Characterisation of major histocompatibility complex class I genes in Japanese Ranidae frogs.

The major histocompatibility complex (MHC) is a key component of adaptive immunity in all jawed vertebrates, and understanding the evolutionary mechanisms that have shaped these genes in amphibians, one of the earliest terrestrial tetrapods, is important. We characterised MHC class I variation in three common Japanese Rana species (Rana japonica, Rana ornativentris and Rana tagoi tagoi) and identified a total of 60 variants from 21 individuals. We also found evolutionary signatures of gene duplication, recombination and balancing selection (including trans-species polymorphism), all of which drive increased MHC diversity. A unique feature of MHC class I from these three Ranidae species includes low synonymous differences per site (d S) within species, which we attribute to a more recent diversification of these sequences or recent gene duplication. The resulting higher d N/d S ratio relative to other anurans studied could be related to stronger selection pressure at peptide binding sites. This is one of the first studies to investigate MHC in Japanese amphibians and permits further exploration of the polygenetic factors associated with resistance to infectious diseases

Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs

Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection

The neutral theory and natural selection in the HLA region

Based on available DNA sequence data in the HLA region of 4 Mb, we review the degree of polymorphism at 39 loci of which most are involved in the immune system. The extent of nucleotide differences per silent site differs greatly from locus to locus. It is exceptionally high at classical MHC loci, intermediate at six MHC-related pseudogenes as well as at some loci in class I and II regions, and low in the class III region. Different exons of individual MHC loci show also different degrees of silent polymorphism; high in the exons encoding for the peptide binding region (PBR) and low in the exons encoding for trans-membranes and cytoplasmic tails. The degree of polymorphism within MHC allelic lineages is not much smaller than that between allelic lineages, contrary to the expectation where intra-allelic sequence exchanges are restricted. The observation that many allelic lineages at the HLA-DRB1 locus are combinations of distinct motifs in the beta pleated sheet and alpha helix of PBR indicates that sequence exchanges occur even within exon 2. Semi-quantitative analysis is presented about the rate of sequence exchanges between selected and linked neutral regions, although more sequence information is necessary to make definite conclusions. The extraordinary MHC polymorphism is viewed from the dual function of MHC molecules that controls the acquired immune system

ヒトの精神活動に関わる遺伝子の進化と集団遺伝学

2016～2018研究成果の概要（和文）：ヒトの疾病に関わる遺伝子のリスクSNPsの多くが他の霊長類で保存されている祖先型であることが知られている。ヒト特異的な社会的あるいは環境の変化によりこれらのSNPsがヒトの疾病と関わるようになったとの仮説を立て、これまで明らかになっている128の統合失調症関連SNPsをコアとして、連鎖不平衡(LD)、正の自然選択、SNPsの分岐時間等を解析している。東アジア集団で調べたところ、66SNPsで強いLDブロックを、その内15SNPsで自然選択の可能性を検出した。これら15SNPsの分岐時間は半数が最近5万年以降であった。これは考古学的遺物からヒトの脳活動が亢進したと考えられる時期と一致している。研究成果の学術的意義や社会的意義現生人類は30万年ほど前にアフリカ大陸で誕生後、およそ5～8万年前に全世界へとその生息域を広げた。これに伴い、洞窟の壁画、遺跡から発掘される装飾品や石器などに見られるようにヒトは文化や技術の面で大きな発展を遂げた。この文化的・技術的な発展にはヒトの脳機能の亢進がともなっていることは想像に難くない。統合失調症は認知や思考の障害であり、その発症に関わる遺伝子は、そのようなヒトの脳機能の亢進に関わると考えられる。そこで本研究では、最近、大規模関連解析で同定された統合失調症に関連する128個のSNPを対象に、ヒトの脳機能の亢進に関与したと思われる遺伝子を検出し、その適応的役割を明らかにする。研究成果の概要（英文）：It is known that many disease-related SNPs (risk SNPs) in humans areancestral, shared by non-human primates, implying that human-specific environmental or socialchanges would be a trigger of the onset of SNP-related diseases. To examine this hypothesis, westudied linkage disequilibrium (LD) surrounding target SNPs, a signal of positive selection onancestral and derived SNPs and estimated the divergence time of a derived allele group. A recentlarge-scale association study has identified 128 schizophrenia-related SNPs. Of these, 66 derivedSNPs in East Asia showed strong LD blocks. Our newly developed statistical test revealed significantsignals of ongoing positive selection at 15 SNPs and the most recent common ancestor of a derivedallele group at a half of the SNPs occurred no earlier than 50,000 years ago. This age of positivelyselected alleles at each target SNP coincides with the time of drastic changes in human brainactivities that became evident in archaeological remains

The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesian Cemani and Chinese Silkie breeds.

Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involve the endothelin 3 gene, EDN3. A genomic region, DR1 of 127 kb, together with another region, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversion of one DR2. Quantitative PCR and copy number variation analyses on the Cemani genome sequence confirmed the duplication of EDN3. These genetic arrangements are identical in Cemani and Silkie, indicating a single origin of the genetic cause of Fm. The two DR1s harbor two distinct EDN3 haplotypes in a form of permanent heterozygosity, although they remain allelic in the ancestral Red Jungle Fowl population and some domesticated chicken breeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemani and Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguous record for selective sweep that extends in both directions from tandemly duplicated EDN3 loci. This highly homozygous tract is different in length between Cemani and Silkie, reflecting their distinct breeding histories. It is estimated that the Fm phenotype came into existence at least 6600-9100 years ago, prior to domestication of Cemani and Silkie, and that throughout domestication there has been intense artificial selection with strength s > 50% in each breed

Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations.

A key characteristic of MHC genes is the persistence of allelic lineages over macroevolutionary periods, often through multiple speciation events. This phenomenon, known as trans-species polymorphism (TSP), is well documented in several major taxonomic groups, but has less frequently been observed in birds. The order Passeriformes is arguably the most successful terrestrial vertebrate order in terms of diversity of species and ecological range, but the reasons for this success remain unclear. Passerines exhibit the most highly duplicated MHC genes of any major vertebrate taxonomic group, which may generate increased immune response relative to other avian orders with fewer MHC loci. Here, we describe phylogenetic patterns of the MHC IIB in the passerine family Corvidae. Our results indicate wide-spread TSP within this family, with at least four supported MHC IIB allelic lineages that predate speciation by many millions of years. Markov chain Monte Carlo simulations indicate that divergence of these lineages occurred near the time of the divergence of the Passeriformes and other avian orders. We suggest that the current MHC diversity observed in passerines is due in part to the multiple duplication of a single MHC locus, DAB1, early in passerine evolution and that subsequent duplications of these paralogues have contributed to the enormous success of this order by increasing their ability to recognize and mount immune responses to novel pathogens

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

BackgroundThe major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations. ResultsAmong 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected. ConclusionsThe low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population