Japanese Clade Research Articles

Secondary contact of two cryptic Hokou gecko groups in the Izu Islands, Japan

We analyzed the mitochondrial DNA of Gekko hokouensis collected from the Izu Islands (maybe an introduced population) and the Nansei Islands (native population), both in Japan. A molecular phylogenetic analysis suggested that G. hokouensis of Japan belongs to a cryptic monophyletic group different from that of the currently discovered sample of China. Furthermore, the Japanese clade of G. hokouensis is differentiated into two subclades (Clade 1 and Clade 2 in this article). In the Nansei Islands, these two subclades form a complicated nested-distribution pattern and do not coexist on any of the islands, whereas both clades appear to coexist in the Izu Islands. The two clades exhibit high genetic diversity in the Nansei islands, which are the source population. Surprisingly, it has been revealed that high genetic diversity has also been maintained in the Izu Islands, which are the introduced population, in each clade. AMOVA has also revealed that the genetic differentiation between the populations in the Izu Islands and the Nansei Islands was not significant in each clade. These results suggest that the population of the Izu Islands is now in secondary contact between two clades by multiple migrations from various regions of the Nansei Islands.

Nationwide and long-term molecular epidemiologic studies of mumps viruses that circulated in Japan between 1986 and 2017.

In Japan, major mumps outbreaks still occur every 4-5 years because of low mumps vaccine coverage (30-40%) owing to the voluntary immunization program. Herein, to prepare for a regular immunization program, we aimed to reveal the nationwide and long-term molecular epidemiological trends of the mumps virus (MuV) in Japan. Additionally, we performed whole-genome sequencing (WGS) using next-generation sequencing to assess results from conventional genotyping using MuV sequences of the small-hydrophobic (SH) gene. We analyzed 1,064 SH gene sequences from mumps clinical samples and MuV isolates collected from 25 prefectures from 1986 to 2017. The results showed that six genotypes, namely B (110), F (1), G (900), H (3), J (41), and L (9) were identified, and the dominant genotypes changed every decade in Japan since the 1980s. Genotype G has been exclusively circulating since the early 2000s. Seven clades were identified for genotype G using SH sequence-based classification. To verify the results, we performed WGS on 77 representative isolates of genotype G using NGS and phylogenetically analyzed them. Five clades were identified with high bootstrap values and designated as Japanese clade (JPC)-1, -2, -3, -4, -5. JPC-1 and -3 accounted for over 80% of the total genotype G isolates (68.3 and 13.8%, respectively). Of these, JPC-2 and -5, were newly identified clades in Japan through this study. This is the first report describing the nationwide and long-term molecular epidemiology of MuV in Japan. The results provide information about Japanese domestic genotypes, which is essential for evaluating the mumps elimination progress in Japan after the forthcoming introduction of the mumps vaccine into Japan's regular immunization program. Furthermore, the study shows that WGS analysis using NGS is more accurate than results obtained from conventional SH sequence-based classification and is a powerful tool for accurate molecular epidemiology studies.

Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan

Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.

Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific.

Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.

Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data.

To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.

Phylogenetic position of the Atlantic Gnomefish, Scombrops oculatus (Teleostei: Scombropidae), within the genus Scombrops, inferred from the sequences of complete mitochondrial genome and cytochrome c oxidase subunit I genes

We determined the complete mitochondrial genome of the Atlantic Gnomefish, Scombrops oculatus (Scombropidae). The total length of mitochondrial DNA (mtDNA) was 16,515 bp and included 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene arrangement of S. oculatus was identical to those of three Japanese scombropid species and those of other teleosts. The phylogenetic analysis using the whole mtDNA, excluding the control region, indicates the Atlantic species is distinct from the Japanese clade, whereas that using cytochrome c oxidase subunit I gene showed the Atlantic species is most closely related to the African species.

Taxonomic revision of Dictyosiphon (Ectocarpales s.l., Phaeophyceae) from the north-western Pacific, with descriptions of D. asiaticus sp. nov. and D. sparsus sp. nov

ABSTRACT Dictyosiphon asiaticus sp. nov. and D. sparsus sp. nov. are newly described from Japan and the north-western Pacific. Molecular phylogenies based on the mitochondrial cox1 and cox3 and chloroplast atpB, psaA, psbA and rbcL DNA sequences revealed that Dictyosiphon comprises at least seven lineages worldwide. Japanese Dicytosiphon species formed two clades with high support and were sister to a clade including specimens from the cold-water regions of the northern Pacific, the Arctic, and the north-western Atlantic. Specimens of one of the Japanese clades (= D. asiaticus sp. nov.) were morphologically similar to D. foeniculaceus (generitype described from Scotland, UK), having densely branched thalli with fine branches, and were epiphytic on Scytosiphon spp. and Chordaria spp. Specimens of the other Japanese clade (= D. sparsus sp. nov.) were morphologically similar to D. chordaria, having somewhat thicker, sparse branches with blunt tips, and were epiphytic on Chordaria spp. We assign the third clade distributed on both sides of the North Pacific to D. sinicola, which was described from Washington, USA, for the following reasons: Dictyosiphon specimens in the region having relatively densely branched thalli with fine tips have been identified as D. foeniculaceus, and D. sinicola was distinguished from them by its remarkably larger thallus, while anatomically they are very similar. However, D. foeniculaceus is not widely distributed in the region, with only one genetic lineage (species) reported, so that those two taxa are considered to be ecotypes of the same species, and D. sinicola is the valid name for the taxon.

East Asian origin of the widespread alpine snow‐bed herb, Primula cuneifolia (Primulaceae), in the northern Pacific region

AbstractAimThe evolutionary importance of southern mountain ranges has been noted for alpine as well as arctic–alpine plants. However, it remains unclear whether these isolated marginal populations of cold‐adapted species have contributed to the establishment of their current widespread distribution. We aim to explore the molecular evidence for the recent northward migration of alpine snow‐bed species in the northern Pacific region.LocationJapanese Archipelago, Kamchatka Peninsula, Alaska.TaxonPrimula cuneifolia Ledeb., the wedgeleaf primrose, distributed in high mountains across the northern Pacific region and its sister species, Primula nipponica Yatabe, which is endemic to northern Japan.MethodsThe phylogenetic relationships and genetic structure of P. cuneifolia and its sister species were estimated using multiple loci from genotyping by random amplicon sequencing‐direct (GRAS‐Di) analyses. The temporal framework of genetic divergence was estimated using the isolation‐with‐migration model. The post‐glacial range shift was inferred using approximate Bayesian computation and ecological niche modelling.ResultsPhylogenetic analyses revealed that P. cuneifolia diverged into four clades, among which the southernmost clade in Japan diverged earlier than the northern clades. The Japanese clade likely diverged during the last glacial period, followed by further post‐glacial divergence of clades in the Kamchatka Peninsula and Alaska.Main conclusionOur study demonstrated that P. cuneifolia originated in Japan and spread northward into the northern Pacific region during and after the last glacial period. This finding provides the first evidence suggesting that population persistence and genetic divergence as well as speciation in the less glaciated mountains in Japan play important roles in the diversity and distribution of alpine plants in the northern Pacific region.

Molecular phylogeny and historical biogeography of the genus Platycerus (Coleoptera, Lucanidae) in East Asia

AbstractThe genus Platycerus is a cool temperature zone taxon widely distributed in the Northern Hemisphere. In East Asia, 10, one and 28 species are known in Japan, Korea and China, respectively. Recent studies of Platycerus have revealed the divergence pattern in Japan and South Korea, but that of Chinese Platycerus is unknown. We conducted a phylogenetic and biogeographical study of Platycerus in East Asia, including China, using 68, 87 and 296 sequence data of the nuclear wingless gene, internal transcribed spacer (ITS) region and mitochondrial COI gene, respectively. Although the introgression of mitochondrial genes had been known in Japanese Platycerus, the essential contradiction was not recognized between the phylogenetic trees of nuclear genes and COI in Chinese Platycerus. In the COI tree, the Japanese clade and Asian continental clade diverged around 10.84 million years ago, and four major clades were recognized in the latter. For the shape of the posterolateral corner of the Platycerus pronotum, sharp (S)‐type species are distributed in higher latitudinal and lower altitudinal areas than round (R)‐type species in the Asian continent. S‐type species have evolved from R‐type species at least three times in more northerly areas, where the annual amplitude of temperature change is large. The genus Platycerus has been differentiated and speciated by a process unique to South Korea, Japan and China, according to regional topography. Thus, genetic differentiation and speciation in Platycerus are related to latitudinal and altitudinal gradients, as well as the site topographical profile and niche differentiation.

Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago.

The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times—based on three molecular clock node calibrations—using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades—that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.

Molecular Detection of Severe Fever with Thrombocytopenia Syndrome Virus in Korean Domesticated Pigs.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne virus in China, Japan, and Korea. Although the incidence of SFTS has been increasing annually since the first SFTSV case was reported in Korea, the prevalence of SFTSV in Korean livestock has not conducted. The purpose of this study was to investigate the prevalence of SFTSV in domesticated pigs (Sus scrofa domesticus) throughout Korea. A total of 240 sera were collected from 30 domesticated pigs in eight provinces. To detect SFTSV, one-step reverse transcription RT nested PCR was conducted using SFTSV genome-specific primer sets. The amplified PCR products were cloned and then sequenced. Four of 240 (1.7%) pig sera tested positive for SFTSV through one-step RT nested PCR. Two of the four obtained sequences were included in the Japanese clade, whereas the other two sequences were related to the Chinese clade based on phylogenetic analysis. Moreover, the obtained SFTSV sequences from this study were distinct from human SFTSV strains. This study is the first to attempt the identification of SFTSV sequences from domesticated pigs and the first molecular detection of SFTSV in Korean livestock. Our findings indicate that a new subclade of SFTSV-different from that in humans-may be present in domesticated pigs; the surveillance of SFTSV in livestock is required to better understand the life cycle of SFTSV.

Prevalence of severe fever with thrombocytopenia syndrome virus in black goats (Capra hircus coreanae) in the Republic of Korea

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne pathogen in China, Japan, and the Republic of Korea (ROK). The aim of this study was to investigate the prevalence of SFTSV antigens and anti-SFTSV antibodies in black goats (Capra hircus coreanae) throughout the ROK. Sera were collected from 737 black goats in nine provinces in the ROK. Eighteen of 737 (2.4%) goat sera were positive for SFTSV on one-step reverse transcription nested polymerase chain reaction. The amplified 346-bp S segments of SFTSV sequences were classified into three genotypes (BG1, BG2, and BG3), and were included in the Japanese clade rather than the Chinese clade, based on phylogenetic analysis. Forty-three of 624 (6.9%) serum samples were seropositive for anti-SFTSV antibodies on enzyme-linked immunosorbent assay analysis. This study is the first to examine the molecular prevalence of SFTSV in goats and the first to perform serological detection of anti-SFTSV antibodies in livestock in the ROK. Moreover, the results indicate that SFTSV is widely distributed in goats and that additional monitoring for SFTSV is needed in livestock in the ROK.

Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan.

Buergeria japonica is a widely distributed treefrog occurring from Ryukyu Archipelago to Taiwan. Across this wide distributional range, we combined molecular, acoustic, morphological, and behavioral characters to clarify the taxonomic status among these insular populations. Genetic differentiation in mitochondrial sequences indicated an over 16% divergence among two deeply divergent clades: Japanese clade distributes in Ryukyu Archipelago and northwestern drainages of Taiwan, while Taiwanese clade distributes in the remaining drainages on Taiwan. The Taiwanese clade can be distinguished from the nominative species not only by molecular and morphological differences, but also distinguishable by considerable acoustic differentiation, which is extraordinarily noticeable for an additional type of long call that never recorded from Japanese clade. The two clades form a parapatric distribution pattern with narrow contact zones both in western and eastern Taiwan. Playback experiments indicated that male frogs show significantly stronger defensiveness against conspecific calls rather than heterospecific calls, indicating that these signals play a crucial role in species recognition. Here we describe the Taiwanese clade as a new species; the behavioral response and the magnitude of gene flow across their contact zones are especially worth for detailed studies.

Corrigendum to: Against the odds of unusual mtDNA inheritance, introgressive hybridisation and phenotypic plasticity: systematic revision of Korean freshwater gastropods (Semisulcospiridae, Cerithioidea)

The systematics of Semisulcospiridae in Korea is critically revised by means of comparative anatomy, including comprehensive review of type material and mitochondrial phylogenetics (sequences of COI and 16S). The family is represented by two genera with different reproductive modes: Semisulcospira Boettger, 1886 is viviparous and contains three species (S. coreana (Martens, 1886), S. gottschei (Martens, 1886) and S. forticosta (Martens, 1886)) while Koreoleptoxis Burch &amp; Jung, 1988 is oviparous and also contains three species (K. globus (Martens, 1886), K. nodifila (Martens, 1886), K. tegulata (Martens, 1894)). Koreanomelania Burch &amp; Jung, 1988 is synonymised with Koreoleptoxis. Species can be distinguished by differences in shell shape and sculpture. They form well-differentiated clusters in the mitochondrial phylogeny, consistently revealing lower intraspecific than interspecific genetic distances. Sequences of Japanese Semisulcospira species fall into three distinct major clades (A–C), rendering Semisulcospira non-monophyletic in the mitochondrial tree. Only a small number of Japanese samples were closely related to the Korean clade (Clade C). The numerically predominant Japanese mitochondrial Clade B exhibited increased lineage divergence and, when translated into amino acids, significantly more amino acid substitutions in comparison with Korean species. I conclude that these Japanese sequences may be paralogous and/or may undergo non-neutral evolution. Hence, they are not suitable for inferring phylogenetic relationships.

Against the odds of unusual mtDNA inheritance, introgressive hybridisation and phenotypic plasticity: systematic revision of Korean freshwater gastropods (Semisulcospiridae, Cerithioidea)

The systematics of Semisulcospiridae in Korea is critically revised by means of comparative anatomy, including comprehensive review of type material and mitochondrial phylogenetics (sequences of COI and 16S). The family is represented by two genera with different reproductive modes: Semisulcospira Boettger, 1886 is viviparous and contains three species (S. coreana (Martens, 1886), S. gottschei (Martens, 1886) and S. forticosta (Martens, 1886)) while Koreoleptoxis Burch &amp;amp; Jung, 1988 is oviparous and also contains three species (K. globus (Martens, 1886), K. nodifila (Martens, 1886), K. tegulata (Martens, 1894)). Koreanomelania Burch &amp;amp; Jung, 1988 is synonymised with Koreoleptoxis. Species can be distinguished by differences in shell shape and sculpture. They form well-differentiated clusters in the mitochondrial phylogeny, consistently revealing lower intraspecific than interspecific genetic distances. Sequences of Japanese Semisulcospira species fall into three distinct major clades (A–C), rendering Semisulcospira non-monophyletic in the mitochondrial tree. Only a small number of Japanese samples were closely related to the Korean clade (Clade C). The numerically predominant Japanese mitochondrial Clade B exhibited increased lineage divergence and, when translated into amino acids, significantly more amino acid substitutions in comparison with Korean species. I conclude that these Japanese sequences may be paralogous and/or may undergo non-neutral evolution. Hence, they are not suitable for inferring phylogenetic relationships.

Is the Kuroshio Current a strong barrier for the dispersal of the gizzard shad (Konosirus punctatus) in the East China Sea?

The gizzard shad (Konosirus punctatus) is a common pelagic fish in the East China Sea. To evaluate the influence of Kuroshio Current in shaping the genetic structure of marine species, 10 populations of K. punctatus from Chinese and Japanese coastal waters were collected for analysis based on the mitochondrial DNA marker. All the Japanese populations exhibited higher nucleotide diversity than did Chinese populations. Two distinct clades were identified by the neighbour-joining tree based on haplotypes of Cyt b and the control region. Both AMOVA and pairwise Fst strongly supported the significant genetic divergence between Chinese and Japanese clades, which suggested strictly limited gene exchange. The mismatch distribution of Chinese clade and Japanese Clade B appeared to be unimodal, and Tajima’s D and Fu’s Fs statistics were significantly negative, and, therefore, the hypothesis of selective neutrality was rejected. The results indicated that the Kuroshio Current may not be the strong barrier for the dispersal of K. punctatus in the East China Sea. The climate of Pleistocene periods had played an important role in phylogeographical patterns of K. punctatus and the dispersal strategy of coastal species may be the major current physical barrier for the gene flow among populations from Chinese and Japanese coastal waters.

Complex geographic- and habitat-based niche partitioning of an East Asian habitat generalist mayflyIsonychia japonica(Ephemeroptera:Isonychiidae) with reference to differences in genetic structure

AbstractWe focused on the genetic structure and evolutionary divergence of a typical habitat generalist mayfly, Isonychia japonica, inhabiting rivers widely distributed across eastern Asia. In the Japanese Archipelago, they are distributed across a wide range of environments, including up- and downstream areas in 1 river basin. We analyzed DNA sequences of this mayfly from both the mitochondrial (cytochrome oxidase c subunit I [COI] and 16S ribosomal RNA) and nuclear genomes (Histone H3 and ITS2) of specimens from populations across the eastern Asian region, with emphasis on the Japanese Archipelago. Isonychia japonica is genetically differentiated into 2 major clades (C = continental clade, J = Japanese Archipelago clade). Furthermore, clade J is composed of 2 subclades (clades J-U and J-D). Clade J is separated by environment, with specimens constituting clade J-U occurring in small-scale rivers of the upstream regions and specimens constituting clade J-D occurring in large-scale rivers of downstream re...

Phylogenetic and Geographic Relationships of Severe Fever With Thrombocytopenia Syndrome Virus in China, South Korea, and Japan.

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne acute infectious disease caused by the SFTS virus (SFTSV). SFTS has been reported in China, South Korea, and Japan as a novel Bunyavirus. Although several molecular epidemiology and phylogenetic studies have been performed, the information obtained was limited, because the analyses included no or only a small number of SFTSV strains from Japan. The nucleotide sequences of 75 SFTSV samples in Japan were newly determined directly from the patients' serum samples. In addition, the sequences of 7 strains isolated in vitro were determined and compared with those in the patients' serum samples. More than 90 strains that were identified in China, 1 strain in South Korea, and 50 strains in Japan were phylogenetically analyzed. The viruses were clustered into 2 clades, which were consistent with the geographic distribution. Three strains identified in Japan were clustered in the Chinese clade, and 4 strains identified in China and 26 in South Korea were clustered in the Japanese clade. Two clades of SFTSV may have evolved separately over time. On rare occasions, the viruses were transmitted overseas to the region in which viruses of the other clade were prevalent.

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.

Contrasting genetic structure of closely related giant water bugs: Phylogeography of Appasus japonicus and Appasus major (Insecta: Heteroptera, Belostomatidae)

Appasus japonicus and A. major, two belostomatid species of the giant water bug found in parts of East Asia, have very similar morphological characteristics and ecological niches, and also overlapping habitats. However, the results of our previous published study utilizing molecular phylogenetic analyses of mitochondrial and nuclear DNA revealed extensive genetic differences, which indicated that the possibility of inter-specific hybridization was extremely unlikely. We collected A. japonicus and A. major from the Japanese Archipelago, Korean Peninsula, and Russian Far East, and conducted molecular analyses of mitochondrial DNA COI and 16S rRNA to compare phylogenetic relationships between these species. Three major clades were recognized within A. japonicus. Specimens from the Korean population constituted a monophyletic clade, and were a sister group of the western region of the Japanese Archipelago. The Eastern Japanese clade was clearly differentiated. Four major clades were recognized within A. major. Specimens from the Japanese and Korean populations revealed two distinct monophyletic clades. Significant differentiation was clearly observed between their genetic structures. Furthermore, the results of mismatch distribution and Bayesian skyline plot analyses suggested the possibility of a bottleneck effect or founder effect in two of the A. major clades. Collectively, these results demonstrated both similarities and differences in these two species even though their distribution widely overlaps in East Asia, with their morphological characteristics and ecological niches being very similar. These differences in genetic structures are considered to be due to their evolutionary history.