each of two natural populations possessed high allelic richness (15-16 alleles), whereas only three or fewer DAB alleles were amplified from ornamental guppies. The disparity in allelic richness between wild and ornamental fish cannot be fully explained by fixation of alleles by inbreeding, nor by the presence of non-amplified sequences (ie null alleles). Rather, we suggest that the same allele is fixed at duplicated MHC DAB loci owing to gene conversion. Alternatively, the number of loci in the ornamental strains has contracted during >100 generations in captivity, a hypothesis consistent with the accordion model of MHC evolution. We furthermore analysed the substitution patterns by making pairwise comparisons of sequence variation at the putative peptide binding region (PBR). The rate of non-synonymous substitutions (dN) only marginally exceeded synonymous substitutions (dS) in PBR codons. Highly diverged sequences showed no evidence for diversifying selection, possibly because synonymous substitutions have accumulated since their divergence. Also, the substitution pattern of similar alleles did not show evidence for diversifying selection, plausibly because advantageous non-synonymous substitutions have not yet accumulated. Intermediately diverged sequences showed the highest relative rate of non-synonymous substitutions, with dN/dS>14 in some pairwise comparisons. Consequently, a curvilinear relationship was observed between the dN/dS ratio and the level of sequence divergence.     

Gene duplication and evidence for balancing selection acting on MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis)

Allelic polymorphism and evolution mechanism of major histocompatibility complex (MHC) genes has been investigated in many mammals, however, much less is known in teleost. In order to investigate the mechanisms creating and maintaining variability at the MHC class II DAA locus, we examined the polymorphism, gene duplication and balancing selection of MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis). We described 33 alleles in the C. semilaevis, recombination and gene duplication seems to play more important roles in the origin of new alleles. The rate of non-synonymous substitutions (d(N)) occurred at a significantly higher frequency than that of synonymous substitutions (d(S)) in peptide-binding region (PBR) and non-PBR, suggesting balancing selection for maintaining polymorphisms at the MHC II DAA locus. Many positive selection sites were found to act very intensively on antigen-binding sites. Our founding suggests a snapshot in an evolutionary process of MHC-DAA gene evolution of the C. semilaevis.     

MHC class II variation in the endangered European mink <Emphasis Type="Italic">Mustela lutreola</Emphasis> (L. 1761)—consequences for species conservation

The polymorphic major histocompatibility complex (MHC) has gained a specific relevance in pathogen resistance and mate choice. Particularly the antigen-binding site (ABS), encoded by exon 2 of the DRB class II gene, exhibits numerous alleles and extensive sequence variations between alleles. A lack of MHC variability has attributed to instances such as bottleneck effects or relaxed selection pressure and has a certain impact on the long-term viability of the species concerned. As a result of seriously decreased population density during the last century, the current population of the endangered European mink (Mustela lutreola, L. 1761) has suffered from geographic isolation. In this study, we amplified a partial sequence of the MHC class II DRB exon 2 (229 bp), assessed the degree of genetic variation and compared the variability with those of other Mustelidae. As a result, nine alleles were detected in 20 investigated individuals, which differ from each other by four to 25 nucleotide substitutions (two to 11 amino acid substitutions). Whilst an equal ratio for synonymous and non-synonymous substitutions was found inside the ABS, synonymous substitutions were significantly higher than non-synonymous substitutions in the non-ABS region. Results might indicate that no positive selection exists within the ex situ population of M. lutreola, at least in the analysed fragment. In addition, phylogenetic analyses support the trans-species model of evolution. Becker and Nieberg have contributed equally to this work.     

Sequence diversity of the MHC Ⅱ DRB gene in Chinese tree shrews (Tupaia belangeri chinensis)

The major histocompatibility complex (MHC) is a cluster of genes involved in vertebrate immune response regulation. MHC class I and II cell surface proteins are crucial for discrimination of self versus non-self by the adaptive immune system. Due to their special phylogenetic position within the Euarchontoglires and as a relative of primates, tree shrews have been proposed as an alternative experimental animal model for biomedical studies. However, information about the genetic structure of the tree shrew populations is largely unknown. In this study, we characterized diversity in exon 2 of the MHC II DRB gene isolated from Chinese tree shrews (Tupaia belangeri chinensis). We identified 12 different DRB exon 2 alleles from 15 Chinese tree shrews, 1 to 4 alleles were observed per individual with high levels of sequence divergence between alleles. There were more non-synonymous than synonymous substitutions in the functionally important antigen-binding site (dN/dS = 2.7952, P < 0.01), indicating that the DRB exon 2 in Chinese tree shrews has been influenced by positive selection.     

Evolution of Mhc class II B genes in Darwin's finches and their closest relatives: birth of a new gene

The 15 extant species of Darwin's finches on the Galápagos and Cocos Islands are the products of an unfinished adaptive radiation from a founder flock of birds related to the South American species Tiaris obscura. Molecular characterization of their major histocompatibility complex ( Mhc) class II B genes has revealed the existence of several related groups of sequences (presumably encoded in distinct loci) from which one (group 5) stands out because of its low divergence over extended time periods. Analysis of group 5 exon 2 and intron 2 sequences has revealed that the encoding locus apparently arose 2-3 million years ago in the Tiaris group of South and Central American Thraupini. The locus shows no evidence of inactivation, but displays a very low degree of polymorphism, both in terms of number of alleles and genetic distances between alleles. Some of the polymorphism, however, appears to be trans-specific. All the observed intergenic differences can be explained by point mutations and most of the exon 2 changes represent non-synonymous substitutions, although the rate of non-synonymous and synonymous substitutions appears to be the same. The origin of the new locus is explained by the birth-and-death model of Mhc evolution with two important extensions. First, the ancestor of the group 5 genes may have arisen without new gene duplication and second, the birth of the new group may have been brought about by a switch from balancing to directional selection. The ancestor of the group 5 genes may have been a classical class II B allele (one of many) which directional selection fixed in the ancestral population and drove into the category of nonclassical genes.     

藏鸡主要组织相容性复合体B-LBⅡ基因第二外显子序列遗传变异分析

根据鸡主要组织相容性复合体B-LBⅡ基因序列设计特异性引物,在藏鸡基因组中扩增了一个包括其第二外显子和第二内含子在内长度为374 bp的片段,并通过克隆和PCR直接测序获得了该片段的核苷酸序列。发现了15个B-LBⅡ新等位基因。对18个B-LBⅡ等位基因核苷酸序列和其所编码的MHCB-LBⅡ分子β1结构域的氨基酸序列分析显示,第二外显子核苷酸序列遗传多态性异常丰富,存在着62个多态变异位点(共包括80个突变),其中41个为简约性多态位点;衡量该序列遗传多样性的π值为0.0718;反映其群体内遗传变异度的平均遗传距离为0.056±0.008,低于在5个外来品种所估算的平均遗传距离。该编码区核苷酸相对异义替换率(15.61±2.69%)显著高于其同义替换率(3.25±0.94%),进一步分析表明,基因重组和平衡选择机制可能是引起B-LBⅡ基因序列变异的主要因素。在β1结构域氨基酸序列中,存在11个同义替换和27个异义替换;在24个肽结合位点中有12个变异位点;与其他6个中国地方鸡品种和一个外来品种比较发现,有11个异义氨基酸替换仅出现在藏鸡群体中,并被认为与藏鸡的免疫特异性有关,可为鸡的抗病力研究提供分子依据。     

Allelic variation, balancing selection and positive selected sites detected from MHC class Iα gene of olive flounder

Major histocompatibility complex (MHC) genes play an important role in the immune response of vertebrates. Allelic polymorphism and pattern of evolution in MHC genes has been investigated in many mammals, however, much less is known in teleost. In the present study, we have investigated complete MHC Iα gene consists of 7 exons and 6 introns in Olive flounder (Paralichthys olivaceus). Genetic variation in the MHC class Iα gene was also tested in flounder. In 32 individuals, a total of 62 alleles were detected from exon 2 of MHC class Iα gene. The rate of non-synonymous substitutions (d ( N )) occurred at a significantly higher frequency than that of synonymous substitutions (d ( S )) in PBR and non-PBR, suggesting that balancing selection for maintaining polymorphisms at the MHC Iα locus. Many positive selection sites were found to act very intensively on antigen binding sites. Our founding suggests a snapshot in an evolutionary process of MHC Iα gene evolution of the P. olivaceus.     

Major histocompatibility complex variation and evolution at a single, expressed DQA locus in two genera of elephants

Genes of the vertebrate major histocompatibility complex (MHC) are crucial to defense against infectious disease, provide an important measure of functional genetic diversity, and have been implicated in mate choice and kin recognition. As a result, MHC loci have been characterized for a number of vertebrate species, especially mammals; however, elephants are a notable exception. Our study is the first to characterize patterns of genetic diversity and natural selection in the elephant MHC. We did so using DNA sequences from a single, expressed DQA locus in elephants. We characterized six alleles in 30 African elephants (Loxodonta africana) and four alleles in three Asian elephants (Elephas maximus). In addition, for two of the African alleles and three of the Asian alleles, we characterized complete coding sequences (exons 1–5) and nearly complete non-coding sequences (introns 2–4) for the class II DQA loci. Compared to DQA in other wild mammals, we found moderate polymorphism and allelic diversity and similar patterns of selection; patterns of non-synonymous and synonymous substitutions were consistent with balancing selection acting on the peptides involved in antigen binding in the second exon. In addition, balancing selection has led to strong trans-species allelism that has maintained multiple allelic lineages across both genera of extant elephants for at least 6 million years. We discuss our results in the context of MHC diversity in other mammals and patterns of evolution in elephants.     

Major histocompatibility complex alleles associated with parasite susceptibility in wild giant pandas

Major histocompatibility complex (MHC) polymorphism is thought to be driven by antagonistic coevolution between pathogens and hosts, mediated through either overdominance or frequency-dependent selection. However, investigations under natural conditions are still rare for endangered mammals which often exhibit depleted variation, and the mechanism of selection underlying the maintenance of characteristics remains a considerable debate. In this study, 87 wild giant pandas were used to investigate MHC variation associated with parasite load. With the knowledge of the MHC profile provided by the genomic data of the giant panda, seven DRB1, seven DQA1 and eight DQA2 alleles were identified at each single locus. Positive selection evidenced by a significantly higher number of non-synonymous substitutions per non-synonymous codon site relative to synonymous substitutions per synonymous codon site could only be detected at the DRB1 locus, which leads to the speculation that DRB1 may have a more important role in dealing with parasite infection for pandas. Coprological analyses revealed that 55.17% of individuals exhibited infection with 1–2 helminthes and 95.3% of infected pandas carried Baylisascaris shroederi. Using a generalized linear model, we found that Aime-DRB1*10 was significantly associated with parasite infection, but no resistant alleles could be detected. MHC heterozygosity of the pandas was found to be uncorrelated with the infection status or the infection intensity. These results suggested that the possible selection mechanisms in extant wild pandas may be frequency dependent rather than being determined by overdominance selection. Our findings could guide the candidate selection for the ongoing reintroduction or translocation of pandas.     

Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress

Population-level studies using the major histocompatibility complex (Mhc) have linked specific alleles with specific diseases, but data requirements are high and the power to detect disease association is low. A novel use of Mhc population surveys involves mapping allelic substitutions onto the inferred structural molecular model to show functional differentiation related to local selective pressures. In the estuarine fish Fundulus heteroclitus, populations experiencing strong differences in antigenic challenges show significant differences in amino acid substitution patterns that are reflected as variation in the structural location of changes between populations. Fish from a population genetically adapted to severe chemical pollution also show novel patterns of DNA substitution at a highly variable Mhc class II B locus including strong signals of positive selection at inferred antigen-binding sites and population-specific signatures of amino acid substitution. Heavily parasitized fish from an extreme PCB-contaminated (U.S. Environmental Protection Agency Superfund) site show enhanced population-specific substitutions in the a-helix portion of the inferred antigen-binding region. In contrast, fish from an unpolluted site show a significantly different pattern focused on the first strand of the B-pleated sheet. Whether Mhc population profile differences represent the direct effects of chemical toxicants or indirect parasite-mediated selection, the result is a composite habitat-specific signature of strong selection and evolution affecting the genetic repertoire of the major histocompatibility complex.     

Patterns of polymorphism in the MHC class II of a non-passerine bird,the great snipe (<Emphasis Type="Italic">Gallinago media</Emphasis>)

The genomic organisation of the major histocompatibility complex (MHC) seems to vary considerably between different bird species. In order to understand this variation it is important to gather information from different species. We have, for the first time, investigated MHC class II polymorphism in a wader species, the great snipe (Gallinago media). Eleven alleles were found in five sequenced individuals; these come from at least three different loci, but RFLP data suggest that a larger number of genes may be present. For MHC genes, amino acid substitutions followed the, for MHC genes, general pattern of high non-synonymous substitution rates in peptide-binding regions, suggesting that the sequenced alleles may be expressed. The number of genes, lengths of introns and exon sequences of the great snipe MHC seem to be intermediate between those of chicken and passerine birds.     

Balancing selection,sexual selection and geographic structure in MHC genes of Great Snipe

Signatures of balancing selection are often found when investigating the extremely polymorphic regions of major histocompatibility complex (MHC) genes, and it is generally accepted that selective forces maintain this polymorphism. However, the exact nature of the selection is controversial. Theoretical studies have mainly focused on overdominance and/or frequency dependent selection while laboratory studies have emphasised the role of mate choice. Empirical field data, on the other hand, have been relatively scarce. Previously we have found that geographic structure in MHC class II genes of the Great Snipe (Gallinago media) is too pronounced to be explained by neutral forces alone. Here we test the hypothesis that sexual selection on MHC alleles may be influencing this geographic structure between mountain and lowland populations. We found evidence of balancing selection acting on MHC genes in the form of a higher rate of amino-acid changing substitutions compared to silent substitutions in the peptide binding regions. Not only natural selection but also sexual selection may influence MHC polymorphism in this bird because certain MHC alleles have been found to be associated with higher male mating success. Contrary to predictions from negative frequency dependent selection, males carrying locally rare alleles did not have a mating advantage. Instead, the mating success of alleles in a mountain population was positively correlated to their relative frequency in the mountains compared to the lowlands, implying that locally adapted MHC alleles may also be favoured by sexual selection.     

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the ‘minimal essential’ MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.     

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.     

Sequence diversity of the MHC DRB gene in the Eurasian beaver (Castor fiber)

Major histocompatibility complex (MHC) genes, coding molecules which play an important role in immune response, are the most polymorphic genes known in vertebrates. However, MHC polymorphism in some species is limited. MHC monomorphism at several MHC class I and II loci was previously reported for two neighbouring northern European populations of the Eurasian beaver (Castor fiber) and reduced selection for polymorphism has been hypothesized. Here, we analysed a partial sequence of the second exon of the MHC II DRB locus from seven relict European and Asian beaver populations. We detected 10 unique alleles among 76 beavers analysed. Only a western Siberian population was polymorphic, with four alleles detected in 10 individuals. Each of the remaining populations was fixed for a different allele. Sequences showed considerable divergence, suggesting the long persistence of allelic lineages. A significant excess of nonsynonymous substitutions was detected at the antigen binding sites, indicating that sequence evolution of beaver DRB was driven by positive selection. Current MHC monomorphism in the majority of populations may be the result of the superimposition of the recent bottleneck on pre-existing genetic structure resulting from population subdivision and differential pathogen pressure.     

Patterns of Historical Balancing Selection on the Salmonid Major Histocompatibility Complex Class II β Gene

Allelic variation in the major histocompatibility class (MHC) IIB gene of salmonids is analyzed for patterns indicative of natural selection acting at the molecular level. Sequence data for the second exon of this MHC gene were generated for 11 species in three salmonid genera: Oncorhynchus, Salmo, and Salvelinus. Phylogenetic analysis of nucleotide sequences revealed: (1) monophyletic grouping of alleles from each genus, (2) transspecies evolution of alleles within Salmo and Salvelinus, and (3) differential patterns of transspecies evolution within the genus Oncorhynchus. Within Oncorhynchus, five of seven species had alleles that were species-specific or nearly so, while the remaining two, O. mykiss and O. clarkii, retained ancestral polymorphisms. The different patterns in Oncorhynchus and the other two genera could be due to historical demographic effects or functional differences in MHC molecules in the three genera, but the two hypotheses could not be distinguished with the current dataset. An analysis of recombination/gene conversion identified numerous recombinant alleles, which is consistent with what has been found in other vertebrate taxa. However, these gene conversion events could not account for the species-specific allelic lineages observed in five of the Oncorhynchus species. Analyses of the relative rates of nonsynonymous and synonymous substitutions revealed the signature of selection on the class IIB gene in all 11 of the salmonid species for both the ABS and the non-ABS codons. Codon-based analyses of selection identified seven codons that have experienced selection in the majority of the species. More than half of these sites were mammalian ABS codons, but several were not, suggesting subtle functional differences in the mammalian and teleost fish MHC molecules.     

Polymorphism and Balancing Selection at Major Histocompatibility Complex Loci

Amino acid replacements in the peptide-binding region (PBR) of the functional major histocompatibility complex (Mhc) genes appear to be driven by balancing selection. Of the various types of balancing selection, we have examined a model equivalent to overdominance that confers heterozygote advantage. As discussed by A. Robertson, overdominance selection tends to maintain alleles that have more or less the same degree of heterozygote advantage. Because of this symmetry, the model makes various testable predictions about the genealogical relationships among different alleles and provides ways of analyzing DNA sequences of Mhc alleles. In this paper, we analyze DNA sequences of 85 alleles at the HLA-A, -B, -C, -DRB1 and -DQB1 loci with respect to the number of alleles and extent of nucleotide differences at the PBR, as well as at the synonymous (presumably neutral) sites. Theory suggests that the number of alleles that differ at the sites targeted by selection (presumably the nonsynonymous sites in the PBR) should be equal to the mean number of nucleotide substitutions among pairs of alleles. We also demonstrate that the nucleotide substitution rate at the targeted sites relative to that of neutral sites may be much larger than 1. The predictions of the presented model are in surprisingly good agreement with the actual data and thus provide means for inferring certain population parameters. For overdominance selection in a finite population at equilibrium, the product of selection intensity (s) against homozygotes and the effective population size (N) is estimated to be 350-3000, being largest at the B locus and smallest at the C locus. We argue that N is of the order of 10(5) and s is several percent at most, if the mutation rate per site per generation is 10(-8).     

High allelic variation of MHC class II alpha antigen and the role of selection in wild and cultured Sparus aurata populations

Genetic polymorphism and differentiation in wild and cultured sea bream samples were studied after amplification, cloning, and partial sequence of the major histocompatibility complex (MHC) class II alpha antigen. Forty-one alleles were detected from 43 unrelated individuals and sequence alignment of the obtained alleles revealed 28 polymorphic sites. High heterozygosity values and allelic richness were unveiled for both wild and cultured populations. The substitution pattern (d_N /d_S = 0.7) is not consistent with the effect of diversifying selection, indicating lower selection pressure on the a2 domain, as well as that too few advantageous non-synonymous mutations have accumulated as substrate for the diversifying selection to act. Comparison with previously published results on microsatellite markers suggests that balancing selection in MHC genes reduces the genetic drift and bottleneck effects that are common in aquaculture and which are known to reduce genetic variation at neutral markers. The present study stresses that both coding and non-coding loci should be analyzed for designing proper management strategies.     

MHC Variability of a Small Lemur in the Littoral Forest Fragments of Southeastern Madagascar

Habitat fragmentation inhibits gene flow between populations often resulting in a loss of genetic diversity with possible negative effects on fitness parameters. In vertebrates, growing evidence suggests that such genetic diversity is particularly important at the level of the major histocompatibility complex (MHC) because its gene products play an important role in immune functions. Diversity in the MHC is assumed to improve population viability. Here, we investigated the impact of forest fragmentation on the genetic variability of one of the functionally important parts of the MHC, DRB exon 2, of the endemic mouse lemur Microcebus murinus by comparing populations inhabiting two littoral forest fragments of different size in southeastern Madagascar. Twelve different alleles of DRB exon 2 were found in 145 individuals of M. murinus with high levels of sequence divergence between alleles. In both subpopulations, levels of genetic diversity were high, and the genetic analyses revealed only limited effects of fragmentation. Significantly more non-synonymous than synonymous substitutions were found in the functionally important antigen recognition and binding sites indicating selection processes maintaining MHC polymorphism. This is the first study on MHC variation in a free-ranging Malagasy lemur population.     

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.