Natural selection at major histocompatibility complex loci of vertebrates

Body size, inbreeding, and lifespan in domestic dogs

Inbreeding poses a real or potential threat to nearly every species of conservation concern. Inbreeding leads to loss of diversity at the individual level, which can cause inbreeding depression, and at the population level, which can hinder ability to respond to a changing environment. In closed populations such as endangered species and ex situ breeding programs, some degree of inbreeding is inevitable. It is therefore vital to understand how different patterns of breeding and inbreeding can affect fitness in real animals. Domestic dogs provide an excellent model, showing dramatic variation in degree of inbreeding and in lifespan, an important aspect of fitness that is known to be impacted by inbreeding in other species. There is a strong negative correlation between body size and lifespan in dogs, but it is unknown whether the higher rate of aging in large dogs is due to body size per se or some other factor associated with large size. We used dense genome-wide SNP array data to calculate average inbreeding for over 100 dog breeds based on autozygous segment length and found that large breeds tend to have higher coefficients of inbreeding than small breeds. We then used data from the Veterinary medical Database and other published sources to estimate life expectancies for pure and mixed breed dogs. When controlling for size, variation in inbreeding was not associated with life expectancy across breeds. When comparing mixed versus purebred dogs, however, mixed breed dogs lived about 1.2 years longer on average than size-matched purebred dogs. Furthermore, individual pedigree coefficients of inbreeding and lifespans for over 9000 golden retrievers showed that inbreeding does negatively impact lifespan at the individual level. Registration data from the American Kennel Club suggest that the molecular inbreeding patterns observed in purebred dogs result from specific breeding practices and/or founder effects and not the current population size. Our results suggest that recent inbreeding, as reflected in variation within a breed, is more likely to affect fitness than historic inbreeding, as reflected in variation among breeds. Our results also indicate that occasional outcrosses, as in mixed breed dogs, can have a substantial positive effect on fitness.

HLA Allele and Haplotype Frequencies in Three Urban Mexican Populations: Genetic Diversity for the Approach of Genomic Medicine

Genetic variability defends us against pathogen-driven antigens; human leucocyte antigens (HLA) is the immunological system in charge of this work. The Mexican mestizo population arises mainly from the mixture of three founder populations; Amerindian, Spaniards, and a smaller proportion of the African population. We describe allele and haplotype frequencies of HLA class I (-A and -B) and class II (-DRB1 and -DQB1), which were analyzed by PCR-SSP in Mexican mestizo from three urban populations of Mexico: Chihuahua-Chihuahua City (n = 88), Mexico City-Tlalpan (n = 330), and Veracruz-Xalapa (n = 84). The variability of the allele HLA class I and class II among the three regions of Mexico are in four alleles: HLA-A*24:02 (36.39%), -B*35:01 (16.04%), -DRB1*04:07 (17.33%), and -DQB1*03:02 (31.47%), these alleles have been previously described in some indigenous populations. We identified 5 haplotypes with a frequency >1%: HLA-A*02:01-B*35:01-DRB1*08:02-DQB1*04:02, A*68:01-B*39:01-DRB1*08:02-DQB1*04:02, A*02:01-B*35:01-DRB1*04:07-DQB1*03:02, A*68:01-B*39:01-DRB1*04:07-DQB1*03:02, and A*01:01-B*08:01-DRB1*03:01-DQB1*02:01. Also, the haplotype A*02:01-B*35:01-DRB1*08:02-DQB1*04:02 was identified in Tlalpan and Xalapa regions. Haplotype A*01:01-B*08:01-DRB1*03:01-DQB1*02:01 was found only in Tlalpan and Chihuahua. In the Xalapa region, the most frequent haplotype was A*24:02-B*35:01-DRB1*04:07-DQB1*03:02. These alleles and haplotypes have been described in Amerindian populations. Our data are consistent with previous studies and contribute to the analysis of the variability in the Mexican population.

The MHC Class Ia Genes in Chenfu's Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Simple Summary

Amphibians, the first terrestrial vertebrates, provide materials for adaptive evolutionary studies, such as the evolution of the major histocompatibility complex (MHC). To date, various MHC evolutionary mechanisms have been identified in frogs, but more research is needed to determine the evolutionary mechanisms of the frog MHC. The main purpose of this study was to evaluate polymorphisms in the MHC class Ia genes of the Chenfu’s Treefrog. The MHC class Ia genes of the Chenfu’s Treefrog have high polymorphism. The mechanisms responsible for the formation of the polymorphisms include gene duplication, recombination, and selection.

Abstract

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

Molecular evolution of MHC class II DRB exon 2 in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae)

Raccoon dogs, Nyctereutes procyonoides, are native to East Asia, but have been introduced into western Russia and eastern Europe. To determine allelic diversity and elucidate the evolution of major histocompatibility complex (MHC) class II genes in the raccoon dog, we analysed a 237-bp region of DRB exon 2 from 36 individuals of native and introduced populations from Japan and Russia. We detected 23 DRB alleles (Nypr-DRBs), 22 of which were novel. Some alleles were found across the species’ range, while others were geographically restricted. For both native and introduced populations, the ratio of non-synonymous to synonymous substitution rates for codons at predicted antigen-binding sites was significantly greater than 2, indicating that Nypr-DRBs have evolved under positive selection. Mixed effect model evolution analysis and an algorithm to detect recombination showed five positively selected codons and one recombination breakpoint, respectively. Overall, our results suggest that the diversity of MHC class II DRB in N. procyonoides was influenced and maintained by recombination, pathogen-driven positive selection, geographical barriers and the founder effect. A Bayesian phylogenetic tree revealed no evidence of trans-species polymorphism (TSP), but instead showed monophyly for the Nypr-DRB alleles within a larger clade of canid sequences. The lack of TSP may have been due to long-term divergence of raccoon dogs from other canids, or to their having encountered different sets of pathogens due to occupying a different ecological niche.

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.

Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy

Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes^1-3. However, the effect of sequence divergence between HLA-I alleles-a quantifiable measure of HLA-I evolution-on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient's genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex-peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.

MHC structuring and divergent allele advantage in a urodele amphibian: a hierarchical multi-scale approach

Proteins encoded by extraordinarily polymorphic major histocompatibility complex (MHC) genes are involved in the adaptive immune response. Balancing selection is believed to maintain MHC polymorphism in the long term, although neutral processes also play a role in shaping MHC diversity. However, the relative contribution of these processes is poorly understood. Here we characterized MHC class II variation of a low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted, geographically structured area. We aimed to (1) evaluate the contribution of selection and neutral processes to shaping MHC diversity at two geographic scales, and (2) test for signatures of divergent allele advantage (DAA), which is a potentially important mechanism of balancing selection. The dominant role of selection in shaping MHC variation was suggested by the lack of correlation between MHC and neutral (microsatellite) variation. Although most variation occurred within populations for both types of markers, they differed in the extent of structuring at the two spatial scales. MHC structuring was more pronounced at local scales, suggesting the role of local selection, while structuring was not detectable at a larger scale, possibly due to the effect of balancing selection. Microsatellites showed the opposite pattern. As expected under DAA, the observed genotypes combined more sequence diversity than expected under a random association of alleles. Thus, DAA may contribute to maintaining MHC polymorphism, which is ancient, as supported by signatures of historical positive selection and trans-species polymorphism. Our results point to the importance of a multi-scale approach in studying MHC variation, especially in low-dispersal taxa, which are genetically structured at fine spatial scales.

Deletion of a Seminal Gene Cluster Reinforces a Crucial Role of SVS2 in Male Fertility

Multiple genes, whose functions or expression are overlapping, compensate for the loss of one gene. A gene cluster in the mouse genome encodes five seminal vesicle proteins (SVS2, SVS3, SVS4, SVS5, and SVS6). These proteins are produced by male rodents and function in formation of the copulatory plug following mating. SVS2 plays an essential role in the successful internal fertilization by protecting the sperm membrane against a uterine immune attack. We hypothesized that the four remaining seminal vesicle proteins (SVPs) of this gene cluster may partially/completely compensate for the deficiency of SVS2. For confirming our hypothesis, we generated mice lacking the entire SVP-encoding gene cluster and compared their fecundity with Svs2-deficient (Svs2^−/−) mice; that is, mice deficient in Svs2 alone. A single loxP site remained after the deletion of the Svs2 gene. Therefore, we inserted another loxP site by combining the CRISPR/Cas9 system with single-stranded oligodeoxynucleotides (ssODN). Male mice lacking the entire SVP-encoding gene cluster (Svs2–6^−/− mice) and thereby all five SVP proteins, generated by the deletion of 100kbp genomic DNA, showed low fecundity. However, the fecundity level was comparable with that from Svs2^−/− male mice. Our results demonstrate that SVS3, SVS4, SVS5, and SVS6 do not function in the protection of sperm against a uterine immune attack in the absence of SVS2. Thus, Svs2 is the critical gene in the SVP gene cluster.

Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC

The major histocompatibility complex (MHC) is a central component of the vertebrate immune system and hence evolves in the regime of a host-pathogen evolutionary race. The MHC is associated with quantitative traits which directly affect fitness and are subject to selection pressure. The evolution of haplotypes at the MHC HLA (HLA) locus is generally thought to be governed by selection for increased diversity that is manifested in overdominance and/or negative frequency-dependent selection (FDS). However, recently, a model combining purifying selection on haplotypes and balancing selection on alleles has been proposed. We compare the predictions of several population dynamics models of haplotype frequency evolution to the distributions derived from 6.59-million-donor HLA typings from the National Marrow Donor Program registry. We show that models that combine a multiplicative fitness function, extremely high haplotype discovery rates, and exponential fitness decay over time produce the best fit to the data for most of the analyzed populations. In contrast, overdominance is not supported, and population substructure does not explain the observed haplotype frequencies. Furthermore, there is no evidence of negative FDS. Thus, multiplicative fitness, rapid haplotype discovery, and rapid fitness decay appear to be the major factors shaping the HLA haplotype frequency distribution in the human population.

Parallel adaptation of rabbit populations to myxoma virus

In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein's antiviral effect.

Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae)

Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.

Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations

Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology.

Whereas specialist major histocompatibility complex (MHC) molecules initiate immune response against only relatively few pathogens, generalists provide protection against a broad range. Accordingly, this study shows that the geographical distribution of generalist MHC alleles in human populations reflects exposure to diverse infectious diseases.

Variation in the human genome influences our susceptibility to infectious diseases, but the causal link between disease and underlying mutation often remains enigmatic. Major histocompatibility complex II (MHC class II) molecules shape both our immune response against pathogens and our tolerance of self-peptides. The genomic region that encodes MHC molecules is of particular interest, as it is home to more genetic disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Here, we propose that MHC class II molecules can be categorized into two major types; specialists initiate effective immune response against only relatively few pathogens, while generalists provide protection against a broad range of pathogens. As support, we demonstrate that generalist MHC class II variants are more prevalent in human populations residing in pathogen-rich areas.

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.

Analysis of peptide-SLA binding by establishing immortalized porcine alveolar macrophage cells with different SLA class II haplotypes

Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells’ short lifespan. We immortalized primary PAMs by transfecting them with both hTERT and SV40LT and established two immortalized cell lines (iPAMs) actively proliferating even after 35 passages. These cells possessed the characteristics of primary PAMs, including strong expression of swine leukocyte antigen (SLA) class II genes and the inability to grow anchorage-independently. We characterized their SLA genes and subsequently performed peptide-SLA binding assays using a peptide from porcine circovirus type 2 open reading frame 2 to experimentally measure the binding affinity of the peptide to SLA class II. The number of peptides bound to cells measured by fluorescence was very low for PK15 cells (7.0% ± 1.5), which are not antigen-presenting cells, unlike iPAM61 (33.7% ± 3.4; SLA-DQA*0201/0303, DQB1*0201/0901, DRB1*0201/1301) and iPAM303 (73.3% ± 5.4; SLA DQA*0106/0201, DQB1*0202/0701, DRB1*0402/0602). The difference in peptide binding between the two iPAMs was likely due to the allelic differences between the SLA class II molecules that were expressed. The development of an immortal PAM cell panel harboring diverse SLA haplotypes and the use of an established method in this study can become a valuable tool for evaluating the interaction between antigenic peptides and SLA molecules and is important for many applications in veterinary medicine including vaccine development.

Bridging immunogenetics and immunoproteomics: Model positional scanning library analysis for Major Histocompatibility Complex class II DQ in Tursiops truncatus

The Major Histocompatibility Complex (MHC) is a critical element in mounting an effective immune response in vertebrates against invading pathogens. Studies of MHC in wildlife populations have typically focused on assessing diversity within the peptide binding regions (PBR) of the MHC class II (MHC II) family, especially the DQ receptor genes. Such metrics of diversity, however, are of limited use to health risk assessment since functional analyses (where changes in the PBR are correlated to recognition/pathologies of known pathogen proteins), are difficult to conduct in wildlife species. Here we describe a means to predict the binding preferences of MHC proteins: We have developed a model positional scanning library analysis (MPSLA) by harnessing the power of mixture based combinatorial libraries to probe the peptide landscapes of distinct MHC II DQ proteins. The algorithm provided by NNAlign was employed to predict the binding affinities of sets of peptides generated for DQ proteins. These binding affinities were then used to retroactively construct a model Positional Scanning Library screen. To test the utility of the approach, a model screen was compared to physical combinatorial screens for human MHC II DP. Model library screens were generated for DQ proteins derived from sequence data from bottlenose dolphins from the Indian River Lagoon (IRL) and the Atlantic coast of Florida, and compared to screens of DQ proteins from Genbank for dolphin and three other cetaceans. To explore the peptide binding landscape for DQ proteins from the IRL, combinations of the amino acids identified as active were compiled into peptide sequence lists that were used to mine databases for representation in known proteins. The frequency of which peptide sequences predicted to bind the MHC protein are found in proteins from pathogens associated with marine mammals was found to be significant (p values <0.0001). Through this analysis, genetic variation in MHC (classes I and II) can now be associated with the binding repertoires of the expressed MHC proteins and subsequently used to identify target pathogens. This approach may be eventually applied to evaluate individual population and species risk for outbreaks of emerging diseases.

Positive selection and climatic effects on MHC class II gene diversity in hares (Lepus capensis) from a steep ecological gradient

In natural populations, allelic diversity of the major histocompatibility complex (MHC) is commonly interpreted as resulting from positive selection in varying spatiotemporal pathogenic landscapes. Composite pathogenic landscape data are, however, rarely available. We studied the spatial distribution of allelic diversity at two MHC class II loci (DQA, DQB) in hares, Lepus capensis, along a steep ecological gradient in North Africa and tested the role of climatic parameters for the spatial distribution of DQA and DQB proteins. Climatic parameters were considered to reflect to some extent pathogenic landscape variation. We investigated historical and contemporary forces that have shaped the variability at both genes, and tested for differential selective pressure across the ecological gradient by comparing allelic variation at MHC and neutral loci. We found positive selection on both MHC loci and significantly decreasing diversity from North to South Tunisia. Our multinomial linear models revealed significant effects of geographical positions that were correlated with mean annual temperature and precipitation on the occurrence of protein variants, but no effects of co-occurring DQA or DQB proteins, respectively. Diversifying selection, recombination, adaptation to local pathogenic landscapes (supposedly reflected by climate parameters) and neutral demographic processes have shaped the observed MHC diversity and differentiation patterns.

Comparative analysis of the blood transcriptomes between wolves and dogs

Dogs were domesticated by human and originated from wolves. Their evolutionary relationships have attracted much scientific interest due to their genetic affinity but different habitats. To identify the differences between dogs and wolves associated with domestication, we analysed the blood transcriptomes of wolves and dogs by RNA-Seq. We obtained a total of 30.87 Gb of raw reads from two dogs and three wolves using RNA-Seq technology. Comparisons of the wolf and dog transcriptomes revealed 524 genes differentially expressed genes between them. We found that some genes related to immune function (DCK, ICAM4, GAPDH and BSG) and aerobic capacity (HBA1, HBA2 and HBB) were more highly expressed in the wolf. Six differentially expressed genes related to the innate immune response (CCL23, TRIM10, DUSP10, RAB27A, CLEC5A and GCH1) were found in the wolf by a Gene Ontology enrichment analysis. Immune system development was also enriched only in the wolf group. The ALAS2, HMBS and FECH genes, shown to be enriched by the Kyoto Encyclopedia of Genes and Genomes analysis, were associated with the higher aerobic capacity and hypoxia endurance of the wolf. The results suggest that the wolf might have greater resistance to pathogens, hypoxia endurance and aerobic capacity than dogs do.

Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America

Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.

Signatures of diversifying selection and convergence acting on passerine Toll-like receptor 4 in an evolutionary context

Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD-2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host-related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.

The ash dieback invasion of Europe was founded by two genetically divergent individuals

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

Selection outweighs drift at a fine scale: Lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops

The highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with that at neutral genetic loci. Differences in MHC and neutral genetic variation are useful for inferring the relative influence of selection, gene flow and drift on MHC variation. To date, such investigations have usually been undertaken at a broad spatial scale. Yet, evolutionary and ecological processes can occur at a fine spatial scale, particularly in small or fragmented populations. We investigated spatial patterns of MHC variation among three geographically close, naturally discrete, sampling sites of Egernia stokesii, an Australian lizard. The MHC of E. stokesii has recently been characterized, and there is evidence for historical selection on the MHC. We found E. stokesii MHC weakly differentiated among sites compared to microsatellites, suggesting selection, acting similarly at each site, has outweighed any effects of low gene flow or of genetic drift on E. stokesii MHC variation. Our findings demonstrate the strength of selection in shaping patterns of MHC variation or consistency at a fine spatial scale.

Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence

Numerous approaches have been developed to infer natural selection based on the comparison of polymorphism within species and divergence between species. These methods are especially powerful for the detection of uniform selection operating across a gene. However, empirical analyses have demonstrated that regions of protein-coding genes exhibiting clusters of amino acid substitutions are subject to different levels of selection relative to other regions of the same gene. To quantify this heterogeneity of selection within coding sequences, we developed Model Averaged Site Selection via Poisson Random Field (MASS-PRF). MASS-PRF identifies an ensemble of intragenic clustering models for polymorphic and divergent sites. This ensemble of models is used within the Poisson Random Field framework to estimate selection intensity on a site-by-site basis. Using simulations, we demonstrate that MASS-PRF has high power to detect clusters of amino acid variants in small genic regions, can reliably estimate the probability of a variant occurring at each nucleotide site in sequence data and is robust to historical demographic trends and recombination. We applied MASS-PRF to human gene polymorphism derived from the 1,000 Genomes Project and divergence data from the common chimpanzee. On the basis of this analysis, we discovered striking regional variation in selection intensity, indicative of positive or negative selection, in well-defined domains of genes that have previously been associated with neurological processing, immunity, and reproduction. We suggest that amino acid-altering substitutions within these regions likely are or have been selectively advantageous in the human lineage, playing important roles in protein function.

High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations

Background

Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes.

Results

We identified a total of 19 DRB sequences, in which five alleles were novel. We found high DRB variation in R. roxellana and three branches of evidence suggesting that balancing selection has contributed to maintaining MHC polymorphism over the long term in this species: i) different patterns of both genetic diversity and population differentiation were detected at MHC and neutral markers; ii) an excess of non-synonymous substitutions compared to synonymous substitutions at antigen binding sites, and maximum-likelihood-based random-site models, showed significant positive selection; and iii) phylogenetic analyses revealed a pattern of trans-species evolution for DRB genes.

Conclusions

High levels of DRB diversity in these R. roxellana populations may reflect strong selection pressure in this species. Patterns of genetic diversity and population differentiation, positive selection, as well as trans-species evolution, suggest that pathogen-mediated balancing selection has contributed to maintaining MHC polymorphism in R. roxellana over the long term. This study furthers our understanding of the role pathogen-mediated balancing selection has in maintaining variation in MHC genes in small and fragmented populations of free-ranging vertebrates.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1148-7) contains supplementary material, which is available to authorized users.

Generation and characterization of the blood transcriptome of Macaca thibetana and comparative analysis with M. mulatta

Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison. Using RNA-seq technology, 138 million sequencing reads of the M. thibetana transcriptome were generated. The assembly included 327 871 transcripts with an N50 of 1571 bp. According to the sequence similarity search, 80 317 (24.5%) transcripts were annotated in the nr protein database. All transcripts from M. thibetana and M. mulatta were functionally classified and compared using GO and KEGG analyses. The two transcriptomes were different in the GO term of nutrient reservoir activity, and in the KEGG subcategories of signaling molecules and interaction, infectious diseases, cell growth and death, and immune system. The transcriptomes in this study would provide a valuable resource for future functional and comparative genomic studies, and even for biological studies of this non-human primate.

Genetic variation and selection of MHC class I loci differ in two congeneric frogs

Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.

Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing

The major histocompatibility complex (MHC) is a key genomic model region for understanding the evolution of gene families and the co-evolution between host and pathogen. To date, MHC studies have mostly focused on species from major vertebrate lineages. The evolution of MHC classical (Ia) and non-classical (Ib) genes in pigs has attracted interest because of their antigen presentation roles as part of the adaptive immune system. The pig family Suidae comprises over 18 extant species (mostly wild), but only the domestic pig has been extensively sequenced and annotated. To address this, we used a DNA-capture approach, with probes designed from the domestic pig genome, to generate MHC data for 11 wild species of pigs and their closest living family, Tayassuidae. The approach showed good efficiency for wild pigs (~80% reads mapped, ~87× coverage), compared to tayassuids (~12% reads mapped, ~4× coverage). We retrieved 145 MHC loci across both families. Phylogenetic analyses show that the class Ia and Ib genes underwent multiple duplications and diversifications before suids and tayassuids diverged from their common ancestor. The histocompatibility genes mostly form orthologous groups and there is genetic differentiation for most of these genes between Eurasian and sub-Saharan African wild pigs. Tests of selection showed that the peptide-binding region of class Ib genes was under positive selection. These findings contribute to better understanding of the evolutionary history of the MHC, specifically, the class I genes, and provide useful data for investigating the immune response of wild populations against pathogens.

Discovery of gorilla MHC-C expressing C1 ligand for KIR

In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic sequence data for a reassessment of allelic diversity at Gogo-C, the gorilla orthologue of HLA-C. Through the combination of long-range amplifications and long-read sequencing technology, we obtained, among the 35 gorillas reanalyzed, three novel full-length genomic sequences including a coding region sequence that has not been previously described. The newly identified Gogo-C*03:01 allele has a divergent recombinant structure that sets it apart from other Gogo-C alleles. Domain-by-domain phylogenetic analysis shows that Gogo-C*03:01 has segments in common with Gogo-B*07, the additional B-like gene that is present on some gorilla MHC haplotypes. Identified in ~ 50% of the gorillas analyzed, the Gogo-C*03:01 allele exclusively encodes the C1 epitope among Gogo-C allotypes, indicating its important function in controlling natural killer cell (NK cell) responses via KIR. We further explored the hypothesis whether gorillas experienced a selective sweep which may have resulted in a general reduction of the gorilla MHC class I repertoire. Our results provide little support for a selective sweep but rather suggest that the overall low Gogo class I diversity can be best explained by drastic demographic changes gorillas experienced in the ancient and recent past.

Selection on MHC in a Context of Historical Demographic Change in 2 Closely Distributed Species of Tuco-tucos (Ctenomys australis and C. talarum)

Selection necessarily acts within the same current and historical demographic framework as neutral evolutionary processes, and the outcome of the interplay between these forces may vary according to their relative strength. In this study, we compare the variation at a major histocompatibility complex (MHC) locus (DRB exon 2), typically subject to strong diversifying selection, and mitochondrial diversity (D-loop) across populations encompassing the entire distribution of 2 species of South American subterranean rodents: Ctenomys australis and C. talarum (tuco-tucos). Although these species are parapatric along most of their distribution, historically they have followed distinct demographic trajectories associated with sea level changes during the Quaternary. We surveyed 8 populations of C. australis and 15 of C. talarum, from which we analyzed 70 and 212 D-loop haplotypes and 91 and 346 DRB genotypes, respectively. Both species have gone through a recent demographic expansion; however, the signal of this process only encompasses the entire distribution of one of the species: C. australis. While balancing selection on MHC in C. talarum-enhanced DRB diversity at the local level compared to D-loop, although not promoting divergence among populations, in C. australis local diversifying selection may have driven higher population differentiation at DRB than at D-loop. Our findings reinforce the idea that the relative strength of selection acting on MHC genes varies spatially and temporally within and among species, even between species using the same macrohabitat and exposed to similar immune challenges.

Effects of Population Bottleneck and Balancing Selection on the Chinese Alligator Are Revealed by Locus-Specific Characterization of MHC Genes

Chinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0.009) at all sites, the deviation from Hardy-Weinberg Equilibrium/heterozygote deficiency, and the significant Tajima’s D values, indicating the MHC class I and class II loci being at different stages of bottleneck. We also obtained 3 pieces of evidence for balancing selection on this severely bottlenecked reptile: an obvious excess of nonsynonymous substitutions over synonymous at the antigen-binding positions, the mean synonymous substitution rate of MHC exons significantly higher than mean nucleotide substitution rate of introns, and the differentiation coefficient F_ST of MHC loci significantly lower than that of microsatellite loci. Consequently, we emphasize that the Chinese alligator holds a pretty low adaptive ability and requires scientific conservation strategies to ensure the long-term population development.

Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan

Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.

Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny

Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean amphibians, the Asiatic toad (Bufo gargarizans) and the Japanese tree frog (Hyla japonica). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that B. gargarizans and H. japonica cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.

Avian and Human Seasonal Influenza Hemagglutinin Proteins Elicit CD4 T Cell Responses That Are Comparable in Epitope Abundance and Diversity

Avian influenza viruses remain a significant concern due to their pandemic potential. Vaccine trials have suggested that humans respond poorly to avian influenza vaccines relative to seasonal vaccines. It is important to understand, first, if there is a general deficiency in the ability of avian hemagglutinin (HA) proteins to generate immune responses and, if so, what underlies this defect. This question is of particular interest because it has been suggested that in humans, the poor immunogenicity of H7 vaccines may be due to a paucity of CD4 T cell epitopes. Because of the generally high levels of cross-reactive CD4 T cells in humans, it is not possible to compare the inherent immunogenicities of avian and seasonal HA proteins in an unbiased manner. Here, we empirically examine the epitope diversity and abundance of CD4 T cells elicited by seasonal and avian HA proteins. HLA-DR1 and HLA-DR4 transgenic mice were vaccinated with purified HA proteins, and CD4 T cells to specific epitopes were identified and quantified. These studies revealed that the diversity and abundance of CD4 T cells specific for HA do not segregate on the basis of whether the HA was derived from human seasonal or avian influenza viruses. Therefore, we conclude that failure in responses to avian vaccines in humans is likely due to a lack of cross-reactive CD4 T cell memory perhaps coupled with competition with or suppression of naive, HA-specific CD4 T cells by memory CD4 T cells specific for more highly conserved proteins.

Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations

The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change.

A genomic survey on the immune differences among Sinocyclocheilus fishes

In our previous work, we reported comparative genomics studies on 3 Sinocyclocheilus fishes, including the surface-dwelling S. graham (Sg), the semi-cave-dewlling S. rhinocerous (Sr) and the cave-restricted S. anshuiensis (Sa). Here, we performed a genomic survey on the immunity differences among the 3 fishes by combination of the genome and transcriptome data. Our results demonstrate that immune-related genetic pathways in Sa and Sr present more similarities than Sg. The innate immune activity in Sa seems to be higher than Sg and Sr, while Sr owns more copy numbers of MHC-related genes (related with the acquired immune system) than Sg and Sa. These differential immune activities in the 3 Sinocyclocheilus species may be due to their differential habitats. Generally speaking, most immunity genes transcribe the lowest levels in Sa when compared with Sg and Sr, which may be associate with a less various microbial environment in the cave-restricted habitat. However, Sr has more members of MHC-related genes than those in Sg and Sa, suggesting a great contribution from the semi-cave-dwelling condition.

Variation in Major Histocompatibility Complex diversity in invasive cane toad populations

Context The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via toxicity to predators. The invasion process has taken its toll on the cane toad, with changes in the immunological capacity across the Australian invasive population. Aims To investigate the immunogenetic underpinnings of these changes, we studied the diversity of the Major Histocompatiblity Complex (MHC) genes in introduced cane toad populations. Methods We studied the diversity of two MHC genes (the classical class I UA locus and a class II DAB locus) and compared these with neutral microsatellite markers in toads from the Australian site of introduction and the Australian invasion front. We also included toads from Hawai’i, the original source of the Australian toads, to infer founder effect. Key results Diversity across all markers was low across Australian and Hawai’ian samples, consistent with a reduction in genetic diversity through multiple founder effects during the course of the successive translocations. In Australia, allelic diversity at the microsatellite markers and the UA locus was reduced at the invasion front, whereas all three alleles at the DAB locus were maintained in the invasion-front toads. Conclusions Loss of allelic diversity observed at the microsatellite markers and the UA locus could be the result of drift and bottlenecking along the invasion process, however, the persistence of DAB diversity warrants further investigation to disentangle the evolutionary forces influencing this locus. Implications Through the use of different molecular markers, we provide a preliminary description of the adaptive genetic processes occurring in this invasive population. The extremely limited MHC diversity may represent low immunogenetic competence across the Australian population, which could be exploited for invasive species management.

Primary immunodeficiencies suggest redundancy within the human immune system

Pathogen-driven evolution has shaped the complexity of the human immune system. Our genome contains at least 1854 gene products involved in immune responses. However, the redundancy and robustness of the immune system need further characterization. One way to examine this redundancy is through the study of monogenic primary immunodeficiencies (PIDs) associated with infections. Causal mutations affecting innate immunity genes are, in relative terms, close to seven times less frequent than those affecting adaptive immunity genes in PIDs. Loss-of-function mutations of innate immunity genes encoding pattern-recognition receptors (PRRs) and associated pathways rarely cause susceptibility to infections, which suggests that PRR pathways are partially redundant in the immune responses to infection. This dispensability has also been observed for constitutive products of the immune system, such as secretory immunoglobulin A, and for innate immune cells, such as natural killer and innate lymphoid cell subsets, which are not essential for viability. This Review discusses these findings in the context of their implications for the identification of previously unknown classes of PIDs and assessment of the susceptibility to infection associated with various targeted immunotherapies.

Natural Selection in the Great Apes

Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh.

Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana

Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e., a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.