論文 - 木村　亮介

Admixture and natural selection shaped genomes of an Austronesian-speaking population in the Solomon Islands.

Isshiki M, Naka I, Watanabe Y, Nishida N, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Eddie R, Ohtsuka R, Ohashi J

Scientific reports ( Scientific Reports )  10 ( 1 ) 6872   2020年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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ゲノムで解き明かされるヒトの遺伝適応：ヒトは如何にして厳しい環境や病原体を克服したのか？

木村 亮介

日本マススクリーニング学会誌   30   237 - 245   2020年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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琉球諸語研究における方言系統地理学の可能性

狩俣 繁久, 木村 亮介

フィールドと文献から見る日琉諸語の系統と歴史   -   2020年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Evidence for sympatric speciation in a Wallacean ancient lake.

Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K

Evolution; international journal of organic evolution ( Evolution )  73 ( 9 ) 1898 - 1915   2019年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Sympatric speciation has been demonstrated in few empirical case studies, despite intense searches, because of difficulties in testing the criteria for this mode of speciation. Here, we report a possible case of sympatric speciation in ricefishes of the genus Oryzias on Sulawesi, an island of Wallacea. Three species of Oryzias are known to be endemic to Lake Poso, an ancient tectonic lake in central Sulawesi. Phylogenetic analyses using RAD-seq-derived single nucleotide polymorphisms (SNPs) revealed that these species are monophyletic. We also found that the three species are morphologically distinguishable and clearly separated by population-structure analyses based on the SNPs, suggesting that they are reproductively isolated from each other. A mitochondrial DNA chronogram suggested that their speciation events occurred after formation of the tectonic lake, and existence of a historical allopatric phase was not supported by coalescent-based demographic inference. Demographic inference also suggested introgressive hybridization from an outgroup population. However, differential admixture among the sympatric species was not supported by any statistical tests. These results all concur with criteria necessary to demonstrate sympatric speciation. Ricefishes in this Wallacean lake provide a promising new model system for the study of sympatric speciation.

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Study on existence of the fisheries resources abundance by using environmental deoxyribonucleic acid (e-DNA) approach at fishing grounds in the Sulawesi Sea, Indonesia

Masengi K, Mandagi IF, Manu L, Silooy F, Labaro IL , Masengi AWR, Sebua N, Masengi EIKG, Pinontoan B, Hutabarat Y, Hukom F, Iwata M, Abe Y, Sato Y, Kimura R, Yamahira K

IOP Conference Series: Materials Science and Engineering ( IOP Conference Series: Materials Science and Engineering )  567 ( 1 )   2019年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits.

Koganebuchi K, Kimura R

Annals of human biology ( Annals of Human Biology )  46 ( 4 ) 354 - 366   2019年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Context: The Ryukyu Islands stretch across a southwestern area of the Japanese Archipelago. Because of their unique geographical and historical backgrounds, Ryukyuans have their own genetic and phenotypic characteristics, which have been disclosed in previous anthropological and biomedical studies. Objective: The history, peopling and biomedical and genetic characteristics of Ryukyuans are reviewed and future research directions are discussed. Conclusion: Morphological and genetic studies have suggested the complex demographic history of Ryukyuans and their relationships with other Asian populations. Knowledge of population formation processes is important to understand the distribution of pathogens. In viral infectious diseases, some strains that may be associated with disease symptoms are specific to Ryukyuans. Dramatic changes in diet have played an important role among Ryukyuans in terms of increases in lifestyle-related diseases and mortality risks. To achieve a better understanding of pathogenic disease factors, further integration of findings regarding the genetic and biomedical characteristics of the Ryukyuans is needed.

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Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic <i>Papilio polytes</i> in multiple islands in the Ryukyus, Japan.

Tsurui-Sato K, Sato Y, Kato E, Katoh M, Kimura R, Tatsuta H, Tsuji K

Ecology and evolution ( Ecology and Evolution )  9 ( 10 ) 5991 - 6002   2019年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Batesian mimicry is a well-studied adaptation for predation avoidance, in which a mimetic species resembles an unpalatable model species. Batesian mimicry can be under positive selection because of the protection gained against predators, due to resemblance to unpalatable model species. However, in some mimetic species, nonmimetic individuals are present in populations, despite the benefits of mimicry. The mechanism for evolution of such mimetic polymorphism remains an open question. Here, we address the hypothesis that the abundance of mimics is limited by that of the models, leading to mimetic polymorphism. In addition, other forces such as the effects of common ancestry and/or isolation by distance may explain this phenomenon. To investigate this question, we focused on the butterfly, Papilio polytes, that exhibits mimetic polymorphism on multiple islands of the Ryukyus, Japan, and performed field surveys and genetic analysis. We found that the mimic ratio of P. polytes was strongly correlated with the model abundance observed on each of the five islands, suggesting negative frequency-dependent selection is driving the evolution of polymorphism in P. polytes populations. Molecular phylogenetic analysis indicated that the southern island populations are the major source of genetic diversity, and the middle and northern island populations arose by relatively recent migration. This view was also supported by mismatch distribution and Tajima's D analyses, suggesting a recent population expansion on the middle and northern islands, and stable population persistence on the southern islands. The frequency of the mimetic forms within P. polytes populations is thus explained by variations in the model abundance rather than by population structure. Thus, we propose that predation pressure, rather than neutral forces, have shaped the Batesian mimicry polymorphism in P. polytes observed in the Ryukyus.

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Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan.

Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C

Scientific reports ( Scientific Reports )  9 ( 1 ) 6575   2019年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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東アジアにおけるヒトの遺伝適応の痕跡を求めて

木村 亮介

日本生理人類学会誌 ( 日本生理人類学会 )  24 ( 2 ) 87 - 91   2019年

掲載種別: 研究論文（学術雑誌）

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Modern humans dispersed into East Asia approximately 40K years ago and genetically adapted to unprecedentedenvironmental conditions. Signatures of local genetic adaptations, which are engraved in our genome, can bedetected using population genomics approaches. Human genome variation data have enabled a comprehensive searchfor genetic variants showing such signatures as well as for those associated with phenotypic variation. Although ourknowledge about local genetic adaptations has increased due to recent research efforts, little is known about whatselective pressures acted on the selected variants.

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Association of an intronic SNP of the EFEMP1 gene with height in Tongans

Isshiki M.

Meta Gene ( Meta Gene )  17   172 - 176   2018年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Growth hormone receptor gene is related to root length and tooth length in human teeth.

Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R

The Angle orthodontist   88 ( 5 ) 575 - 581   2018年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Association between the FGFR1 rs13317 single nucleotide polymorphism and orbitale-nasion depth based on cephalometric images.

Adel M, Yamaguchi T, Tomita D, Kim YI, Takahashi M, Nakawaki T, Hikita Y, Haga S, Nadim M, Kawaguchi A, Isa M, El-Kenany W, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R

Journal of human genetics ( Journal of Human Genetics )  63 ( 8 ) 901 - 909   2018年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The fibroblast growth factor receptor 1 (FGFR1) gene plays an important role in craniofacial morphogenesis. In our previous study, an association between FGFR1 single nucleotide polymorphisms (SNPs) and craniofacial morphology was demonstrated in Japanese and Korean subjects. The present study aimed to evaluate the relationship between a common FGFR1 SNP (rs13317) with craniofacial morphology, increasing the number of measurements and examining Egyptian subjects (n = 191) in addition to the Japanese (n = 211) and Korean (n = 226) subjects. Genotyping for rs13317 was performed using the TaqMan assay, and its associations with 81 craniofacial measurements derived from lateral and posteroanterior cephalograms were analyzed by multiple regression analysis controlling sex and facial size. The results from each of the populations were then statistically combined. In the Egyptian subjects, rs13317 was significantly associated with the nasion-orbitale depth (P = 0.00040), and a suggestive association was also observed in the Japanese (P = 0.037) and Korean subjects (P = 0.045). The combined analysis revealed that only the nasion-orbitale depth showed a significant association (P = 0.000062) and that several measurements showed a suggestive association. Our results strongly indicate that rs13317 is associated with a smaller depth between the nasion and orbitale, representing a relative protrusion of the cheekbones and retrusion of the nasal root. A similar characteristic is also observed in individuals with Pfeiffer syndrome, which is caused by a dysfunctional FGFR1 mutation.

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Relationship between tooth length and three-dimensional mandibular morphology.

Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R

The Angle orthodontist ( Angle Orthodontist )  88 ( 4 ) 403 - 409   2018年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Association study of CREBRF missense variant (rs373863828:G &gt; A; p.Arg457Gln) with levels of serum lipid profile in the Pacific populations.

Ohashi J, Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R

Annals of human biology ( Annals of Human Biology )  45 ( 3 ) 215 - 219   2018年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Spatial relationships of the bronchial arteries to the left recurrent laryngeal nerve in the sub-aortic arch area.

Hayasaka K, Ishida H, Kimura R, Nishimaki T

Surgery today ( Surgery Today )  48 ( 3 ) 346 - 351   2018年03月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Purpose: To safely perform lymphadenectomy in the sub-aortic arch area during esophagectomy for esophageal cancer, we investigated the spatial relationships between the bronchial arteries (BAs) and the left recurrent laryngeal nerve (LRLN). Methods: For this macro-anatomical study, 72 cadavers were used. Results: Of the 195 dissected BAs, 15 (7.7%) arteries ran dorsally across the LRLN. Such a running pattern of the BA was found in 15 (20.8%) of the 72 cadavers. Fourteen (93.3%) of the 15 arteries ran anteriorly along the left side of the esophagus, and 13 (86.7%) passed further to the lateral side of the left main bronchus to reach the ventral surface of the tracheobronchus we named this running pattern “Type III”. Of the 51 arteries with the Type III pattern, 25.5% ran across the dorsal side of the LRLN. Conclusion: Approximately 20% of the cadavers had BAs running dorsally to the LRLN in the sub-aortic arch area. Most of these arteries had the Type III pattern. One-quarter of the BAs with the Type III pattern showed this running pattern. Care must be practiced to safely perform lymphadenectomy for esophageal cancer in patients with Type III BAs.

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Interferon regulatory factor 6 variants affect nasolabial morphology in East Asian populations.

Tomita D, Yamaguchi T, Nakawaki T, Hikita Y, Adel M, Kim YI, Haga S, Takahashi M, Kawaguchi A, Isa M, Park SB, Ishida H, Maki K, Kimura R

Archives of oral biology ( Archives of Oral Biology )  85   142 - 147   2018年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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OBJECTIVE: The interferon regulatory factor 6 gene (IRF6) is one of the most conspicuous genes among a large number of candidate risk genes for non-syndromic cleft lip with or without cleft palate, which is considered to be a multifactorial defect. Variants of IRF6 are also suggested to affect normal craniofacial variations, especially in the area of the nose and the upper lip. In the present study, we used lateral cephalograms to establish the relationship between IRF6 and sagittal nasolabial morphology in healthy East Asian subjects. DESIGN: Genomic DNA was extracted from 215 Japanese and 226 Korean individuals, and genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs17389541, rs642961, rs2013162, rs2235371, and rs7802. These SNPs were tested by multiple regression analyses for their association with craniofacial measurements obtained from lateral cephalometrics. RESULTS: We detected a significant association between the derived variants, rs2013162 and rs2235371 and the distances between a facial bone plane indicated by distance from Nasion and Point A (NA plane) to soft tissue landmarks; the Subalare (NA-Sbal) and the Subnasale (NA-Sn) in the sagittal plane. CONCLUSION: Our results indicate that IRF6 variants play an important role in the normal range of variation in nasolabial soft-tissue morphology.

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Mitochondrial DNA variations in Austronesian-speaking populations living in the New Georgia Islands, the Western Province of the Solomon Islands.

Issiki M, Naka I, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J

Journal of human genetics ( Journal of Human Genetics )  63 ( 1 ) 101 - 104   2018年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Computed tomography examinations of the surface and internal morphologies of the upper face in Ryukyu Islanders and mainland Japanese population

ITO TSUYOSHI, KIMURA RYOSUKE, RYUKODEN AZUSA, TSUCHIYA NANAE, MURAYAMA SADAYUKI, ISHIDA HAJIME

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  126 ( 3 ) 123 - 133   2018年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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<p>Using computed tomography, we examined the surface and internal morphologies of the upper face of people living on the Ryukyu Islands and mainland Japanese, focusing on the nasal root protrusion and eyeball position. The results showed that the nasal root protrusion on the surface was influenced by a combination of changes in both hard and soft tissues, such as skeletal nasal protrusion, eyeball recession, and skin thickness. The eyeball position became more posterior as the orbital cavity height and depth increased. Compared with people originating from mainland Japan, Ryukyu Islanders had a more prominent nasal root at both surface and skeletal levels, and a lower orbital rim relative to its internal height. However, a significant difference in the eyeball position and skin thickness was not detected. Therefore, the skeletal nasal root protrusion, not soft tissue configuration, is likely to account for the difference in the surface nasal root protrusion between the two populations. These findings will contribute to a better understanding of the association between hard and soft tissue configurations and the diversification of human facial features at the individual and population levels.</p>

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ゲノム情報から人類集団間交配を考える

木村 亮介

生物科学   70   140 - 144   2018年

掲載種別: 研究論文（学術雑誌）

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A missense variant, rs373863828-A (p.Arg457Gln), of CREBRF and body mass index in Oceanic populations.

Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ataka Y, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J

Journal of human genetics ( Journal of Human Genetics )  62 ( 9 ) 847 - 849   2017年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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It has been suggested that a 'thrifty' genotype hypothesis can account for high prevalence of obesity in the island populations of Oceania. A recent genome-wide association study revealed that a missense variant, rs373863828-A (p.Arg457Gln), of the CREBRF gene (encoding CREB3 regulatory factor) was associated with an excessive increase in body mass index (BMI) in Samoans. In the present study, the association of rs373863828-A with an increase in BMI was examined in four Austronesian (AN)-speaking populations in Oceania. We found that rs373863828-A was frequently observed (frequency of 0.15) in Tongans (Polynesians), and was strongly associated with higher BMI (P=6.1 x 10(-4)). A single copy of the rs373863828-A allele increased BMI by 3.09 kg m(-2) after adjustment of age and sex. No significant association was detected in the other three AN-speaking populations (Melanesians and Micronesians) living in Solomon Islands. This was probably due to the low allele frequency (0.02-0.06) of rs373863828-A as well as small sample size. The rs373863828-A allele was not found in both AN-speaking and non-AN-speaking Melanesians living in Papua New Guinea. Our results suggest that rs373863828-A of CREBRF, a promising thrifty variant, arose in recent ancestors of AN-speaking Polynesians.

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