2024年11月, 優秀研究賞, 日本に生息するキタホウネンエビ類の分子系統解析および多型解析, 日本 DNA多型学会
北野誉;田畑光敏;高橋法人;平澤桂;五十嵐聖貴;畠中裕之;大八木昭;五十嵐敬司;梅津和夫

2017年08月, ひらめき☆ときめきサイエンス推進賞, 独立行政法人 日本学術振興会
その他の賞

Integrating Mitochondrial and Nuclear Genomic Data to Decipher the Evolutionary History of Eubranchipus Species in Japan.　　　　　　　　　　　　　　　
Kitano T; Tabata M; Takahashi N; Hirasawa K; Igarashi S; Hatanaka Y; Ooyagi A; Igarashi K; Umetsu K., 筆頭著者
Molecular Phylogenetics and Evolution, 2024年02月, ［査読有り］

Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius.　　　　　　　　　　　　　　　
Nagasawa K; Kitano T., ラスト(シニア)オーサー
Journal of Molecular Evolution, 2023年10月, ［査読有り］

Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan.　　　　　　　　　　　　　　　
Kitano T; Sato H; Takahashi N; Igarashi S; Hatanaka Y; Igarashi K; Umetsu K., 筆頭著者
BMC Zoology, 2022年02月, ［査読有り］

Identification and Characterization of Genes for the Allo A Lectins in Japanese Rhinoceros Beetle (Trypoxylus dichotomus [Allomyrina dichotoma]).　　　　　　　　　　　　　　　
Tabata M; Umetsu K; Kitano T., ラスト(シニア)オーサー, Springer
Biochemical Genetics, 2022年02月, ［査読有り］

Genetic diversity of two populations of the tufted puffin Fratercula cirrhata (Pallas, 1769).　　　　　　　　　　　　　　　
Sakurayama S; Nojima D; Yoshizawa M; Takeuchi T; Ito M; Kitano T., ラスト(シニア)オーサー
Genes & Genetic Systems, 2021年06月, ［査読有り］

Behavior of eukaryotic symbionts in large benthic foraminifers Calcarina gaudichaudii and Baculogypsina sphaerulata under exposure to wastewater.
Akther S; Suzuki J; Pokhrel P; Okada T; Imamura M; Enomoto T; Kitano T; Kuwahara Y; Fujita M, Large benthic foraminifers (LBFs) are significant contributors to coral island formation in the Pacific Ocean. In recent years, the population of LBFs has decreased because of the increase in anthropogenic influences, such as wastewater (WW) discharge. To implement efficient mitigation measures, pollution tolerance in LBFs should be understood. However, the effects of WW on LBFs and their symbionts have not yet been demonstrated. This study examined the changes in the photosynthetic efficiency (Y[II]) of Calcarina gaudichaudii and Baculogypsina sphaerulata in response to WW by using a pulse-amplitude-modulation fluorometer. These LBFs were exposed to WW with different dilution levels for 22 days. The Y(II) values of the LBFs were found to deteriorate within 1-2 days. However, the Y(II) values both deteriorated and were enhanced in the experiments, thus indicating that WW contains both harmful and beneficial components. Baculogypsina sphaerulata showed an earlier response and greater sensitivity to WW and a higher epibiont infestation than C. gaudichaudii. This result can be attributed to the differences in the physiological and morphological responses of distinct LBFs. A sequencing analysis of 18S rDNA confirmed that the dominant eukaryotic symbionts in the two LBFs studied were Ochrophyta and Labyrinthulomycetes. These eukaryotic symbionts were released and attached as epibionts onto LBFs that were exposed to WW, thus leading to an increase in inactive LBFs. The Shannon-Weaver and Simpson diversity indices revealed that eukaryotic symbiont communities decreased in biodiversity after exposure to WW because of the abundance of algal symbionts. On the basis of these results, we conclude that WW, even with 10,000 × dilution, causes a decrease in active LBF populations owing to the release of eukaryotic symbionts, the decrease in biodiversity, and the infestation of epibionts even though Y(II) is temporarily enhanced. These responses are more significant in B. sphaerulata than in C. gaudichaudii., Elsevier
Environmental Pollution, 2020年10月, ［査読有り］

Nucleotide sequencing of the HoxA gene cluster using Gorilla fosmid clones.
Kitano T; Kim CG; Saitou N., 筆頭著者, Ivyspring International Publisher
Journal of Genomics, 2020年08月29日, ［査読有り］

Evolution of the gene of the lectin, Phalera flavescens agglutinin (PFA).　　　　　　　　　　　　　　　
Sasaki K; Umetsu K; Kitano T, ラスト(シニア)オーサー
Agri Gene, 2020年03月, ［査読有り］

Evolution of S100A3 and PAD3, two important genes for mammalian hair.　　　　　　　　　　　　　　　
Minato T; Unno M; Kitano T, ラスト(シニア)オーサー
Gene, 2019年09月10日, ［査読有り］

The northern brown hagfish, Eptatretus walkeri (McMillan and Wisner, 2004) (Myxiniformes:Myxinidae), is widely distributed in Japanese coastal waters.　　　　　　　　　　　　　　　
Kitano T; Sasaki K; Ichinoseki S; Umetsu K; Sugiyama H, 筆頭著者
Asian Fisheries Science, 2019年03月31日, ［査読有り］

Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia.　　　　　　　　　　　　　　　
Takahashi N; Kitano T; Hatanaka Y; Nagahata Y; Tshistjakov YA; Hamasaki M; Moriya H; Igarashi K; Umetsu K, 責任著者
BMC Zoology, 2018年07月, ［査読有り］

Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences
Akinori Suzuki; Hidero Komata; Shogo Iwashita; Shotaro Seto; Hironobu Ikeya; Mitsutoshi Tabata; Takashi Kitano, ラスト(シニア)オーサー, In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined. Lampreys, along with hagfishes, are cyclostomata (jawless fishes), which is a sister group of gnathostomata (jawed vertebrates). Although those results suggested that one gene was orthologous to the gnathostome RHCG genes, we did not identify clear orthologues for other genes. In this study, therefore, we identified three novel cDNA sequences that belong to the RH gene family using de novo transcriptome analysis of another cyclostome: the brown hagfish (Eptatretus atami). We also determined the nucleotide sequences for the RHBG and RHCG genes in a red stingray (Dasyatis akajei), which belongs to the cartilaginous fishes. The phylogenetic tree showed that two brown hagfish genes, which were probably duplicated in the cyclostome lineage, formed a cluster with the gnathostome RHAG genes, whereas another brown hagfish gene formed a cluster with the gnathostome RHCG genes. We estimated that the RH genes had a higher evolutionary rate than the RHAG, RHBG, and RHCG genes. Interestingly, in the RHBG genes, only the bird lineage showed a higher rate of nonsynonymous substitutions. It is likely that this higher rate was caused by a state of relaxed functional constraints rather than positive selection nor by pseudogenization. (C) 2016 Elsevier Inc. All rights reserved., ACADEMIC PRESS INC ELSEVIER SCIENCE
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2017年02月, ［査読有り］

Brown hagfish from the northwest and east coasts of Honshu, Japan are genetically different
Mikihiro Kase; Takayuki Shimizu; Keita Kamino; Kazuo Umetsu; Hideki Sugiyama; Takashi Kitano, ラスト(シニア)オーサー, The brown hagfish (Eptatretus atami) is one of several known hagfish species occurring in Japanese coastal waters. To date, there has been no research studying genetic polymorphisms in the species. In the present study, we analyzed differences in nucleotide sequences between two populations: one from Suruga Bay on the Pacific coast of Honshu, Japan, and the other from the Sea of Japan, off Akita on the northwest coast of Honshu. We sequenced part of the cytochrome oxidase subunit 1 gene (COX1) from the mitochondrial genome, and three G pro-tein-coupled receptor genes from the nuclear genome. Phylogenetic networks of all four genes showed divergence between the two populations. Further, comparison of the COX1 data using a phylogenetic tree for a range of hagfish species indicated clear differences between the populations, suggesting that they differ at the species level. The numbers of their teeth, in particular of fused cusps (anterior/ posterior multicusps), also supported these findings. Individuals of the Suruga Bay population had 3/3 fused cusps, as described for E. atami, whereas individuals of the Akita population had 3/2 fused cusps. These results suggest that the brown hagfish from the Sea of Japan, off the northwest coast of Honshu, is a distinct species from E. atami., Genetics Society of Japan
Genes and Genetic Systems, 2017年, ［査読有り］

No distinction of orthology/paralogy between human and chimpanzee Rh blood group genes.　　　　　　　　　　　　　　　
Kitano T; Kim CG; Blancher A; Saitou N, 筆頭著者
Genome Biology and Evolution, 2016年02月, ［査読有り］

An N-acetyllactosamine-specific lectin, PFA, isolated from a moth (Phalera flavescens), structurally resembles an invertebrate-type lysozyme.
Kazutaka Yokoyama; Michihiko Sato; Toshihiro Haneda; Kentaro Yamazaki; Takashi Kitano; and Kazuo Umetsu, 責任著者, PFA (Phalera flavescens agglutinin) lectin purified from larvae of the lobster moth (P. flavescens) shows a strong binding ability specific to the N-acetyllactosamine (Gal beta 1-4GlcNAc) site. We determined the genomic and cDNA sequences of the PFA gene, which consists of five exons and spans approximately 5 kb of a genomic region. Surprisingly, the amino acid sequence (149 amino acids) was similar to invertebrate-type lysozymes and related proteins. The predicted tertiary structure of the PFA protein was similar to the lysozymes of clams such as the common orient clam (Meretrix lusoria) and Japanese littleneck (Venerupis philippinarum (Tapes japonica)). The PFA, however, lacks a catalytically essential amino acid, an Asp (D), which is one of the two important amino acids (Glu (E) and D) express the function of lysozyme. As a result, lysozyme activity assays indicated that PFA does not have lysozyme activity. Results suggest that the PFA gene evolved from a lysozyme gene through the loss of lysozyme activity sites and the acquisition of lectin activity during evolution of the genus Phalera. (C) 2014 Elsevier Ltd. All rights reserved., PERGAMON-ELSEVIER SCIENCE LTD
Insect Biochemistry and Molecular Biology, 2014年09月, ［査読有り］

Phylogenetic positions of RH blood group-related genes in cyclostomes.
Akinori Suzuki; Kouhei Endo; Takashi Kitano, 責任著者, The RH gene family in vertebrates consists of four major genes (RH, RHAG, RHBG, and RHCG). They are thought to have emerged in the common ancestor of vertebrates after two rounds of whole genome duplication (2R-WGD). To analyze the detailed phylogenetic relationships within the RH gene family, we determined three types of cDNA sequence that belong to the RH gene family in lamprey (Lethenteron reissneri) and designated them as RHBG-like, RHCG-like1, and RHCG-like2. Phylogenetic analyses clearly showed that RHCG-like1 and RHCG-like2 genes, which were probably duplicated in the lamprey lineage, are orthologs of gnathostome RHCG. In contrast, the clear phylogenetic position of the RHBG-like gene could not be obtained. Probably some convergent events for cyclostome RHBG-like genes prevented the accurate identification of their phylogenetic positions. (C) 2014 Elsevier B.V. All rights reserved., ELSEVIER SCIENCE BV
Gene, 2014年06月, ［査読有り］

Analysis of a Larger SNP Dataset from the HapMap Project Confirmed That the Modern Human A Allele of the ABO Blood Group Genes Is a Descendant of a Recombinant between B and O Alleles.
Masaya Itou; Mitsuharu Sato; Takashi Kitano, 責任著者, The human ABO blood group gene consists of three main alleles (A, B, and O) that encode a glycosyltransferase. The A and B alleles differ by two critical amino acids in exon 7, and the major O allele has a single nucleotide deletion (Δ261) in exon 6. Previous evolutionary studies have revealed that the A allele is the most ancient, B allele diverged from the A allele with two critical amino acid substitutions in exon 7, and the major O allele diverged from the A allele with Δ261 in exon 6. However, a recent phylogenetic network analysis study showed that the A allele of humans emerged through a recombination between the B and O alleles. In the previous study, a restricted dataset from only two populations was used. In this study, therefore, we used a large single nucleotide polymorphism (SNP) dataset from the HapMap Project. The results indicated that the A101-A201-O09 haplogroup was a recombinant lineage between the B and O haplotypes, containing the intact exon 6 from the B allele and the two critical A type sites in exon 7 from the major O allele. Its recombination point was assumed to be located just behind Δ261 in exon 6., Hindawi Limited
International Journal of Evolutionary Biology, 2013年10月, ［査読有り］

The PNarec method for detection of ancient recombinations through phylogenetic network analysis.
Naruya Saitou; Takashi Kitano, ラスト(シニア)オーサー, Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through phylogenetic network analysis, and detected five ancient recombinations in gibbon ABO blood group genes [Kitano etal., 2009. Mol. Phylogenet. Evol., 51, 465-471]. We present applications of this method, now named as "PNarec", to various virus sequences as well as HLA genes. (C) 2012 Elsevier Inc. All rights reserved., ACADEMIC PRESS INC ELSEVIER SCIENCE
Molecular Phylogenetics and Evolution, 2013年02月, ［査読有り］

Molecular evolution of the oxytocin–oxytocin receptor system in eutherians.　　　　　　　　　　　　　　　
Kaoru Yamashita; Takashi Kitano, 責任著者
Molecular Phylogenetics and Evolution, 2013年02月, ［査読有り］

The Functional A Allele Was Resurrected via Recombination in the Human ABO Blood Group Gene.
Takashi Kitano; Antoine Blancher; Naruya Saitou, 筆頭著者, Functional A and B alleles are distinguished at two critical sites in exon 7 of the human ABO blood group gene. The most frequent nonfunctional O alleles have one-base deletion in exon 6 producing a frameshift, and it has the A type signature in two critical sites in exon 7. Previous studies indicated that B and O alleles were derived from A allele in human lineage. In this study, we conducted a phylogenetic network analysis using six representative haplotypes: A101, A201, B101, O01, O02, and O09. The result indicated that the A allele, possibly once extinct in the human lineage a long time ago, was resurrected by a recombination between B and O alleles less than 300,000 years ago., OXFORD UNIV PRESS
Molecular Biology and Evolution, 2012年07月, ［査読有り］

Mitochondrial DNA Analysis of Hokkaido Jomon Skeletons: Remnants of Archaic Maternal Lineages at the Southwestern Edge of Former Beringia.
Noboru Adachi; Ken-ichi Shinoda; Kazuo Umetsu; Takashi Kitano; Hirofumi Matsumura Ryuzo Fujiyama; Junmei Sawada; Masashi Tanaka, To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present. Am J Phys Anthropol 146:346-360, 2011. (C) 2011 Wiley-Liss, Inc., WILEY-BLACKWELL
American Journal of Physical Anthropology, 2011年11月, ［査読有り］

Evolution of two Rh blood group-related genes of the amphioxus species Branchiostoma floridae.
Takashi Kitano; Masahiro Satou; Naruya Saitou., 筆頭著者, We determined cDNAs of two genes that belong to the Rhesus (Rh) blood group gene family in an amphioxus species (Branchiostoma floridae) and designated them Rh-related-1 (RhR-1) and Rh-related-2 (RhR-2). RhR-1 and RhR-2 consisted of 10 and 11 exons, respectively. 3' UTR sequences of RhR-1 were shorter (220-272 bp) than those of RhR-2 (1,505-1,650 bp). CDS lengths were 1,344 and 1,476 bp for RhR-1 and RhR-2, respectively, and the average nucleotide difference between their CDS regions was 0.33. The corresponding regions of Rh genes from exons 2 to 7 were relatively conserved among the chordate species examined in this study. Length difference numbers were in multiples of three, which implies that codon frames were conserved among them, and the same exon/intron boundary phases were observed in those regions. This region was used for the phylogenetic analyses. RhR-1 and RhR-2 formed a cluster on the phylogenetic tree of the Rh gene family. Gene duplication time of RhR-1 and RhR-2 was estimated to be ca. 500 million years ago. It is likely that the four Rh family genes in vertebrates emerged by gene duplications in the common ancestor of vertebrates, and functional differentiation has occurred after the first gene duplication., GENETICS SOC JAPAN
Genes & Genetic Systems, 2010年04月, ［査読有り］

Distinct C-terminus of the B subunit of factor XIII in a population-associated major phenotype: the first case of complete allele-specific alternative splicing products in the coagulation and fibrinolytic systems.
Hiroki Iwata; Takashi Kitano; Kazuo Umetsu; Isao Yuasa; Kentaro Yamazaki; Bettina Kemkes-Matthes; Akitada Ichinose., Objectives: The purpose of this study was to elucidate the molecular bases of the heterogeneity of the B subunit of coagulation factor XIII (FXIII-B), classified by isoelectric focusing into its three population-associated major phenotypes. Methods and Results: By genetic sequencing and polymerase chain reaction (PCR)-restriction fragment length polymorphism analyses, a C-to-G change was identified in intron K for the Asian-associated major phenotype FXIII-B*3. A transcript containing the novel exon XII' was detected by reverse transcription PCR using hepatocyte cell lines with this allele. The exclusive existence of a novel C-terminal peptide in a homozygote of FXIII-B*3 was also detected by matrix-assisted laser-desorption ionization time of flight mass spectrometry. The FXIII-B*3 isoform had a C-terminus 15 residues longer than the other isoforms, containing two additional basic amino acids and one extra acidic amino acid. Accordingly, the C-to-G nucleotide substitution created an efficient splice acceptor AG dinucleotide, which resulted in allele-specific alternative splicing in intron K. When compared with FXIII-B*1, the third major phenotype, FXIII-B*2, had an A-to-G change in exon III, converting His95 to Arg, and a rare phenotype, FXIII-B*4, had an A-to-T change in exon VII, converting Glu368 to Val. Conclusions: We found an extremely rare event of complete allele-specific alternative splicing for FXIII-B. The FXIII-B*3 isoform had a distinct C-terminal peptide, while the FXIII-B*2 and FXIII-B*4 isoforms had His95 to Arg and Glu368 to Val substitutions, respectively, which led to differential isoelectric points of these isoforms. Such variations in the amino acid sequence of FXIII-B may have profound effects on its structure-function relationship, plasma FXIII levels, and disease susceptibility., WILEY-BLACKWELL PUBLISHING, INC
Journal of Thrombosis and Haemostasis, 2009年07月, ［査読有り］

Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis.
Takashi Kitano; Reiko Noda; Osamu Takenaka; Naruya Saitou., 筆頭著者, The primate ABO blood group gene encodes a glycosyl transferase (either A or B type), and is known to have large coalescence times among the allelic lineages in human. We determined nucleotide sequences of ca. 2.2 kb of this gene for 23 individuals of three gibbon species (agile gibbon, white-handed gibbon, and siamang), and observed a total of 24 haplotypes. We found relics of five ancient intragenic recombinations, occurred during ca. 2-7 million years ago, through a phylogenetic network analysis. The coalescence time between A and B alleles estimate precede the divergence (ca. 8 MYA) of siamang and common gibbon lineages. This establishes the coexistence of divergent allelic lineages of the ABO blood group gene for a long period in the ancestral gibbon species, and strengthens the non-neutral evolution for this gene. (C) 2009 Elsevier Inc. All rights reserved., ACADEMIC PRESS INC ELSEVIER SCIENCE
Molecular Phylogenetics and Evolution, 2009年06月, ［査読有り］

Allele frequencies of a SNP and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene.
Takashi Kitano; Isao Yuasa; Kentaro Yamazaki; Nori Nakayashiki; Aya Miyoshi; Kyung Sook Park; Kazuo Umetsu., 筆頭著者, Allele frequencies for a SNP (rs17822931) and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene were investigated in seven Japanese, one Korean, and one German populations. The SNP will be useful as one of ancestry information markers, because it showed marked difference in frequencies between Asian and European populations. © 2007 Elsevier Ireland Ltd. All rights reserved.
Legal Medicine, 2008年03月, ［査読有り］

Mitochondrial DNA Sequence Phylogeny of 4 Populations of the Widely Distributed Cynomolgus Macaque (Macaca fascicularis fascicularis).
Antoine Blancher; Maxime Bonhomme; Brigitte Crouau-Roy; Keiji Terao; Takashi Kitano; Naruya Saitou., We studied the mitochondrial DNA (mtDNA) polymorphism of 304 Macaca fascicularis fascicularis (M. f. fascicularis) individuals, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius). By sequencing a 590-bp fragment in the hypervariable II region of the D-loop region, we defined 70 haplotypes. The homologous region was also characterized in 22 Chinese Macaca mulatta and 2 Macaca sylvanus. The phylogenetic analysis confirms the monophyly of M. f. fascicularis and defines 2 haplotype groups inside the M. f. fascicularis clade: one "insular," encompassing 6 Philippines, 2 Mauritius, and 31 Indonesian haplotypes, the other "continental" that contains all Indochinese and 6 Indonesian haplotypes. Continental and insular group divergence time was estimated to be approximately 106 years before present (BP). Among Indonesian haplotypes, some have a continental origin. This suggests either direct migration from mainland to Indonesia or that remnant lineages from an ancient population genetically close to the mainland (i.e., in the Sunda Shelf, <
550 000 years BP) were subsequently brought southward to Indonesia. The low nucleotide diversity in the Philippines population suggests a bottleneck following colonization by Indonesian individuals, around 110 000 years BP. mtDNA and further observations of nuclear genetic data corroborate the mixed origin (Indonesian/continental) hypothesis of Mauritius individuals and a population bottleneck. © The American Genetic Association. 2008. All rights reserved.
Journal of Heredity, 2008年03月, ［査読有り］

Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies.
Yu-Hua Liu; Aya Takahashi; Takashi Kitano; Tsuyoshi Koide; Toshihiko Shiroishi; Kazuo Moriwaki; Naruya Saitou., Patterns of genetic variation provide insight into the evolutionary history of a species. Mouse (Mus musculus) is a good model for this purpose. Here we present the analysis of genealogies of the 21 nuclear loci and one mitochondrial DNA region in M. musculus based on our nucleotide sequences of nine inbred strains from three M. musculus subspecies (musculus, domesticus, and castaneus) and one M. spicilegus strain as an outgroup. The mitochondrial DNA gene genealogy of those strains confirmed the introgression pattern of one musculus strain. V hen all the nuclear DNA data were concatenated to produce a phylogenetic tree of nine strains, musculus and domesticus strains formed monophyletic clusters with each other, while the two castaneus strains were paraphyletic. When each DNA region was treated independently, the phylogenetic networks revealed an unnegligibly high level of subspecies admixture and the mosaic nature of their genome. Estimation of ancestral and derived population sizes and migration rates suggests the effects of ancestral polymorphism and gene flow on the pattern of genetic variation of the current subspecies. Gene genealogies of Fut4 and Dfy loci also suggested existence of the gene flow between M. musculus and M. spicilegus or other distant species., GENETICS SOC JAPAN
Genes & Genetic Systems, 2008年02月, ［査読有り］

Two universal primer sets for species identification among vertebrates.
Takashi Kitano; Kazuo Umetsu; Wei Tian; Motoki Osawa., 筆頭著者, The aim of this study was to develop a simple method using universal primers for species identification based on direct PCR sequencing. Two primer sets were designed based on the conserved regions of the 12S and 16S rRNA loci detected by the comprehensive sequence comparison among 30 mammalian whole mitochondrial genomes. In humans, the expected sizes of PCR products of the 12S and 16S rRNAs were 215 and 244 bp, respectively. Both primer sets successfully amplified the expected PCR products from various kinds of vertebrates including mammals, birds, reptiles, amphibians, and fish, and the sequenced segments contained sufficient nucleotide differences to identify each animal species. A case example of the identification of a piece of buried bone of unknown species is presented, and the species was identified as a pig by this method., SPRINGER
International Journal of Legal Medicine, 2007年09月, ［査読有り］

Tempo and mode of evolution of the Rh blood group genes before and after gene duplication.
Takashi Kitano; Kazuo Umetsu; Wei Tian; Kentaro Yamazaki; Naruya Saitou., 筆頭著者, The Rh blood group genes became duplicated in a common ancestor of human-chimpanzee-gorilla. We compared the evolutionary rates of the Rh blood group genes for each exon for branches connecting to humans, having duplicated Rh loci, and to orangutan, gibbon, and Old World monkeys, species having a single Rh locus. Our results show that evolutionary rates of nonsynonymous substitutions at exon 7 became accelerated in the human lineage. Furthermore, we surveyed the sequence variation in the region surrounding exon 7 of gibbons to clarify whether the diversity of the human exon 7 was introduced after the duplication or had been maintained before it. Two amino acid polymorphisms in white-handed gibbons were observed in the immediate vicinity of the D-specific motif in the human exon 7. Although the evolutionary rate of exon 7 was accelerated after the gene duplication, our results suggest that exon 7 had the potential for change even before the gene duplication., SPRINGER
Immunogenetics, 2007年05月, ［査読有り］

Origin and evolution of gene for prolactin-induced protein.
Takashi Kitano; Wei Tian; Kazuo Umetsu; Isao Yuasa; Kentaro Yamazaki; Naruya Saitou; Motoki Osawa., 筆頭著者, Prolactin-induced protein (PIP) is a small protein secreted into the fluid in several glands. We determined the PIP coding sequences of 5 hominoid species and estimated the numbers of synonymous and nonsynonymous substitutions for each branch of the mammalian PIP gene tree. The branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions. These changes tended to be accumulated in the fibronectin-binding domain. Many other primate branches also showed higher nonsynonymous than synonymous substitutions, thus suggesting that the PIP genes of primates have experienced some kind of positive selection. We also considered the phylogenetic relationship of the PIP gene with the alpha-2-macroglobulin gene family. The results indicate that the PIP gene arose by partial gene duplication from a member of the alpha-2-macroglobulin gene family after the divergence between amphibians and other tetrapods. (c) 2006 Elsevier B.V. All rights reserved., ELSEVIER SCIENCE BV
Gene, 2006年11月, ［査読有り］

Conservation of a platelet activating domain of Aggrus/podoplanin as a platelet aggregation-inducing factor.
Mika Kato-Kaneko; Yukinari Kato; Takashi Kitano; Motoki Osawa., Human Aggrus/podoplanin is an identified platelet aggregation-inducing factor of cancer cells, which is also known as a specific marker of lymphatic endothelium. Human Aggrus was known to be expressed in seminoma, squamous cell carcinoma, malignant mesothelioma, sarcomas and several brain tumors. In our previous studies, the sialylated O-glycan of human and mouse Aggrus were shown to be critical for its platelet aggregation-inducing activity in the experiments using the glycosylation-deficient Chinese hamster ovary (CHO) cell lines. We newly cloned Aggrus homologues from rat, hamster, dog and bovine cDNAs, in addition to the human and mouse CDNAs, and confirmed there are three tandem repeats of the platelet aggregation-stimulating (PLAG) domain in Aggrus, which were conserved in all homologues. We found that bovine Aggrus has a sporadic deletion mutation in the first PLAG domain, and lacks platelet aggregation-inducing activity. We introduced point mutation in the PLAG domain of Aggrus and showed that either the first or last PLAG domain is critical for activity, but not the middle domain. In addition, we studied the molecular evolutionary process of the PLAG domain of Aggrus. The PLAG domain and its activity appeared after the divergence of avians and mammals. In conclusion, we provide evidence that Aggnis homologues conserved the segment of EDxxVTPG in their extracellular domain which are critical for their platelet aggregation-inducing activities. (c) 2006 Elsevier B.V. All rights reserved., ELSEVIER SCIENCE BV
Gene, 2006年08月, ［査読有り］

Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes.
Takashi Kitano; Naruya Saitou., 筆頭著者, Nucleotide sequences of nine 5' upstream gene regions for human, chimpanzee, gorilla, and orangutan were determined. We estimated nucleotide differences (d) for each region between human and great apes. The overall d was 0.027 (ranged from 0.004 to 0.052). Rates of nucleotide substitution were estimated by using d and divergence times of human, chimpanzee, gorilla, and orangutan. The overall rate of nucleotide substitution between human and other hominoids was estimated to be 0.52-0.85 x 10(-9). This rate in 5' upstream regions was lower than that of synonymous sites, suggesting that 5' upstream regions have evolved under some functional constraints. Because lower rates have been reported for coding sequences in primates compared to rodents, we also estimated the rate (1.17-1.76 x 10-9) of nucleotide substitutions for the corresponding 5' upstream regions in rodents (mouse/rat comparison). Thus the primate rate was lower than rodent rate also for the 5' upstream regions., GENETICS SOC JAPAN
Genes & Genetic Systems, 2005年06月, ［査読有り］

Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes.
Shimada MK; Kim CG; Kitano T; Ferrell RE; Kohara Y; Saitou N., Chromosome rearrangement has been considered to be important in the evolutionary process. Here, we demonstrate the evolutionary relationship of the rearranged human chromosome 12 and the corresponding chromosome XII in apes (chimpanzee, bonobo, gorilla, orangutan, and gibbon) by examining PCR products derived from the breakpoints of inversions and by conducting shotgun sequencing of a gorilla fosmid clone containing the breakpoint and a "duplicated segment" (duplicon). We confirmed that a pair of 23-kb duplicons flank the breakpoints of inversions on the long and short arms of chimpanzee chromosome XII. Although only the 23-kb duplicon on the long arm of chimpanzee chromosome XII and its telomeric flanking sequence are found to be conserved among the hominoids (human, great apes, and gibbons), the duplicon on the short arm of chimpanzee chromosome XII is suggested to be the result of a duplication from that on the long arm. Furthermore, the shotgun sequencing of a gorilla fosmid indicated that the breakpoint on the long arm of the gorilla is located at a different position 1.9 kb from that of chimpanzee. The region is flanked by a sequence homologous to that of human chromosome 6q22. Our findings and sequence analysis suggest a close relationship between segmental duplication and chromosome rearrangement (or breakpoint of inversion) in Hominoidea. The role of the chromosome rearrangement in speciation is also discussed based on our new results. Copyright (C) 2005 S. Karger AG, Basel., KARGER
Cytogenetic and Genome Research, 2005年01月, ［査読有り］

Polymorphisms in the trace amine receptor 4 (TRAR4) gene on chromosome 6q23.2 are associated with susceptibility to schizophrenia.
Jubao Duan; Maria Martinez; Alan R Sanders; Cuiping Hou; Naruya Saitou; Takashi Kitano; Bryan J Mowry; Raymond R Crowe; Jeremy M Silverman; Douglas F Levinson; Pablo V Gejman., Several linkage studies across multiple population groups provide convergent support for a susceptibility locus for schizophrenia-and, more recently, for bipolar disorder-on chromosome 6q13-q26. We genotyped 192 European-ancestry and African American (AA) pedigrees with schizophrenia from samples that previously showed linkage evidence to 6q13-q26, focusing on the MOXD1-STX7-TRARs gene cluster at 6q23.2, which contains a number of prime candidate genes for schizophrenia. Thirty-one screening single-nucleotide polymorphisms (SNPs) were selected, providing a minimum coverage of at least 1 SNP/20 kb. The association observed with rs4305745 (P = .0014) within the TRAR4 (trace amine receptor 4) gene remained significant after correction for multiple testing. Evidence for association was proportionally stronger in the smaller AA sample. We performed database searches and sequenced genomic DNA in a 30-proband subsample to obtain a high-density map of 23 SNPs spanning 21.6 kb of this gene. Single-SNP analyses and also haplotype analyses revealed that rs4305745 and/or two other polymorphisms in perfect linkage disequilibrium (LD) with rs4305745 appear to be the most likely variants underlying the association of the TRAR4 region with schizophrenia. Comparative genomic analyses further revealed that rs4305745 and/or the associated polymorphisms in complete LD with rs4305745 could potentially affect gene expression. Moreover, RT-PCR studies of various human tissues, including brain, confirm that TRAR4 is preferentially expressed in those brain regions that have been implicated in the pathophysiology of schizophrenia. These data provide strong preliminary evidence that TRAR4 is a candidate gene for schizophrenia
replication is currently being attempted in additional clinical samples., University of Chicago Press
American Journal of Human Genetics, 2004年09月, ［査読有り］

Human specific amino acid changes found in 103 protein coding genes.
Takashi Kitano; Yu-Hua Liu; Shintaroh Ueda; Naruya Saitou., 筆頭著者, humans have many characteristics that are different from those of the great apes. These human-specific characters must have arisen through mutations accumulated in the genome of our direct ancestor after the divergence of the last common ancestor with chimpanzee. Gene trees of human and great apes are necessary for extracting these human-specific genetic changes. We conducted a systematic analysis of 103 protein-coding genes for human, chimpanzee, gorilla, and orangutan. Nucleotide sequences for 18 genes were newly determined for this study, and those for the remaining genes were retrieved from the DDBJ/EMBL/GenBank database. The total number of amino acid changes in the human lineage was 147 for 26,199 codons (0.56%). The total number of amino acid changes in the human genome was, thus, estimated to be about 80,000. We applied the acceleration index test and Fisher's synonymous/nonsynonymous exact test for each gene tree to detect any human-specific enhancement of amino acid changes compared with ape branches. Six and two genes were shown to have significantly higher nonsynonymous changes at the human lineage from the acceleration index and exact tests, respectively. We also compared the distribution of the differences of the nonsynonymous substitutions on the human lineage and those on the great ape lineage. Two genes were more conserved in the ape lineage, whereas one gene was more conserved in the human lineage. These results suggest that a small proportion of protein-coding genes started to evolve differently in the human lineage after it diverged from the ape lineage., OXFORD UNIV PRESS
Molecular Biology and Evolution, 2004年05月, ［査読有り］

DNA sequence and comparative analysis of chimpanzee chromosome 22.
Hidemi Watanabe et al., Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized., NATURE PUBLISHING GROUP
Nature, 2004年05月, ［査読有り］

Gene diversity patterns at ten X-chromosomal loci in humans and chimpanzees.
Takashi Kitano; Carsten Schwarz; Birgit Nickel; Svante Paabo., 筆頭著者, We have investigated the pattern and extent of nucleotide diversity in 10 X-chromosomal genes where mutations are known to cause mental retardation in humans. For each gene, we sequenced the entire coding region from cDNA in humans, chimpanzees, and orangutans, as well as about 3 kb of genomic DNA in 20 humans sampled worldwide and in 10 chimpanzees representing two "subspecies." Overall nucleotide diversity in these genes is about twofold lower in humans than in chimpanzees, and nucleotide diversity within and between species is low, suggesting that a high level of functional constraint acts on these genes. Strikingly, we find that a summary of the allele frequency spectrum is significantly correlated in humans and chimpanzees, perhaps reflecting very similar levels of constraint at these genes in the two species. A possible exception is FMR2, which shows a higher number of nonsynonymous than synonymous substitutions on the human lineage, suggesting the action of positive selection., OXFORD UNIV PRESS
Molecular Biology and Evolution, 2003年08月, ［査読有り］

Evolution of the cystatin B gene: implications for the origin of its variable dodecamer tandem repeat in humans.
Motoki Osawa; Mika Kaneko; Hidekazu Horiuchi; Takashi Kitano; Yoshi Kawamoto; Naruya Saitou; Kazuo Umetsu., The human cystatin B gene contains a variable number of 12-bp tandem repeats in its promoter region, of which the common alleles contain two or three copies and unusual expansion causes progressive myoclonus epilepsy of the Unverricht-Lundborg type. We undertook a comprehensive analysis of the genomic sequence to address the evolutionary events of this variable repeat. By examination of a contiguous genome sequence spanning 5.0 kb and linkage analysis of detected polymorphic changes, we identified six major intragenic haplotypes in unrelated Japanese subjects. The number of normal repeats was closely correlated with these alleles, indicating that changes in the array should be comparatively rare events during human evolution. To examine the origin of the repeat array further, we also analyzed five primate genomes. Repetitive polymorphism was unlikely in hominoids, and the array originated with the dodecamer itself in the course of primate evolution. The variability conceivably developed after the separation to humans. (C) 2003 Elsevier Science (USA). All rights reserved., ACADEMIC PRESS INC ELSEVIER SCIENCE
Genomics, 2003年01月, ［査読有り］

Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication
Y Sakaki; H Watanabe; T Taylor; M Hattori; A Fujiyama; A Toyoda; Y Kuroki; T Itoh; N Saitou; S Oota; CG Kim; T Kitano; H Lehrach; ML Yaspo; R Sudbrak; A Kahla; R Reinhardt; M Kube; M Platzer; S Taenzer; P Galgoczy; A Kel; H Bloecker; M Scharfe; G Nordsiek; Hellmann, I; P Khaitovich; S Paabo; Z Chen; SY Wang; SX Ren; XL Zhang; HJ Zheng; GF Zhu; BF Wang; GP Zhao; SF Tsai; K Wu; TT Liu; KJ Hsiao; HS Park; YS Lee; JE Cheong; SH Choi, COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY, 2003年

Molecular evolution of FOXP2, a gene involved in speech and language.
Wolfgang Enard; Molly Przeworski; Simon E Fisher; Cecilia SL Lai; Victor Wiebe; Takashi Kitano; Anthony P Monaco; Svante Paabo., Language is a uniquely human trait likely to have been a prerequisite for the development of human culture. The ability to develop articulate speech relies on capabilities, such as fine control of the larynx and mouth(1), that are absent in chimpanzees and other great apes. FOXP2 is the first gene relevant to the human ability to develop language(2). A point mutation in FOXP2 co-segregates with a disorder in a family in which half of the members have severe articulation difficulties accompanied by linguistic and grammatical impairment(3). This gene is disrupted by translocation in an unrelated individual who has a similar disorder. Thus, two functional copies of FOXP2 seem to be required for acquisition of normal spoken language. We sequenced the complementary DNAs that encode the FOXP2 protein in the chimpanzee, gorilla, orang-utan, rhesus macaque and mouse, and compared them with the human cDNA. We also investigated intraspecific variation of the human FOXP2 gene. Here we show that human FOXP2 contains changes in amino-acid coding and a pattern of nucleotide polymorphism, which strongly suggest that this gene has been the target of selection during recent human evolution., NATURE PUBLISHING GROUP
Nature, 2002年08月, ［査読有り］

Extreme mtDNA homogeneity in continental Asian populations.
Hiroki Oota; Takashi Kitano; Feng Jin; Isao Yuasa; Li Wang; Shintaroh Ueda; Naruya Saitou; Mark Stoneking., Mitochondrial DNA (mtDNA) variation in continental Asia has not been well-studied. Here, we report mtDNA HV1 sequences for 84 Xi'an and 82 Changsha Han Chinese, 89 Honshu Japanese, and 35 Vietnamese. Comparison of these sequences with other Asian mtDNA sequences reveals high variability within populations, but extremely low differentiation among Asian populations. Correlations between genetic distance and geographic distance, based on mtDNA and Y chromosome variation, indicate a higher migration rate in females than in males. This may reflect patrilocality, as suggested previously, but another plausible hypothesis is that the demographic expansion associated with the spread of agriculture in Asia may be responsible for the extreme genetic homogeneity in Asia. (C) 2002 Wiley-Liss., WILEY-LISS
American Journal of Physical Anthropology, 2002年06月, ［査読有り］

Functional genomics in the chimpanzee. In: Progress-Report 1999-2002.　　　　　　　　　　　　　　　
Enard W; Ebersberger I; Fischer A; Heissig F; Hellmann I; Hoffner B; Khaitovich P; Kitano T; Kohler K; Metzler D; Nickel B; Przeworski M; Schwarz C; Nowick K; Wiebe V; Winkler M; Zollner S; Paabo S
German Human Genome Project, 2002年

Haplotype analysis of the human alpha2-HS glycoprotein (fetuin) gene.
Motoki Osawa; Isao Yuasa; Takashi Kitano; Jürgen Henke; Mika Kaneko; Toshifumi Udono; Naruya Saitou; Kazuo Umetsu., Alpha2-HS glycoprotein (AHSG), which is equivalent to fetuin in other species, is a protein found in human plasma. AHSG is polymorphic with two common alleles and many variants. To examine the intragenic haplotypes and their diversity at this locus, a contiguous genomic DNA sequence (10.3 kb) was analyzed in 20 samples (40 chromosomes), and haplotypes were determined for 309 subjects. Judging from the aligned nucleotide sequences and the conserved amino acid residues comparing human and chimpanzee AHSG, it was concluded that the type 1 allele is probably older and has evolved into four major suballeles. The type 2 allele was generated from one branch of the type 1 allele. AHSG*3 and *5 variants were each found to have a single nucleotide change in exon 7, resulting in the change of an amino acid residue from Arg(299) to Cys and from Asp(258) to Asn, respectively. It was noted that the AHSG*3 mutation gives rise to an additional cysteine residue, which possible affects the conformation of the protein. The AHSG gene was found to have a low mutation rate adn no apparent recombination events. Furthermore, the detected substitutions were nonhomogeneously distributed at this locus. In particular, four nonsynonymous substitutions were concentrated in the carboxyl-terminal domain., CAMBRIDGE UNIV PRESS
Annals of Human Genetics, 2001年01月, ［査読有り］

Gene diversity of chimpanzee ABO blood group genes elucidated from exon 7 sequences.
Sumiyama K; Kitano T; Noda R; Ferrell RE; and Saitou N., Human and non-human primate ABO blood group genes show relatively large numbers of nucleotide differences. In this study, we determined exon 7 sequences for 10 individuals of common chimpanzee and for four individuals of bonobo to estimate nucleotide diversities among them. Sequence data showed the existence of chimpanzee specific 9-base deletion in the beginning of the exon 7 coding region. From a phylogenetic network of exon 7 sequences of ABO blood group genes for human, common chimpanzee, bonobo and gorilla, effects of parallel substitutions and/or some kinds of convergent events are inferred in the chimpanzee lineage. We also estimated nucleotide diversities for common chimpanzee and bonobo ABO blood group genes, and these values were 0.4% and 0.2%, respectively. These values are higher than that of most human genes. (C) 2000 Elsevier Science B.V. All rights reserved., ELSEVIER SCIENCE BV
Gene, 2000年12月, ［査読有り］

Evolutionary history of the Rh blood group-related genes in vertebrates.
Kitano T; Saitou N., 筆頭著者, Rh and its homologous Rh50 gene products are considered to form heterotetramers on erythrocyte membranes. Rh protein has Rh blood group antigen sites, while Rh50 protein does not, and is more conserved than Rh protein. We previously determined both Rh and Rh50 gene cDNA coding regions from mouse and rat, and carried out phylogenetic analyses. In this study, we determined Rh50 gene cDNA coding regions from African clawed frog and Japanese medaka fish, and examined the long-term evolution of the Rh blood group and related genes. We constructed the phylogenetic tree from amino acid sequences. Rh50 genes of African clawed frog and Japanese medaka fish formed a cluster with mammalian Rh50 genes. The gene duplication time between Rh and Rh50 genes was estimated to be about 510 million years ago based on this tree. This period roughly corresponds to the Cambrian, before the divergence between jawless fish and jawed vertebrates. We also BLAST-searched an amino acid sequence database, and the Rh blood group and related genes were found to have homology with ammonium transporter genes of many organisms. Ammonium transporter genes can he classified into two major groups (amt alpha and amt beta). Both groups contain genes from three domains (bacteria, archaea, and eukaryota). The Rh blood group and related genes are separated from both amt alpha and beta groups., SPRINGER-VERLAG
Immunogenetics, 2000年08月, ［査読有り］

Evolution of the ABO blood group gene in Japanese macaque.
Noda R; Kitano T; Takenaka O; and Saitou N., We determined 5 sequences of Japanese macaque ABO blood group gene exon 7 (ca. 0.5kb) and 2 sequences for exon 5 and intron 6 (ca. 1.7kb). We compared those data with published sequences of other Old World monkey species, and the results suggest that alleles A and B were polymorphic in the ancestral species of macaques, and that B type allele evolved independently in macaque and baboon lineages., GENETICS SOC JAPAN
Genes & Genetic Systems, 2000年06月, ［査読有り］

Gene diversity of chimpanzee ABO blood group genes elucidated from intron 6 sequences.
Takashi Kitano; Reiko Noda; Kenta Sumiyama; Robert E Ferrell; Naruya Saitou., 筆頭著者, The human and nonhuman primate ABO blood group gene shows relatively large numbers of nucleotide differences around the exon 7 region. In this study we determined intron 6 sequences for 9 alleles of common chimpanzee and for 3 alleles of bonobo to estimate nucleotide diversities among them. Sequence length polymorphisms are observed in this region as a repeat appears one to five times. From a phylogenetic network of intron 6 sequences of ABO blood group genes for humans, common chimpanzee, and bonobo, parallel substitutions and/or some kinds of convergent events are predicted in the chimpanzee lineage. We also estimated nucleotide diversities for common chimpanzee and bonobo ABO blood group genes; these values were 0.219% and 0.208%, respectively., OXFORD UNIV PRESS INC
Journal of Heredity, 2000年, ［査読有り］

Evolution of Rh blood group genes have experienced gene conversions and positive selection.
Kitano T; Saitou N., 筆頭著者, There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having 12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of human and nonhuman primate Ph genes, and the network patterns suggested the occurrences of gene conversions. We therefore used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions. After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher nonsynonymous than synonymous substitutions; this suggests that the Ph genes have experienced some kind of positive selection., SPRINGER VERLAG
Journal of Molecular Evolution, 1999年11月, ［査読有り］

Molecular evolutionary analyses of the Rh blood group genes and Rh50 genes in mammals.
Kitano T; OOta S; and Saitou N., 筆頭著者, All mammals probably possess the Rh blood group gene and its homologous Rh50 gene coded membrane proteins. In this study, we compared nucleotide sequences of Rh and Rh50 genes for primates and rodents. We found that the rates of synonymous substitutions of both genes were roughly constant, and the divergence time between mouse and rat was estimated to be about 30 million years ago (mya). Heterogeneity of the evolutionary rate between primates and rodents was suggested. We also compared amino acid changes of outer-, inner-, and trans-membrane regions of the Rh and Rh50 proteins. Amino acid changes of outer-membrane regions were more frequent except for primate Rh genes. To obtain an improved estimation of divergence time, it is better to have multiple calibration points for the molecular clock. The time of gene duplication that produced the Rh and Rh50 genes was estimated to be about 340-380 mya., ACAD SINICA INST ZOOLOGY
Zoological Studies, 1999年10月, ［査読有り］

DDBJのホームページを用いた配列解析
北野 誉; 斎藤成也, The DDBJ (DNA Data Bank of Japan) home page features a submission system of nucleotide sequence data (SAKURA) and various tools for analyses of nucleotide and amino acid sequence data.
In this manuscript, we explain the methods of data retrieval by key words search, homology search, and multiple alignment using the DDBJ home page., GAKUSHIN PUBL CO
Trends in Glycoscience and Glycotechnology, 1999年05月

Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene.
Kitano T; Sumiyama K; Shiroishi T; and Saitou N., 筆頭著者, We have sequenced the complete coding region of the Rh blood group gene for mouse and rat and that of Rh-related 50 kD glycoprotein (Rh50) for mouse, rat, and crab-eating macaque. Phylogenetic analyses of Rh and Rh50 amino acid sequences indicate that the Rh50 gene has been evolving about two times more slowly than the Rh blood group gene in both primates and rodents. This conservative nature of the Rh50 gene suggests its relative importance to the Rh blood group gene. The time of gene duplication that produced the Rh and Rh50 genes was estimated to be about 240-310 million years ago. We also conducted window analyses of synonymous and nonsynonymous nucleotide substitutions for those two genes. Some peaks where nonsynonymous substitutions are higher than synonymous ones were located on outer membrane regions. This suggests the existence of positive Darwinian selection on Rh and Rh50 genes through host-parasite interactions. (C) 1998 Academic Press., ACADEMIC PRESS INC
Biochemical and Biophysical Research Communications, 1998年08月, ［査読有り］

Phylogenetic relationship of the genus Oncorhynchus species inferred from nuclear and mitochondrial markers.
Kitano T; Matsuoka N; Saitou N., 筆頭著者, The phylogenetic relationship among the salmonid fishes of the genus Oncorhynchus has been analyzed using various kinds of markers for a long time. However, there are three major disagreements among those studies; (1) the authenticity of the Pacific salmon group as a monophyletic cluster, (2) the phylogenetic relationship among three Pacific salmons (pink salmon, sockeye salmon, and chum salmon), and (3) the phylogenetic position of masu salmon. We used allozyme electrophoresis to clarify the phylogenetic relationship between the Pacific salmon group and the Pacific trout group. Furthermore, we reanalysed published mitochondrial DNA D-loop sequences (Shedlock et al., 1992). Allozymic data and mtDNA data indicated the following consistent results; (1) all Pacific salmons formed a monophyletic cluster, (2) chum salmon and pink salmon were clustered within those Pacific salmons, (3) masu salmon formed a cluster with other Pacific salmons and diverged first in this group., GENETICS SOC JAPAN
Genes & Genetic Systems, 1997年02月, ［査読有り］

Biochemical evidence for the genetic differentiation between the two osmerid fishes, Hypomesus nipponensis and H. pretiosus japonicus　　　　　　　　　　　　　　　
Matsuoka N; Kitano T; Yamazaki M
The Science Reports of the Hirosaki University, 1995年

Detection of recombinations through phylogenetic network construction
Naruya Saitou; Takashi Kitano
GENES & GENETIC SYSTEMS, 2012年12月

類人猿とヒトのゲノム進化研究
北野誉; 斎藤成也
生体の科学, 2004年

〔主要な業績〕Genomics of Foraminiferal Symbionts. In Reference Module in Life Sciences　　　　　　　　　　　　　　　
Akther S; Kitano T; Fujita M, 共著
Elsevier, 2023年02月28日, ［査読有り］

日本に生息するキタホウネンエビ類の分子系統解析および多型解析　　　　　　　　　　　　　　　
北野誉; 田畑 光敏; 高橋 法人; 平澤 桂; 五十嵐 聖貴; 畠中 裕之; 大八木 昭; 五十嵐 敬司; 梅津 和夫
日本DNA多型学会第33回学術集会, 2024年11月28日

日本の鵜飼漁に使用されるウミウPhalacrocorax capillatusの遺伝的多様性に関する研究　　　　　　　　　　　　　　　
古門裕貴; 石塚龍太; 中根理充; 北野誉
第26回日本進化学会神奈川大会, 2024年08月21日

下北半島の固有種である半陸半水生の淡水性巻貝シモキタシブキツボFukuia ooyagiiの分子系統地理学的解析　　　　　　　　　　　　　　　
北野誉; 大八木昭; 梅津和夫
第26回日本進化学会神奈川大会, 2024年08月21日

ミトコンドリアD-loopの塩基配列を用いたウミウの集団遺伝学的解析　　　　　　　　　　　　　　　
北野誉、古門裕貴、石塚龍太、中根理充
日本DNA多型学会第32回学術集会, 2023年11月17日

トワダカワゲラScopura longaの地域集団の分子系統学的解析から日本列島の成り立ちを考える　　　　　　　　　　　　　　　
伊村理雄、北野誉、大八木昭、草刈広一、清水洋樹、梅津和夫
日本DNA多型学会第32回学術集会, 2023年11月16日

SLC4A遺伝子ファミリーの進化　　　　　　　　　　　　　　　
山崎 紘平,北野 誉
第45回日本分子生物学会年会, 2022年12月02日

ヒトの祖先におけるABO式血液型のA型遺伝子の解析　　　　　　　　　　　　　　　
三上 修平,北野 誉
第45回日本分子生物学会年会, 2022年12月02日

SFTP遺伝子ファミリーの進化過程の解析　　　　　　　　　　　　　　　
長澤 協美,北野 誉
第45回日本分子生物学会年会, 2022年12月02日

キタホウネンエビ類におけるミトコンドリアゲノムと核ゲノムの系統樹の不一致　　　　　　　　　　　　　　　
北野 誉
第45回日本分子生物学会年会, 2022年12月02日

MIG-seq 法を用いたシモキタシブキツボFukuia ooyagii Minato, 1982 の遺伝的多様性の解析　　　　　　　　　　　　　　　
北野 誉,梅津 和夫,大八木 昭
日本DNA多型学会第31回学術集会, 2022年11月18日

ミトコンドリアの制御領域および MIG-seq 法を用いたウミウの遺伝的多様性の解析　　　　　　　　　　　　　　　
中根 理充,北野 誉
日本DNA多型学会第31回学術集会, 2022年11月17日

鵜飼のウミウの性判別：偏った性比の要因とペアの繁殖行動の意義　　　　　　　　　　　　　　　
亀田 佳代子,村山 美穂,中根 理充,北野 誉
日本鳥類学会2022年度大会, 2022年11月04日

下北半島の固有種シモキタシブキツボ Fukuia ooyagii Minato, 1982 の生物地理学的研究　　　　　　　　　　　　　　　
北野 誉,梅津 和夫,大八木 昭
日本DNA多型学会第30回学術集会, 2021年12月03日

ミトコンドリア DNA の制御領域の塩基配列を用いたウミウ Phalacrocorax capillatus の多様性の解析　　　　　　　　　　　　　　　
中根 理充,北野 誉
日本DNA多型学会第30回学術集会, 2021年12月03日

後口動物におけるSLC4遺伝子族の進化　　　　　　　　　　　　　　　
山崎 紘平,北野 誉
第44回日本分子生物学会年会, 2021年12月01日

毛のキューティクルに関係する遺伝子のクジラ亜目とネコ亜目における偽遺伝子化過程の解析　　　　　　　　　　　　　　　
長澤 協美,山崎 紘平,北野 誉
日本進化学会 2021 東京, 2021年08月19日

日本近海のヌタウナギ類Eptatretus属の系統解析および多型解析　　　　　　　　　　　　　　　
槇修杜,一関晋太朗,猿渡敏郎,梅津和夫,杉山秀樹,北野誉
日本DNA多型学会第29回学術集会 東京, 2020年11月26日

キタホウネンエビのミトコンドリアゲノム　　　　　　　　　　　　　　　
日本進化学会第22回大会, 2020年09月08日

飼育下エトピリカの遺伝的多様性に関する研究　　　　　　　　　　　　　　　
櫻山静香; 野島大貴; 吉澤円; 川上壮太郎; 竹内智弘; 伊藤槙子; 北野誉
日本DNA多型学会第28回学術集会 京都, 2019年11月29日

日本近海に生息するヌタウナギ類の遺伝的多様性　　　　　　　　　　　　　　　
北野誉,槇修杜,一関晋太朗,猿渡敏郎,梅津和夫,杉山 秀樹
日本DNA多型学会第28回学術集会 京都, 2019年11月28日

融雪プールに生息するキタホウネンエビ類の系統解析　　　　　　　　　　　　　　　
高橋 法人,北野 誉,畠中 裕之,永幡 嘉之,Yu A. Tshistjakov,濱崎 眞克,守谷 開,五十嵐 敬司,梅津 和夫
日本進化学会 2018 東京, 2018年08月23日

Evolution of S100A3 and PADI3 genes during the mammalian lineage　　　　　　　　　　　　　　　
Takashi Kitano; Tadashi Minato
Society for Molecular Biology and Evolution 2018 Yokohama, 2018年07月09日

Phylogenetic trees of Eptatretus species constructed by the neighbor-joining method.　　　　　　　　　　　　　　　
Special Symposium to Celebrate over 50,000 citations of Saitou & Nei (1987)'s Neighbor-Joining Method paper, 2018年06月02日, ［招待有り］

モンクロシャチホコのN-アセチルラクトサミン特異的レクチンPFAの進化　　　　　　　　　　　　　　　
佐々木 一樹,横山 和卓,梅津 和夫,北野 誉
第40回日本分子生物学会年会（2017年度生命科学系学会合同年次大会）, 2017年12月08日

脊椎動物におけるS100A遺伝子族とPADI遺伝子族の進化　　　　　　　　　　　　　　　
湊 理,北野 誉
第40回日本分子生物学会年会（2017年度生命科学系学会合同年次大会）, 2017年12月08日

カブトムシN-アセチルラクトサミン特異的レクチン遺伝子の進化　　　　　　　　　　　　　　　
田畑 光敏、梅津 和夫、北野 誉
日本進化学会 2017 京都, 2017年08月25日

真獣下綱におけるABO式血液型遺伝子の進化　　　　　　　　　　　　　　　
小野 久志、北野 誉
日本進化学会 2017 京都, 2017年08月25日

系統樹の拡張としての系統ネットワーク　　　　　　　　　　　　　　　
日本進化学会第19回大会, 2017年08月25日

類人猿のABO式血液型遺伝子の解析　　　　　　　　　　　　　　　
北野 誉,斎藤 成也
第39回日本分子生物学会年会, 2016年11月30日

鳥類RHBG遺伝子の進化速度変化の解析　　　　　　　　　　　　　　　
加瀨 幹大,鈴木 昭徳,北野 誉
第39回日本分子生物学会年会, 2016年11月30日

日本産カブトムシ新規レクチン遺伝子の解析　　　　　　　　　　　　　　　
田畑 光敏,梅津 和夫,北野 誉
第39回日本分子生物学会年会, 2016年11月30日

Rh式血液型遺伝子ゲノム領域の解析　　　　　　　　　　　　　　　
北野 誉
日本進化学会 2016 東京, 2016年08月26日

ヒトABO式血液型ハプロタイプの進化　　　　　　　　　　　　　　　
伊藤 正哉、斎藤 成也、北野 誉
日本進化学会 2015 東京, 2015年08月22日

カブトムシレクチン遺伝子の進化　　　　　　　　　　　　　　　
田畑 光敏、梅津 和夫、北野 誉
日本進化学会 2015 東京, 2015年08月22日

クロヌタウナギ2集団の遺伝的分化　　　　　　　　　　　　　　　
加瀬 幹大、神野 圭太、小又 秀朗、杉山 秀樹、梅津 和夫、北野 誉
日本進化学会 2015 東京, 2015年08月22日

Genome Sequence Analysis of the Chimpanzee RH Blood Group Gene Cluster　　　　　　　　　　　　　　　
Takashi Kitano; Antoine Blancher; Naruya Saitou
Society for Molecular Biology and Evolution 2015 Vienna, 2015年07月13日

モンクロシャチホコのN-アセチルラクトサミン特異的レクチンは無脊椎動物のリゾチームと構造的類似性がある　　　　　　　　　　　　　　　
横山 和卓,佐藤 道比古,羽田 俊裕,山崎 健太郎,北野 誉,梅津 和夫
第37回日本分子生物学会年会 2014 横浜, 2014年11月27日

ヒトのABO式血液型遺伝子における組換えの解析　　　　　　　　　　　　　　　
伊藤 正哉,北野 誉
第37回日本分子生物学会年会 2014 横浜, 2014年11月26日

系統ネットワーク法を用いたヒトABO式血液型遺伝子の解析　　　　　　　　　　　　　　　
伊藤 正哉、北野 誉
日本進化学会 2014 大阪, 2014年08月22日

脊椎動物の初期におけるRH式血液型遺伝子族の進化　　　　　　　　　　　　　　　
鈴木昭徳,北野誉
第36回日本分子生物学会年会 2013 神戸, 2013年12月03日

系統ネットワーク法を用いたヒトABO式血液型遺伝子のSNP解析　　　　　　　　　　　　　　　
伊藤 正哉,佐藤 允治,北野 誉
日本遺伝学会第85回大会 2013 東京, 2013年09月21日

無顎類のRH式血液型遺伝子族の解析　　　　　　　　　　　　　　　
鈴木昭徳,北野誉
日本遺伝学会第85回大会 2013 東京, 2013年09月21日

系統ネットワーク構築による組換えの検出　　　　　　　　　　　　　　　
斎藤成也、北野 誉
日本遺伝学会 第84回大会, 2012年09月26日

無顎類のRH式血液型遺伝子族の解析　　　　　　　　　　　　　　　
鈴木昭徳、池谷弘伸、遠藤康平、北野 誉
日本進化学会 2012 東京, 2012年08月22日

有胎盤哺乳類の共通祖先におけるオキシトシンレセプターの進化速度の変化　　　　　　　　　　　　　　　
山下 薫、北野 誉
日本進化学会 2012 東京, 2012年08月22日

Evolution of the Rh family genes and the AVPR-OXTR family genes expressing in the kidney　　　　　　　　　　　　　　　
Akinori Suzuki; Hironobu Ikeya; Mari Sugaya; Kaoru Yamashita; Kouhei Endo; Takashi Kitano
Society for Molecular Biology and Evolution 2012 Dublin, 2012年06月25日

鳥類におけるRHBGの進化速度の加速　　　　　　　　　　　　　　　
菅谷麻理; 小林 純; 岡田淳之; 北野 誉
日本進化学会 2011 京都, 2011年07月31日

系統ネットワーク法を用いたABO式血液型遺伝子の解析　　　　　　　　　　　　　　　
佐藤允治; 矢沢博史; 北野 誉
日本進化学会 2011 京都, 2011年07月31日

The functional A allele was resurrected via recombination in the human ABO blood group gene　　　　　　　　　　　　　　　
Takashi Kitano
Society for Molecular Biology and Evolution 2011 Kyoto, 2011年07月28日

動物のミトコンドリアDNAにおける転位と転換の比率　　　　　　　　　　　　　　　
佐藤允治; 繪幡愛子; 北野 誉
日本進化学会 2010 東京, 2010年08月03日

A type allele was resurrected in modern human ABO blood group genes　　　　　　　　　　　　　　　
Takashi Kitano; Naruya Saitou
Society for Molecular Biology and Evolution 2010 Lyon, 2010年07月05日

アオメエソ類魚類の集団遺伝学的研究　　　　　　　　　　　　　　　
武内 瞳; 北野 誉
日本ＤＮＡ多型学会 第17回学術集会, 2008年11月20日

Relic of ancient recombinations deciphered through phylogenetic network analysis　　　　　　　　　　　　　　　
Takashi Kitano
Society of Evolutionary Studies, Japan, 2008 Tokyo, 2008年08月22日

発話とFoxP2遺伝子　　　　　　　　　　　　　　　
北野 誉
日本進化学会 2007 京都, 2007年09月02日

Genetic and Molecular Bases for Phenotypes of the B Subunit for Factor XIII　　　　　　　　　　　　　　　
XXIst Congress of the International Society on Thrombosis and Haemostasis, 2007年07月

日本進化学会

日本遺伝学会

日本分子生物学会

Society for Molecular Biology & Evolution

日本生物地理学会

日本甲殻類学会

日本DNA多型学会