Positive selection on mammalian MHC-DQ genes revisited from a multispecies perspective

Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analysed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.

Investigating the development of diarrhoea through gene expression analysis in sheep genetically resistant to gastrointestinal helminth infection

Gastrointestinal helminths infect livestock causing health problems including severe diarrhoea. To explore the underlying biological mechanisms relating to development and control of diarrhoea, we compared 4 sheep that were susceptible to development of diarrhoea with 4 sheep that were diarrhoea-resistant. Transcriptomes in the tissues where the parasites were located were analyzed using RNASeq. By considering low-diarrhoea sheep as control, we identified 114 genes that were down-regulated and 552 genes that were up-regulated genes in the high-diarrhoea phenotype. Functional analysis of DEGs and PPI sub-network analysis showed that down-regulated genes in the high-diarrhoea phenotype were linked to biological processes and pathways that include suppression of ‘antigen processing and presentation’, ‘immune response’, and a list of biological functional terms related to ‘suppression in immune tolerance’. On the other hand, up-regulated genes in the high-diarrhoea phenotype probably contribute to repair processes associated with tissue damage, including ‘extracellular matrix organization’, ‘collagen fibril organization’, ‘tissue morphogenesis’, ‘circulatory system development’, ‘morphogenesis of an epithelium’, and ‘focal adhesion’. The genes with important roles in the responses to helminth infection could be targeted in breeding programs to prevent diarrhoea.

Comparative Analysis of SLA-1, SLA-2, and DQB1 Genetic Diversity in Locally-Adapted Kenyan Pigs and Their Wild Relatives, Warthogs

Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.

Mating system is correlated with immunogenetic diversity in sympatric species of Peromyscine mice

The number of reproductive partners per individual varies markedly across animal mating systems. This variation may be an important determinant of patterns of immunogenetic diversity, particularly at Major Histocompatibility Complex (MHC) Class I and II loci. To compare immunogenetic variation in taxa with markedly different mating systems, we used RNAseq-generated data to quantify genotypic diversity in three species of Peromyscine rodents: the monogamous California mouse (Peromyscus californicus) and the polygynandrous deer mouse (P. maniculatus) and brush mouse (P. boylii). By sampling populations of these species from multiple localities in California, we were able to conduct replicated analyses of the relationship between mating system and immunogenetic variation. Across the four localities sampled, diversity at MHC Class I and II genes was consistently higher in the two polygynandrous species. We found no evidence that sampling location (i.e., variation in habitat conditions) contributed to observed differences in MHC variation among populations or species. Collectively, our data indicate that immunogenetic variation in Peromyscine mice is associated with reproductive behavior, rather than geographic locality or habitat type. The consistently greater variability detected in the polygynandrous species examined suggests that balancing selection imposed by behaviorally-mediated pathogen exposure is important in maintaining variation at MHC genes in these animals.

Comparative analysis of host resistance to Sarcoptes scabiei var. cuniculi in two different rabbit breeds

BACKGROUND

Scabies, caused by infestation of the mite Sarcoptes scabiei, is one of the most severe ectoparasitic diseases in rabbits. Scabies seriously affects the commercial rabbit breeding, causing severe economic losses. Host resistance to S. scabiei is an important factor in further development of the rabbit industry. In the present study, we compared the host resistance to S. scabiei var. cuniculi of a new breed of domestic rabbit propagated by the Sichuan Animal Sciences Academy (QiXing rabbit, QX) compared with that of a traditional rabbit breed in the domestic rabbit industry (IRA rabbit, IRA).

METHODS

Both QX and IRA rabbits were experimentally infested with live S. scabiei var. cuniculi mites for 48 h. Then, during the course of four-week experimental infestation period, the body weight of rabbits was recorded every two weeks for calculating body-weight variations in comparison to the non-infested control rabbits. Skin lesions in the foot area were assessed on weekly basis and serum samples were tested weekly for the estimation of changes in the total antibody levels (IgG, IgE and IgM). Moreover, DNA extracted from the blood samples was amplified for analysis of the genetic diversity in the major histocompatibility complex, class II, DQ Alpha (MHC-DQA) gene.

RESULTS

Compared to the IRA rabbits, the QX rabbits showed a significantly higher (P < 0.05) relative body weight gain compared to the non-infested control rabbits and significantly lower (P < 0.05) scores for foot skin lesions and higher levels of IgG, IgE and IgM at weeks 1 to 4, week 2 and week 1 post-infestation, respectively. Furthermore, a polymorphism site at position 103 bp of exon two of MHC-DQA gene and a different gene frequency were found between two rabbit breeds, suggesting the genetic basis for the differential host resistance to the S. scabiei var. cuniculi between two rabbit breeds.

CONCLUSIONS

The QX rabbits showed higher host resistance to S. scabiei var. cuniculi compared to the IRA rabbits at the clinical, immunological and genetic levels. These results provide a reference for the breeding of rabbits with adequately improved and sustained host resistance to scabies in the domestic rabbit industry.

Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare

Background

The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.

Results

Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.

Conclusion

Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.

Positive selection in coding regions and motif duplication in regulatory regions of bottlenose dolphin MHC class II genes

The vertebrate immune response is mediated through highly adaptive, quickly evolving cell surface receptors, the major histocompatibility complex (MHC). MHC molecules bind and present a diverse array of pathogenic molecules and trigger a cascade of defenses. Use of MHC variation as a marker for population health has also evolved quickly following advances in sequencing methods. We applied a combination of traditional and next generation sequencing methodology to characterize coding (peptide binding region) and regulatory (proximal promoter) sequence variation in MHC Class II DQA and DQB genes between estuarine and coastal populations of the bottlenose dolphin, Tursiops truncatus, an apex predator whose health status is indicative of anthropogenic impacts on the ecosystem. The coding regions had 10 alleles each at DQA and DQB; the promoters had 6 and 7 alleles at DQA and DQB, respectively with variation within key regulatory motifs. Positive selection was observed for the coding regions of both genes while both coding and promoter regions exhibited geographic differences in allele composition that likely indicates diversifying selection across habitats. Most notable was the discovery of a complete duplication of a 14-bp T-box motif in the DQA promoter. Four class II promoter regions (DQA, DQB, DRA, DRB) were characterized in species from four cetacean families (Delphinidae, Monodontidae, Lipotidae, and Physeteridae) and revealed substantial promoter structural diversity across this order. Peptide binding regions may not be the only source of adaptive potential within cetacean MHC for responding to pathogenic threats. These findings are the first analysis of cetacean MHC regulatory motifs, which may divulge unique immunogenetic strategies among cetaceans and reveal how MHC transcriptional control continues to evolve. The combined MHC regulatory and coding data provide new genetic context for distinct vulnerability profiles between coastal and estuarine populations, which are key concerns for health and risk management.

Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations

The European rabbit (Oryctolagus cuniculus) natural populations within the species native region, the Iberian Peninsula, are considered a reservoir of genetic diversity. Indeed, the Iberia was a Pleistocene refuge to the species and currently two subspecies are found in the peninsula (Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus). The genes of the major histocompatibility complex (MHC) have been substantially studied in wild populations due to their exceptional variability, believed to be pathogen driven. They play an important function as part of the adaptive immune system affecting the individual fitness and population viability. In this study, the MHC variability was assessed by analysing the exon 2 of the DQA gene in several European rabbit populations from Portugal, Spain and France and in domestic breeds. Twenty-eight DQA alleles were detected, among which 18 are described for the first time. The Iberian rabbit populations are well differentiated from the French population and domestic breeds. The Iberian populations retained the higher allelic diversity with the domestic breeds harbouring the lowest; in contrast, the DQA nucleotide diversity was higher in the French population. Signatures of positive selection were detected in four codons which are putative peptide-binding sites and have been previously detected in other mammals. The evolutionary relationships showed instances of trans-species polymorphism. Overall, our results suggest that the DQA in European rabbits is evolving under selection and genetic drift.

Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

BACKGROUND

Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers.

RESULTS

23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed between the two species.

CONCLUSIONS

Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these macaques. Balancing selection plays an important role in sharing allelic lineages between species, but genetic drift may share balancing selection dominance to maintain MHC diversity. Great divergence at neutral or adaptive markers showed that moderate genetic differentiation had occurred in rhesus macaque populations in western Sichuan, China, due to the habitat fragmentation caused by long-term geographic barriers and human activity. The Heishui population should be paid more attention for its lowest level of genetic diversity and relatively great divergence from others.

Positive selection on MHC class II DRB and DQB genes in the bank vole (Myodes glareolus)

The major histocompatibility complex (MHC) class IIB genes show considerable sequence similarity between loci. The MHC class II DQB and DRB genes are known to exhibit a high level of polymorphism, most likely maintained by parasite-mediated selection. Studies of the MHC in wild rodents have focused on DRB, whilst DQB has been given much less attention. Here, we characterised DQB genes in Swedish bank voles Myodes glareolus, using full-length transcripts. We then designed primers that specifically amplify exon 2 from DRB (202 bp) and DQB (205 bp) and investigated molecular signatures of natural selection on DRB and DQB alleles. The presence of two separate gene clusters was confirmed using BLASTN and phylogenetic analysis, where our seven transcripts clustered according to either DQB or DRB homologues. These gene clusters were again confirmed on exon 2 data from 454-amplicon sequencing. Our DRB primers amplify a similar number of alleles per individual as previously published DRB primers, though our reads are longer. Traditional d N/d S analyses of DRB sequences in the bank vole have not found a conclusive signal of positive selection. Using a more advanced substitution model (the Kumar method) we found positive selection in the peptide binding region (PBR) of both DRB and DQB genes. Maximum likelihood models of codon substitutions detected positively selected sites located in the PBR of both DQB and DRB. Interestingly, these analyses detected at least twice as many positively selected sites in DQB than DRB, suggesting that DQB has been under stronger positive selection than DRB over evolutionary time.

Insight into gene evolution within Cervidae and Bovidae through genetic variation in MHC-DQA in the black muntjac (Muntiacus crinifrons)

The critical role that the major histocompatibility complex plays in the immune recognition of parasites and pathogens makes its evolutionary dynamics exceptionally relevant to ecology, population biology, and conservation studies. The black muntjac is a rare deer endemic to a small mountainous region in eastern China. We found that this species has two DQA loci through cDNA expression and sequence variation analysis. The level of variation at both DQA loci was found to be extremely low (three alleles for DQA1 and four alleles for DQA2), possibly because of past bottlenecks and the species' relatively solitary behavior pattern. The ratio of d(N)/d(S) in the putative peptide binding region of the DQA2 locus (13.36, P = 0.012) was significantly larger than one but not that of DQA1 (0.94, P = 0.95), suggesting strong positive selection at the DQA2 but not at the DQA1 locus. This difference might reflect different sets of evolutionary selection pressures acting on the two loci. The phylogenetic tree showed that DQA1 alleles from two species of Cervidae and two of Bovidae grouped together, as did the DQA2 alleles. However, different genes from the four species were located in separate branches. These results lead us to suggest that these DQA alleles are derived from primordial DQA genes from a common ancestor and are maintained in Cervidae and Bovidae since their divergence around 25.5-27.8 million years ago.

Evolutionary genetics of MHC class II beta genes in the brown hare, Lepus europaeus

The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na = 11, D_est = 0.071 and Na = 15, D_est = 0.409, respectively), but not for the DPB gene (Na = 4, D_est = 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ω > 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids.

Natural selection coupled with intragenic recombination shapes diversity patterns in the major histocompatibility complex class II genes of the giant panda

Ample variations of the major histocompatibility complex (MHC) genes are essential for vertebrates to adapt to various environmental conditions. In this study, we investigated the genetic variations and evolutionary patterns of seven functional MHC class II genes (one DRA, two DRB, two DQA, and two DQB) of the giant panda. The results showed the presence of two monomorphic loci (DRA and DQB2) and five polymorphic loci with different numbers of alleles (seven at DRB1, six at DRB3, seven at DQA1, four at DQA2, six at DQB1). The presence of balancing selection in the giant panda was supported by the following pieces of evidence: (1) The observed heterozygosity was higher than expected. (2) Amino acid heterozygosity was significantly higher at antigen-binding sites (ABS) compared with non-ABS sequences. (3) The selection parameter omega (d(N)/d(S)) was significantly higher at ABS compared with non-ABS sequences. (4) Approximately 95.45% of the positively selected codons (P>0.95) were located at or adjacent to an ABS. Furthermore, this study showed that (1) The Qinling subspecies exhibited high omega values across each locus (all >1), supporting its extensive positive selection. (2) The Sichuan subspecies displayed small omega at DRB1 (omega<0.72) and DQA2 (omega<0.48), suggesting that these sites underwent strong purifying selection. (3) Intragenic recombination was detected in DRB1, DQA1, and DQB1. The molecular diversity in classic Aime-MHC class II genes implies that the giant panda had evolved relatively abundant variations in its adaptive immunity along the history of host-pathogen co-evolution. Collectively, these findings indicate that natural selection accompanied by recombination drives the contrasting diversity patterns of the MHC class II genes between the two studied subspecies of giant panda.

Evolutionary history of an MHC gene in two leporid species: characterisation of Mhc-DQA in the European brown hare and comparison with the European rabbit

We surveyed the genetic diversity of the expressed major histocompatibility complex class II DQA locus in natural populations of European brown hares, Lepus europaeus, from Austria and Belgium (267 individuals in total). Based on cDNA sequences, we designed hare-specific primers to amplify the highly variable second exon of the DQA gene. Using cloning-sequencing methodology and capillary electrophoresis single-strand conformation polymorphism, we found ten alleles of the DQA exon 2 locus across these two European regions, of which eight are described for the first time. To search for signals of selection and recombination in the evolution of the DQA gene within the leporids, we augmented our sample with orthologous DQA alleles from the European rabbit, Oryctolagus cuniculus, in order to carry out a species level, species pairwise comparison. We found evidence of recombination in the history of the DQA sequences in leporids with some recombinant alleles bridging the species divide. In both species, selection on peptide binding site codons can be detected, though stronger for the rabbit. This result suggests that there may be a differential selection pressure in the deeper evolutionary history of these two species due to differences in several demographic and ecological traits likely subjecting them to differential selection by parasites. Finally, evolutionary relationships show a widespread and statistically significant intermingling of alleles from the two species. The many macroparasites shared between hares and rabbits may explain this pattern of trans-species polymorphism.