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動物生態学研究室

北海道大学大学院農学研究院基盤研究部門生物資源科学分野

Araki's Lab Recent Publications

研究発表・論文
P2280320.JPG

研究発表・論文

2024

  • Detection of environmental DNA of finless porpoise (Neophocaena asiaeorientalis) in Osaka Bay, Japan. N. Hashimoto, T. Iwata, N. Kihara, M. K. Sakata, T. Minamoto. Conservation Genetics Resources accepted (2024)

  • Environmental DNA unveils deep phylogeographic structure of a freshwater fish. T. Yatsuyanagi, T. Kanbe, K. Fujii, S. Inoue, H. Araki. Molecular Ecology  accepted (2024)

 

2023

  • Co-occurrence patterns of endangered Sakhalin taimen and introduced rainbow trout in Hokkaido, Japan, inferred by environmental DNA metabarcoding. T. Kanbe, H. Mizumoto, T. Mitsuzuka, N. Nakajima, H. ArakiAquatic Conservation  33: 1492-1500 (2023) https://doi.org/10.1002/aqc.4022

  • Application of eDNA methods to evaluate abundance and reproduction of winter-breeding freshwater mussels (Buldowskia iwakawai) in the Ishikari River floodplain. J. Wu, J. N. Negishi, H. Izumi, T. Kanbe, H. Mizumoto, H. Araki. Hydrobiologia 851: 541-558 (2023) https://link.springer.com/article/10.1007/s10750-023-05343-y

  • Opposite trends in environmental DNA distributions of two freshwater species under climate change. Q. Wu, J. Zhou, T. Komoto, T. Ishikawa, N. Goto, M. K. Sakata, D. Kitazawa, T. Minamoto. Ecosphere 14:e4651. (2023)  https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.4651

  • Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities. G. P. Huston, M. L. D. Lopez, Y. Cheng, L. King, L. C. Duxbury, M. Picard, G. Thomson-Laing, E. Myler, C. C. Helbing, M. T. Kinnison, J. E. Saros, I. Gregory-Eaves, Marie-Eve Monchamp, S. A. Wood, L. Armbrecht, G. F. Ficetola, L. Kurte, J. Von Eggers, J. Brahney, G. Parent, M. K. Sakata, H. Doi, E. Capo. Environmental DNA. (2023) https://onlinelibrary.wiley.com/doi/10.1002/edn3.467

  • The eDNA Society International Meeting 2023, “moving from knowledge into practice”. H. Yamanaka, H. Doi, H. Araki, K. Uchii, T. Minamoto (2023) Environmental DNA 5: 1191-1195. https://onlinelibrary.wiley.com/doi/10.1002/edn3.465

  • Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities. H. Doi, S. Matsuoka, S. S. Matsuzaki, M. Nagano, H. Sato, H. Yamanaka, S. Matsuhashi, S. Yamamoto, T. Minamoto, H. Araki, K. Ikeda, A. Kato, K. Kumei, N. Maki, T. Mitsuzuka, T. Takahara, K. Toki, N. Ueda, T. Watanabe, K. Yamazoe, M. Miya. Freshwater Biology 68: 1346-1358 (2023) https://onlinelibrary.wiley.com/doi/10.1111/fwb.14107

  • An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri).  M. K. Sakata, T. Takeshita, R. Nishizawa, T. Sato, T. Minamoto. Analytical Sciences (2023) https://link.springer.com/article/10.1007/s44211-023-00289-6

  • 環境DNAメタバーコーディングを用いた北日本の溜池における外来魚の影響評価 小粥, 八柳, 神戸, 井上, 荒木​ 保全生態学研究 28:333-345 (2023). https://doi.org/10.18960/2216

  • 金原ダム湖におけるオオクチバスの機能的根絶 坪井, 片野, 水本, 荒木 保全生態学研究 28:437-452 (2023). https://doi.org/10.18960/hozen.2224 

2022

  • Origin and expansion of the world’s most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina). X. Liu, S.R. Schjøtt, S.M. Granquist, A. Rosing-Asvid, R. Dietz, J. Teilmann, A. Galatius, K. Cammen, G. O’Corry-Crowe, K. Harding, T. Härkönen, A. Hall, E.L. Carroll, Y. Kobayashi, M. Hammill, G. Stenson, A. Kirstine Frie, C. Lydersen, K.M. Kovacs, L.W. Andersen, J.I. Hoffman, S.J. Goodman, F.G. Vieira, R. Heller, I. Moltke, M. Tange Olsen. Molecular Ecology 31:1682-1699. (2022https://onlinelibrary.wiley.com/doi/full/10.1111/mec.16365

  • Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan. H. Mizumoto, O. Kishida, K. Takai, N. Matsuura, H. Araki. Biological Invasions 24:1199-1211. (2022https://link.springer.com/article/10.1007/s10530-021-02709-y

2021

  • Time to adjust to a new feeding environment determines survival and growth of wild-caught white-spotted charr (Salvelinus leucomaenis pluvius) K. Miyamoto, M. Dordevic, H. Araki. Environmental Biology of Fishes 104: 959-966. (2021) https://doi.org/10.1007/s10641-021-01128-1

  • Artificially increased habitat complexity reduces predation-induced mortality for juvenile salmon in simplified environments. K. Miyamoto, M. Dordevic, H. Araki. Environmental Biology of Fishes 104: 203-209. (2021) https://doi.org/10.1007/s10641-021-01073-z

  • An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. T. Minamoto, M. Miya, T. Sado, S. Seino, H. Doi, M. Kondoh, K. Nakamura, T. Takahara, S. Yamamoto, H. Yamanaka, H. Araki, W. Iwasaki, A. Kasai, R. Masuda, K. Uchii. Environmental DNA 3:8-13. (2021) https://doi.org/10.1002/edn3.121

  • 北海道の渓流魚を対象とした治山ダムの改良効果の検証:長期モニタリングによる検証と環境DNAの活用可能性

    速水, 石山, 水本, 神戸, 下田, 三坂, 卜部, 長坂, 長坂, 小野, 荒木, 中嶋, 福島

    応用生態工学 24(1) 61-73 (2021) https://doi.org/10.3825/ece.20-00043

2020

  • An environmental DNA survey on distribution of an endangered salmonid species, Parahucho perryi, in Hokkaido, Japan. H. Mizumoto, T. Mitsuzuka, H. Araki. Front. Ecol. Evol. 8:569425. (2020)

  • Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA. T.Yatsuyanagi, H. Araki. PLoS ONE 15: e0239912. (2020)

  • Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus). T. Yatsuyanagi, R. Ishida, M.K. Sakata, T. Kanbe, H. Mizumoto, Y. Kobayashi, S. Kamada, S. Namba, H. Nii, T. Minamoto, H. Araki. Environmental DNA 2:130-139. (2020)

  • When is it good to be shy? Experimental evaluation of predation of juvenile salmon by riparian wildlife. K. Miyamoto, H. Araki. Hydrobiologia 847:713-725 (2020)

  • 市民参加型調査で集めた位置情報付き生物写真にサンプリングバイアスは存在するか? ─市民と専門家の遡河性サケマス関連撮影データの比較から─ 佐橋・丸山・有賀・森田・岡本・向井・水本・植田・藤井・渡辺・大熊・荒木. 保全生態学研究 https://doi.org/10.18960/hozen.1930 (2020)

2019

  • Spatiotemporal distribution of juvenile chum salmon in Otsuchi Bay, Iwate, Japan, inferred from environmental DNA. Y. Minegishi, M.K-S. Wong, T. Kanbe, H. Araki, T. Kashiwabara, M. Ijichi, K. Kogure, S. Hyodo. PLoS ONE 14: e0222052. (2019)

  • Effects of water depth and structural complexity on survival and settlement of white-spotted charr (Salvelinus leucomaenis). K. Miyamoto, H. Araki. Hydrobiologia 840:103-112. (2019)

  • Ongoing localized extinctions of stream-dwelling whitespotted charr populations in small dammed-off habitats of Hokkaido Island, Japan. K. Morita, G. Sahashi, M. Miya, S. Kamada, T. Kanbe, H. Araki. Hydrobiologia 840:207-213. (2019)

2018

  • Modeling fitness changes in wild Atlantic salmon populations faced by spawning intrusion of domesticated escapees. M. Castellani, M. Heino, J. Gilbey, H. Araki, T. Svasand, K.A. Glover. Evolutionary Applications 11:1010-1025. (2018)

  • Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid. H. Mizumoto, H. Urabe, T. Kanbe, M. Fukushima, H. Araki. Limnology 19: 219-227. (2018)

  • Experimental evaluation for predation of stocked salmon by riparian wildlife: the effects of prey size and predator behaviors. K. Miyamoto, T.E. Squires, H. Araki. Marine and Freshwater Research 69: 446-454. (2018)

2017

  • Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions. K.A. Glover, M.F. Sloberg, P. McGinnity, K. Hindar, E. Verspoor, M.W. Coulson, M.M. Hansen, H. Araki, O. Skaala, T. Svasand. Fish and Fisheries 18: 890-927. (2017)

  • Occurrence of the Kuril Harbour Seal (Phoca vitulina) at a small fixed fishing net in Akkeshi Bay, Hokkaido, Japan. Y. Kobayashi, M. Kobayashi, Y. Sakurai, K. Takada. Int. J. Agr. Pol. Res. 5: 18-25. (2017)

  • Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. S. Yamamoto, R. Masuda, Y. Sato, T. Sado, H. Araki, M. Kondoh, T. Minamoto, M. Miya. Scientific Reports 7: 40368. (2017)

  • Differentiated predation risk on hatchery-reared juvenile masu salmon by white-spotted charr with different body sizes. K. Miyamoto, H. Araki. Fish. Sci. 83: 245-250. (2017)

  • Understanding and monitoring the consequences of human impacts on intraspecific variation. M. Mimura, T. Yahara, D.P. Faith, E. Vazquez-Dominguez, R.I. Colautti, H. Araki, F. Javadi, J. Nunez-Farfan, A.S. Mori, S. Zhou, P.M. Hollingsworth, L.E. Neaves, Y. Fukano, G.F. Smith, Y. Sato, H. Tachida, A.P. Hendry. Evol. Appl. 10: 121-139. (2017)

2016

  • Environmental DNA as a ‘Snapshot’ of fish distribution: a case study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan. S. Yamamoto, K. Minami, K. Fukaya, K. Takahashi, H. Sawada, H. Murakami, S. Tsuji, H. Hashizume, S. Kubonaga, T. Horiuchi, M. Hongo, J. Nishida, Y. Okugawa, A. Fujiwara, M. Fukuda, S. Hidaka, K.W. Suzuki, M. Miya, H. Araki, H. Yamanaka, A. Maruyama, K. Miyashita, R. Masuda, T. Minamoto, M. Kondoh. PLoS ONE 11: e0153291. (2016)

  • The eco-evolutionary impacts of domestication and agricultural practices on wild species. M.M. Turcotte, H. Araki, D.S. Karp, K. Poveda, S.R. Whitehead. Phil. Trans. Roy. Soc. B. 372: 20160033. (2016)

2015

  • MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. M. Miya, Y. Sato, T. Fukunaga, T. Sado, J.Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh, W. Iwasaki. Roy. Soc. Open Sci. 2: 150088. (2015)

  • IBSEM: An Individual-Based Atlantic Salmon Population Model. M. Castellani, M. Heino, J. Gilbey, H. Araki, T. Svasand, K.A. Glover. PLoS One 10: e0138444. (2015)

  • Population genetics of non-genetic traits: evolutionary roles of stochasticity in gene expression. K. Mineta, T. Matsumoto, N. Osada, H. Araki. Gene 562: 16-21. (2015)

  • An individual-based diploid model predicts limited conditions under which stochastic gene expression becomes advantageous. T. Matsumoto, K. Mineta, N. Osada, H. Araki. Front. Genet. 6: 336-347. (2015)

2014 or older

See full list in Hitoshi Araki’s short CV here (PDF)

Araki's Personal Publication list (Before HU)

FISH GENETICS, ECOLOGY & EVOLUTION

  • Satake and Araki (2012)
    Stocking of captive-bred fish can cause long-term population decline and gene pool replacement: predictions from a population dynamics model incorporating density-dependent mortality
    Theoretical Ecology 5: 283-296.

  • Bezault, Balaresque, Toguyeni, Fermon, Araki, Baroiller, Rognon (2011)
    Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa.
    BMC Genetics 12: 102 (16 pages).

  • Araki and Schmid. (2010)
    Is hatchery stocking a help or harm? Genetics as a key for enhancement and natural reproduction.
    Aquaculture 308:S2-S11.

  • Blouin, Thuillier, Cooper, Amarasinghe, Araki and Grunau. (2010)
    No evidence for large differences in genomic methylation between wild and hatchery steelhead trout (Oncorhynchus mykiss).
    Canadian Journal of Fisheries and Aquatic Sciences 67, 217-224.

  • Araki, Cooper and Blouin. (2009)
    Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild.
    Biology Letters 5, 621-624. [Media coverage: Scientific American, SwissInfo]

  • Araki, Berejikian, Ford and Blouin. (2008)
    Fitness of hatchery-reared salmonids in the wild.
    Evolutionary Applications 1: 342-355.

  • Araki, Cooper and Blouin. (2007)
    Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild.
    Science 318:100-103. [Media coverage: BBC, The New York Times, AP, Nature News, Nikkei News, F1000]

  • Araki, Waples and Blouin. (2007)
    A potential bias in the temporal method for estimating Ne in admixed populations under natural selection.
    Molecular Ecology 16: 2261-2271.

  • Araki, Waples, Ardren, Cooper and Blouin. (2007) Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms.
    Molecular Ecology 16: 953-966.

  • Araki, Ardren, Olsen, Cooper and Blouin. (2007)
    Reproductive success of captive-bred steelhead trout in the wild: Evaluation of three hatchery programs in the Hood River.
    Conservation Biology 21: 181-190. [Media coverage: AP, Oregonian, Asahi News, F1000]

  • Araki and Blouin. (2005)
    Unbiased estimation of relative reproductive success of different groups: evaluation and correction of bias caused by parentage assignment errors.
    Molecular Ecology 14: 4097-4109.

POPULATION GENETICS & MOLECULAR EVOLUTION

  • Wang, Si, Yao, Tian, Araki and Yang (2012)
    Genome-wide survey of Pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.
    PLoS One 7:e51769 DOI: 10.1371/journal.pone.0051769

  • Yue, Li, Wang, Araki, Tian and Yang (2010)
    Genome-wide investigation reveals high evolutionary rates in annual plants.
    BMC Plant Biology 10: 242 (12 pages).

  • Gu, Tan , Gou, Araki and Tian. (2010)
    Avoidance of long mononucleotide repeats in codon pair usage.
    Genetics 188: 1077-1084.

  • Wang, Ho, Hung, Wang, Huang, Araki, Osada and Chiang. (2010)
    Multi-locus analyses of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.
    New Phytologist 188: 488-500.

  • Zhu, Wang, Tang, Araki and Tian. (2009)
    Genome-wide association between insertions/deletions and the nucleotide diversity in bacteria.
    Molecular Biology and Evolution 26: 2353-2361.

  • Tian, Wang, Zhang, Araki, Yang, Kreitman, Nagylaki, Hudson, Bergelson and Chen. (2008)
    Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes.
    Nature 455: 105-108. [Media coverage: F1000]

  • Zhang, Sun, Yuan, Araki, Wang, Tian. (2008)
    The pattern of insertion/deletion polymorphism in Arabidopsis thaliana.
    Molecular Genetics and Genomics (MGG) 280: 351-361.

  • Du, Gu, Tian, Araki, Yang and Tian. (2008)
    Grouped nucleotide polymorphism: A major contributor to genetic variation in Arabidopsis.
    Gene 426: 1-6.

  • Araki, Innan, Kreitman and Bergelson. (2007)
    Molecular evolution of pathogenicity-island genes in Pseoudomonas viridiflava.
    Genetics 177: 1031-1041.

  • Ding, Araki, Wang, Zhang, Yang, Chen and Tian. (2007)
    Highly asymmetric rice genomes.
    BMC Genomics 8: 154.

  • Orgil, Araki, Tangchaiburana, Berkey and Xiao. (2007)
    Intraspecific genetic variations, fitness cost and benefit of RPW8, a disease resistance locus in Arabidopsis thaliana.
    Genetics 176: 2317-2333.

  • Yang, Jiang, Araki, Ding, Yang and Tian. (2007)
    A molecular isolation mechanism associated with high intra-specific diversity in rice.
    Gene 394: 87-95.

  • Ding, Cheng, Jin, Araki, Yang and Tian. (2007)
    Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis.
    Genetica 129: 235-242.

  • Araki, Tian, Goss, Jakob, Halldorsdottir, Kreitman and Bergelson. (2006)
    Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis.
    Proceedings of the National Academy of Sciences of the USA (PNAS) 103: 5887-5892. [Media coverage: F1000]

  • Shen, Araki, Chen, Chen and Tian. (2006)
    Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana.
    Genetics 172: 1243-1250.

  • Araki, Yoshizumi, Inomata and Yamazaki. (2005)
    Genetic coadaptation of the Amylase gene system in Drosophila melanogaster: Evidence for the selective advantage of the lowest AMY activity and of its epistatic genetic background.
    Journal of Heredity 96: 388-395.

  • Zhou, Wang, Chen, Araki, Jing, Jiang, Shen and Tian. (2004)
    Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.
    Molecular Genetics and Genomics (MGG) 271: 402-415.

  • Jakob, Goss, Araki, Van, Kreitman and Bergelson. (2002)
    Pseudomonas viridiflavaP. syringae – natural pathogens of Arabidopsis thaliana.
    Molecular Plant-Microbe Interact (MPMI) 15: 1195-1203.

  • Tian, Araki, Stahl, Bergelson and Kreitman. (2002)
    Signature of balancing selection in Arabidopsis.
    Proceedings of the National Academy of Sciences of the USA (PNAS) 99: 11525-11530. [Media coverage: F1000]

  • Araki, Inomata and Yamazaki. (2001)
    Molecular evolution of duplicated Amylase gene regions in Drosophila melanogaster: Evidence of positive selection in the coding regions and selective constraints in the cis-regulatory regions.
    Genetics 157: 667-677.

  • Araki and Tachida. (1997)
    Bottleneck effect on evolutionary rate in the nearly neutral mutation model.
    Genetics 147: 907-914.

BOOK SECTIONS

  • Yatsuyanagi, Minegishi, Mizumoto & Araki (2021)
    In 「環境DNA~生態系の真の姿を読み解く」(共立出版)
    – 種特異的環境DNA手法の事例

  • Araki (2008)
    In Fisheries for Global Welfare and Environment, Tsukamoto, Kawamura, Takeuchi, Beard and Kaiser Eds., TERRAPUB, Tokyo, Japan. (in English)
    – “Hatchery stocking for restoring wild populations: A genetic evaluation of the reproductive success of hatchery fish vs. wild fish”

  • Araki (2007)
    In Evolution of Plants, Shimizu and Hasebe Eds., SHUJUNSHA Co. Ltd., Tokyo, Japan. (in Japanese)
    – “Natural selection on a plant-pathogen interaction between Arabidopsis and Pseudomonas”

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