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Publication List (April 21, 2025)
Yoshinori Kumazawa
Peer-reviewed papers
1. Johnson J.A., Athrey G., Anderson C.M., Bell D.A., Dixon A., Kumazawa Y., Maechtle T., Meeks G.W., Mindell D., Nakajima K., Novak B., Talbot S., White C., and Zhan X. (2023) Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies. Ecology and Evolution 13(7): e10347.
2. 黒川景，野呂達哉，熊澤慶伯 (2023) 環境DNAを用いた才井戸流周辺の動物種の予察的分析．なごやの生物多様性 10: 1-12.
3. 小汐晃平，横山悠理，戸田尚希，熊澤慶伯 (2023) 名古屋市産バッタ類のDNAバーコーディングと集団遺伝解析．なごやの生物多様性 10: 13-26.
4. 寺本匡寛#，横山悠理#，熊澤慶伯，島田知彦 (2022) ミトコンドリアDNA塩基配列を用いた名古屋圏のツチガエルの遺伝的解析：近年の生息地分断と遺伝的分化度の上昇．爬虫両棲類学会報 2022(2): 161-175. #共同第一著者
5. Xiaokaiti X., Hashiguchi Y., Ota H., and Kumazawa Y. (2022) Evolution of the noncoding features of sea snake mitochondrial genomes within Elapidae. Genes 13: 1470.
6. Kambayashi C., Kakehashi R., Sato Y., Mizuno H., Tanabe H., Rakotoarison A., Künzel S., Furuno N., Ohshima K., Kumazawa Y., Nagy Z.T., Mori A., Allison A., Donnellan S.C., Ota H., Hoso M., Yanagida T., Sato H., Vences M., and Kurabayashi A. (2022) Geography-dependent horizontal gene transfer from vertebrate predators to their prey. Molecular Biology and Evolution 39: msac052.
7. Nasu K., Yokoyama Y., Sun Y., Suzuki-Matsubara M., Teramoto T., Moriyama A., Kawase M. and Kumazawa Y. (2020) Mitochondrial genome of Cipangopaludina japonica (Gastropoda: Viviparidae) with a tRNA gene rearrangement. Mitochondrial DNA Part B 5(2): 1340-1341.
8. 横山悠理，中島京也，陸田径典，熊澤慶伯 (2020) 名古屋周辺ワシタカ類のDNAバーコーディングと集団遺伝解析．なごやの生物多様性 7: 1-14.
9. Matsubara, K., Kumazawa, Y., Ota, H., Nishida, C., and Matsuda, Y. (2019) Karyotype analysis of four blind snake species (Reptilia: Squamata: Scolecophidia) and karyotypic changes in Serpentes. Cytogenetic and Genome Research 157(1-2): 91-99.
10. 熊澤慶伯，松原美恵子，横山悠理，寺本匡寛，村瀬幸雄，那須健一郎，孫垚，森山昭彦，川瀬基弘 (2019) 名古屋市産淡水貝類のDNAバーコーディング．なごやの生物多様性 6: 1-14.
11. 川瀬基弘，西尾和久，松原美恵子，市原俊，森山昭彦，熊澤慶伯 (2018) 遺伝子解析に基づく中部・西日本産ナミギセルStereophaedusa japonica個体群の種内多様性と名古屋市の個体群の系統的位置づけ．なごやの生物多様性 5: 11-22.
12. Atminarso, D., Wibowo, A., Kusuma, W. E., Prianto, E., Ahnelt, H., Vasemägi, A., and Kumazawa, Y. (2018) The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia. Mitochondrial DNA Part B 3(1): 122-124.
13. Sun, Y., Kurisaki, M., Hashiguchi, Y., and Kumazawa, Y. (2017) Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing. BMC Genomics 18: 665.
14. Kusuma, W. E., Samuel, P. D., Wiadnya, D. G. R., Hariati, A. M., and Kumazawa, Y. (2017) Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae). Mitochondrial DNA Part B 2(2): 373-374.
15. 井上晶次，熊澤慶伯 (2017) 名古屋市を中心とした愛知県及び近隣県産ゾウムシ類のDNAバーコーディング．なごやの生物多様性 4: 23-29.
16. Kusuma, W. E., Ratmuangkhwang, S., and Kumazawa, Y. (2016) Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): cryptic species and west-to-east divergences. Molecular Phylogenetics and Evolution 105: 212-223.
17. Kusuma, W. E., and Kumazawa, Y. (2016) Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). Mitochondrial DNA Part A 27(6): 4222-4223.
18. Matsubara, K., Nishida, C., Matsuda, Y., and Kumazawa, Y. (2016) Sex chromosome evolution in snakes inferred from divergence patterns of two gametologous genes and chromosome distribution of sex chromosome-linked repetitive sequences. Zoological Letters 2: 19.
19. 藤谷武史，能登原盛弘，熊澤慶伯 (2016) ミトコンドリアDNA塩基配列を用いた名古屋市及び周辺地域におけるカスミサンショウウオの遺伝的多様性の研究．爬虫両棲類学会報 2016(1): 1-12.
20. Oba, Y., Ôhira, H., Murase, Y., Moriyama, A., and Kumazawa, Y. (2015) DNA barcoding of Japanese click beetles (Coleoptera, Elateridae). PLoS ONE 10(1): e0116612.
21. Kumazawa, Y., Miura, S., Yamada, C., and Hashiguchi, Y. (2014) Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics 15: 930.
22. Ratmuangkhwang, S., Musikasinthorn, P., and Kumazawa, Y. (2014) Molecular phylogeny and biogeography of air sac catfishes of the Heteropneustes fossilis species complex (Siluriformes: Heteropneustidae). Molecular Phylogenetics and Evolution 79: 82-91.
23. 橋口康之，熊澤慶伯 (2013) 脊椎動物嗅覚受容体遺伝子ファミリーの進化研究における次世代シーケンサーの活用．生物科学 64(3): 131-140.
24. Matsubara, K., Kuraku, S., Tarui, H., Nishimura, O., Nishida, C., Agata, K., Kumazawa, Y., and Matsuda, Y. (2012) Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake. BMC Genomics 13: 604.
25. Dehara, Y., Hashiguchi, Y., Matsubara, K., Yanai, T., Kubo, M., and Kumazawa, Y. (2012) Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach. Genome Biology and Evolution 4(4):602-616.
26. Jonniaux, P., Hashiguchi, Y., and Kumazawa, Y. (2012) Mitochondrial genomes of two African geckos of genus Hemitheconyx. Mitochondrial DNA 23(4):278-279.
27. Amer, S. A. M., Mohamed, M. A., Wilms, T. M., Shobrak, M., and Kumazawa, Y. (2012) Mitochondrial DNA variability within Uromastyx ornata philbyi (Agamidae: Squamata) from southwestern Saudi Arabia. Comparative and Functional Genomics 2012:851379.
28. Amer, S. A. M., Montaser, M. M., and Kumazawa, Y. (2011) Preliminary molecular variability within Uromastyx aegyptia microlepis (Reptilia: Agamidae) inhabiting Saudi Arabia. World Applied Sciences Journal 12(11):1955-1961.
29. Okajima, Y., and Kumazawa, Y. (2010) Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications. BMC Evolutionary Biology 10:141.
30. Okajima, Y., and Kumazawa, Y. (2009) Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines. Gene 441:28-35.
31. Inoue, J. G., Kumazawa, Y., Miya, M., and Nishida, M. (2009) The historical biogeography of the freshwater knifefishes using mitogenomic approaches: a Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular Phylogenetics and Evolution 51:486-499.
32. Amer, S. A. M., and Kumazawa, Y. (2009) Complete sequence of the mitochondrial genome of the endangered Nile soft-shelled turtle Trionyx triunguis. Egyptian Journal of Experimental Biology (Zoology) 5:43-50.
33. Amer, S. A. M., and Kumazawa, Y. (2009) Molecular affinity of Somali and Egyptian mastigures among the Afro-Arabian Uromastyx. Egyptian Journal of Experimental Biology (Zoology) 5:1-7.
34. Kawagoshi, T., Nishida, C., Ota, H., Kumazawa, Y., Endo, H., and Matsuda, Y. (2008) Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis)(Crocodylidae, Crocodylia). Chromosome Research 16:1119-1132.
35. Azuma, Y., Kumazawa, Y., Miya, M., Mabuchi, K., and Nishida, M. (2008) Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evolutionary Biology 8:215.
36. Amer, S. A. M., and Kumazawa, Y. (2008) Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards. Genes and Genetic Systems 83:275-280.
37. Jonniaux P., and Kumazawa Y. (2008) Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae). Gene 407:105-115.
38. Amer S. A. M., and Kumazawa Y. (2007) The mitochondrial genome of the lizard Calotes versicolor and a novel gene inversion in South Asian draconine agamids. Molecular Biology and Evolution 24(6):1330-1339.
39. Kumazawa Y. (2007) Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene 388:19-26.
40. Li X., Musikasinthorn P., and Kumazawa Y. (2006) Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences. Ichthyological Research 53(2):148-159.
41. Dong S., and Kumazawa Y. (2005) Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features. Journal of Molecular Evolution 61(1):12-22.
42. Amer S. A. M., and Kumazawa Y. (2005) Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements. Biological Journal of the Linnean Society 85(2):247-260.
43. Iwabe N., Hara Y., Kumazawa Y., Shibamoto K, Saito Y, Miyata T., and Kato K. (2005) Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Molecular Biology and Evolution 22(4):810-813.
44. Amer S. A. M., and Kumazawa Y. (2005) Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids. Gene 346:249-256.
45. Kumazawa Y., and Endo H. (2004) Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Research 11(2):115-125.
46. Kumazawa Y. (2004) Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes. DNA Research 11(2):137-144.
47. Kumazawa Y., Azuma Y., and Nishida M. (2004) Tempo of mitochondrial gene evolution: can mitochondrial DNA be used to date old divergences? Endocytobiosis and Cell Research 15:136-142.
48. Kobayashi Y., Dokiya Y., Kumazawa Y., and Sugita M. (2002) Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris. Biochemical and Biophysical Research Communications 299(1):57-61.
49. Kumazawa Y., and Nishida M. (2000) Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Molecular Biology and Evolution 17(12):1869-1878.
50. Cao Y., Sorenson M. D., Kumazawa Y., Mindell D. P., and Hasegawa M. (2000) Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene 259:139-148.
51. Kumazawa Y., and Nishida M. (1999) Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles. Molecular Biology and Evolution 16(6):784-792.
52. Kumazawa Y., Ota H., Nishida M., and Ozawa T. (1998) The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150(1):313-329.
53. Taguchi S., Kojima S., Terabe M., Kumazawa Y., KohriyamaH., Suzuki M., Miura K., and Momose H. (1997) Molecular phylogenetic characterization of Streptomyces protease inhibitor family. Journal of Molecular Evolution 44(5):542-551.
54. Kumazawa Y., Ota H., Nishida M., and Ozawa T. (1996) Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Molecular Biology and Evolution 13(9):1242-1254.
55. Kumazawa Y., and Nishida M. (1995) Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Molecular Biology and Evolution 12(5):759-772.
56. Watanabe Y., Kawai G., Yokogawa T., Hayashi N., Kumazawa Y., Ueda T., Nishikawa K., Hirao I., Miura K., and Watanabe K. (1994) Higher-order structure of bovine mitochondrial tRNASerUGA: chemical modification and computer modeling. Nucleic Acids Research 22(24):5378-5384.
57. Tsurui H., Kumazawa Y., Sanokawa R., Watanabe Y., Kuroda T., Wada A., Watanabe K., and Shirai T. (1994) Batchwise purification of specific tRNAs by a solid-phase DNA probe. Analytical Biochemistry 221(1):166-172.
58. Wakita K., Watanabe Y., Yokogawa T., Kumazawa Y., Nakamura S., Ueda T., Watanabe K., and Nishikawa K. (1994) Higher-order structure of bovine mitochondrial tRNAPhe lacking the 'conserved' GG and T_CG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Research 22(3):347-353.
59. Kumazawa Y., and Nishida M. (1993) Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Journal of Molecular Evolution 37(4):380-398.
60. Kumazawa Y., Yokogawa T., Tsurui H., Miura K., and Watanabe K. (1992) Effect of the higher-order structure of tRNAs on the stability of hybrids with oligodeoxyribonucleotides: separation of tRNA by an efficient solution hybridization. Nucleic Acids Research 20(9):2223-2232.
61. Pääbo S., Thomas W. K., Whitfield K. M., Kumazawa Y., and Wilson A. C. (1991) Rearrangements of mitochondrial transfer RNA genes in marsupials. Journal of Molecular Evolution 33(5):426-430.
62. Yokogawa T., Watanabe Y., Kumazawa Y., Ueda T., Hirao I., Miura K., and Watanabe K. (1991) A novel cloverleaf structure found in mammalian mitochondrial tRNASer(UCN). Nucleic Acids Research 19(22):6101-6105.
63. Kumazawa Y., Schwartzbach C. J., Liao H.-X., Mizumoto K., Kaziro Y., Miura K., Watanabe K., and Spremulli L. L. (1991) Interactions of bovine mitochondrial phenylalanyl-tRNA with ribosomes and elongation factors from mitochondria and bacteria. Biochimica et Biophysica Acta 1090(2):167-172.
64. Asakawa S., Kumazawa Y., Araki T., Himeno H., Miura K., and Watanabe K. (1991) Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. Journal of Molecular Evolution 32(6):511-520.
65. Kumazawa Y., Himeno H., Miura K., and Watanabe K. (1991) Unilateral aminoacylation specificity between bovine mitochondria and eubacteria. Journal of Biochemistry 109(3):421-427.
66. Kumazawa Y., Yokogawa T., Hasegawa E., Miura K., and Watanabe K. (1989) The aminoacylation of structurally variant phenylalanine tRNAs from mitochondria and various nonmitochondrial sources by bovine mitochondrial phenylalanyl-tRNA synthetase. Journal of Biological Chemistry 264(22):13005-13011.
67. Yokogawa T., Kumazawa Y., Miura K., and Watanabe K. (1989) Purification and characterization of two serine isoacceptor tRNAs from bovine mitochondria by using a hybridization assay method. Nucleic Acids Research 17(7):2623-2638.
Proceedings of international conferences
1. Kumazawa Y. (2002) Molecular clock estimation in fishes and its application to biogeographical studies. In: Proceedings of International Commemorative Symposium for 70th Anniversary of the Japanese Society of Fisheries Science, Fisheries Science 68(supp 1):357-360.
2. Kumazawa Y., and Nishida M. (2000) Molecular phylogenetic analysis of vertebrate radiations. pp. 137-143 In: IIAS International Symposium on 'Biodiversity' December 3-5, 1998 (IIAS Reports. No. 1999-003) (ed) Iwatsuki K. International Institute for Advanced Studies, Kyoto, Japan.
Books
1. 熊澤慶伯 (2023) 分子系統学．日本古生物学会編、古生物学の百科事典、丸善、東京、pp. 492-493.
2. 熊澤慶伯 (2022) センター・協議会20周年に向けての期待．生物多様性における新たな挑戦の時代．なごや生物多様性センター編、なごや生物多様性センター・なごや生物多様性保全活動協議会 10年のあゆみ、名古屋市環境局環境企画部環境企画課・なごや生物多様性保全活動協議会、名古屋、pp. 105及びpp. 110.
3. 熊澤慶伯 (2022) DNAバーコーディング．小澤岳昌他編、先端の分析法 第２版、NTS、東京、pp. 521-525.
4. 熊澤慶伯 (2018) 大陸移動—淡水魚．日本魚類学会編、魚類学の百科事典 第１版、丸善出版、東京、pp. 168-169.
5. 熊澤慶伯 (2010) 分子系統学．シクリッド．多重置換．分子生物地理学．ミトコンドリアDNA． 日本古生物学会編、古生物学事典 第２版 朝倉書店、東京、pp. 211, 338, 444-445, 476-477.
6. 熊澤慶伯 (2010) 動物の進化．動物の分布の変遷．石原勝敏、末光隆志総編、生物の事典 朝倉書店、東京、pp. 43-45, 47-49.
7. 熊澤慶伯 (2009) 第７章：分子データを用いた魚類の分岐年代の推定．西田睦編、海洋生命系のダイナミクスー第１巻、海洋の生命史ー生命は海 でどう進化したかー 東海大学出版会、神奈川、pp. 122-138.
8. Kumazawa Y., Yamaguchi M., and Nishida M. (1999) Chapter 3, Mitochondrial molecular clocks and the origin of euteleostean biodiversity: Familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary. pp. 35-52 In: The Biology of Biodiversity (ed) Kato M. Springer-Verlag, Tokyo.
9. Kumazawa Y., and Nishida M. (1996) Phylogenetic utility of mitochondrial transfer RNA genes for deep divergence in animals. pp. 29-35 In: Current Topics on Molecular Evolution (eds.) Nei M. and Takahata N. Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, USA, and Graduate School for Advanced Studies, Hayama, Japan.
Reviews and other papers
1. 川瀬基弘，横山悠理，松原和純，西浩孝，横井敦史，熊澤慶伯 (2025) 愛知県および岐阜県に棲息するCristariiniカラスガイ族（ドブガイ類）の種多様性．なごやの生物多様性 12: 201-212.
2. 川瀬基弘，横山悠理，市原俊，西尾和久，横井敦史，熊澤慶伯 (2024) 関東・北陸・中部地方に分布するオクガタギセルMegalophaedusa dorcasのCOI遺伝子からみた分子系統学的位置付け．瀬木学園紀要 24: 22-30.
3. 川瀬基弘，横山悠理，横井敦史，熊澤慶伯 (2023) 名古屋市に棲息するCristariiniカラスガイ族（ドブガイ類）の種多様性．なごやの生物多様性 10: 125-133.
4. 川瀬基弘，横山悠理，山本大輔，熊澤慶伯 (2023) 矢作第二ダム湛水池のミナミタガイ．矢作川研究 27: 43-48.
5. 川瀬基弘，横山悠理，横井敦史，熊澤慶伯 (2021) 愛知県名古屋市，豊橋市，山梨県北杜市で発見されたBuldowskia shadiniヤハズヌマガイ（新称）．瀬木学園紀要 18: 3-9.
6. 川瀬基弘，横山悠理，吉村卓也，茅原田一，熊澤慶伯 (2021) 岐阜県初記録の湿地性稀少種ミズコハクガイ．瀬木学園紀要 18: 10-14.
7. 川瀬基弘，横山悠理，市原俊，西尾和久，尾畑功，熊澤慶伯 (2021) 愛知県で発見されたクチベニマイマイの系統関係．鳳来寺山自然科学博物館館報 50: 23-29.
8. 川瀬基弘，横山悠理，西尾和久，松原美恵子，横井敦史，熊澤慶伯 (2021) 名古屋市に棲息するニッポンマイマイSatsuma japonicaのCOI遺伝子からみた分子系統学的位置付け．なごやの生物多様性 8: 127-132.
9. 川瀬基弘，村松正雄，横山悠理，横井敦史，熊澤慶伯 (2020) 愛知県奥三河地域で発見された日本初記録のBuldowskia shadini．瀬木学園紀要 17: 3-8.
10. 川瀬基弘，横山悠理，松原美恵子，横井敦史，森山昭彦，熊澤慶伯 (2020) 岐阜市に棲息するナミギセルの分布と系統関係．瀬木学園紀要 17: 9-16.
11. 川瀬基弘，西尾和久，松原美恵子，市原俊，森山昭彦，熊澤慶伯 (2020) 名古屋市に棲息するオオケマイマイAegista vulgivagaのCOⅠ遺伝子からみた分子系統学的位置付け．なごやの生物多様性 7: 31-37.
12. 寺本匡寛，宮田賢輔，横山悠理，熊澤慶伯，内藤遊多，鵜飼普 (2019) 外来種タイリククサキリモドキ（新称）の日本初記録と知見．月刊むし 580: 2-5.
13. 熊澤慶伯 (2010) 進化学のすすめ．Annual Review 2009. Graduate School of Natural Sciences, Nagoya City University 14:35-43.
14. 熊澤慶伯 (2004) 淡水魚アロワナが海を挟んで暮らしている理由．中村桂子編、Biohistory 2003 JT生命誌研究館、大阪、pp106-109.
15. 西田睦，宮正樹， 白井滋，斎藤憲治，熊澤慶伯，馬渕浩司 (2002) 脊椎動物の系統進化．月刊海洋 号外29:36-42.
16. 熊澤慶伯 (2001) アロワナ淡水魚類のプレートテクトニクスによる大陸移動：分子時計と地質データの総合による新しい生物進化像の構築．月刊地球 23(3):208-214.
17. 熊澤慶伯，山口素臣，西田睦 (2000) 淡水魚類の分子生物地理学と魚類分子時計の較正．月刊海洋 32(4):275-280.
18. 熊澤慶伯 (1997) ミトコンドリアｔＲＮＡ遺伝子の配置変動と分子系統学．SHINKA 7(2):49-59.
19. 熊澤慶伯 (1995) 分子時計の有用性と課題．日経サイエンス 25(10):24-28.
20. 熊澤慶伯，小澤智生 (1995) 生命と地球の共進化-分子状酸素の発生と消費をめぐる共進化．月刊地球 17(7):464-471.
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