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Animal Ecology Laboratory

Faculty of Agriculture, Hokkaido University

Araki's Lab Recent Publications

研究発表・論文
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Publications

2023

  • 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. (2023) https://link.springer.com/article/10.1007/s10750-023-05343-y

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  • 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. Araki. Aquatic Conservation  (2023) https://doi.org/10.1002/aqc.4022

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  • 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

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  • 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 (2023) Freshwater Biology.  https://onlinelibrary.wiley.com/doi/10.1111/fwb.14107

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2022

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

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  • 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 Invasions24:1199-1211 (2022, Open Access) https://link.springer.com/article/10.1007/s10530-021-02709-y

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  • Impact assessment of alien fish in reservoirs in northern Japan using environmental DNA metabarcoding

    Atsushi Kogayu, Satoshi Yayanagi, Takashi Kanbe, Shoko Inoue, Hitoshi Araki

    conservation ecology research　in press

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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 Fishes104: 959-966. (2021) hhttps://doi.org/10.1007/s10641-021-01128-1

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  • Artificially increased habitat complexity reduces predation-induced mortality for juvenile salmon in simplified environments.K. Miyamoto, M. Dordevic,H. Araki.Environmental Biology of Fishes104: 203-209. (2021) https://doi.org/10.1007/s10641-021-01073-z

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  • 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 DNA3:8-13. (2021) https://doi.org/10.1002/edn3.121

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  • Verification of improvement effects of erosion control dams for mountain stream fish in Hokkaido: Verification by long-term monitoring and potential use of environmental DNA

    Masato Hayami, Nobuo Ishiyama,Hiroki Mizumoto, Takashi Kobe, Kazutaka Shimoda, Naoyuki Misaka, Koichi Urabe, Akiko Nagasaka, Yu Nagasaka, Osamu Ono,Hitoshi Araki, Nobumi Nakajima, Michio Fukushima

    Applied ecological engineering24(1) 61-73 (2021) https://doi.org/10.3825/ece.20-00043

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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)

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  • Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA.T. Yatsuyanagi, H. Araki.PLoS ONE15: e0239912. (2020)

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  • Environmental DNA monitoring for short-term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus).T. Yatsuyanagi, R. Ishida, MK Sakata,T. Kanbe, H. Mizumoto, Y. Kobayashi, S. Kamada, S. Namba, H. Nii, T. Minamoto,H. Araki.Environmental DNA2:130-139. (2020)

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  • When is it good to be shy? Experimental evaluation of predation of juvenile salmon by riparian wildlife.K. Miyamoto, H. Araki.hydrobiology847:713-725 (2020)

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  • Is there a sampling bias in biophotographs with location information collected in citizen-participatory surveys? ─Comparison of photography data related to migratory salmon trout taken by citizens and experts─ Sahashi, Maruyama, Ariga, Morita, Okamoto, Mukai,Mizumoto・Ueda・Fujii・Watanabe・Okuma・Araki.conservation ecology researchhttps://doi.org/10.18960/hozen.1930 (2020)

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2019

  • Spatiotemporal distribution of juvenile chum salmon in Otsuchi Bay, Iwate, Japan, inferred from environmental DNA. Y. Minegishi, MK-S. Wong, T.Kanbe, H. Araki, T. Kashiwabara, M. Ijichi, K. Kogure, S. Hyodo.PLoS ONE14: e0222052. (2019)

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  • Effects of water depth and structural complexity on survival and settlement of white-spotted charr (Salvelinus leucomaenis).K. Miyamoto, H. Araki.hydrobiology840:103-112 (2019)

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  • 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.hydrobiology840:207-213 (2019)

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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, KA Glover.Evolutionary Applications11: 1010-1025 (2018)

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  • 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.Limnology19: 219-227 (2018)

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  • Experimental evaluation for predation of stocked salmon by riparian wildlife: the effects of prey size and predator behaviors.K. Miyamoto, TE Squires, H. Araki.Marine and Freshwater Research69: 446-454 (2018)

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2017

  • Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions. KA Glover, MF Sloberg, P. McGinnity, K. Hindar, E. Verspoor, MW Coulson, MM Hansen,H. Araki, O. Skaala, T. Svasand.Fish and Fisheries18: 890-927 (2017)

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  • Occurrence of the Kuril Harbor 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.Res5: 18-25 (2017)

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  • 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 Reports7: 40368. (2017)

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  • Differentiated predation risk on hatchery-reared juvenile masu salmon by white-spotted charr with different body sizes.K. Miyamoto, H. Araki.Fish.Sci83: 245-250 (2017)

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  • Understanding and monitoring the consequences of human impacts on intraspecific variation. M. Mimura, T. Yahara, DP Faith, E. Vazquez-Dominguez, RI Colautti,H. Araki, F. Javadi, J. Nunez-Farfan, AS Mori, S. Zhou, PM Hollingsworth, LE Neaves, Y. Fukano, GF Smith, Y. Sato, H. Tachida, AP Hendry.Evol. Appl.10: 121-139 (2017)

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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, KW Suzuki, M. Miya,H. Araki, H. Yamanaka, A. Maruyama, K. Miyashita, R. Masuda, T. Minamoto, M. Kondoh.PLoS ONE11: e0153291. (2016)

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  • The eco-evolutionary impacts of domestication and agricultural practices on wild species. MM Turcotte,H. Araki, DS Karp, K. Poveda, SR Whitehead.Phil.Trans.Roy.Soc.B372: 20160033. (2016)

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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, JY Poulsen, K. Sato, T. Minamoto , S. Yamamoto, H. Yamanaka,H. Araki, M. Kondoh, W. Iwasaki.Roy. Soc. Open Sci2: 150088. (2015)

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  • IBSEM: An Individual-Based Atlantic Salmon Population Model. M. Castellani, M. Heino, J. Gilbey,H. Araki, T. Svasand, KA Glover.PLoS One10: e0138444. (2015)

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  • Population genetics of non-genetic traits: evolutionary roles of stochasticity in gene expression. K. Mineta, T. Matsumoto, N. Osada,H. Araki. Gene562: 16-21 (2015)

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  • An individual-based diploid model predicts limited conditions under which stochastic gene expression becomes advantageous. T. Matsumoto, K. Mineta, N. Osada,H. Araki. Front Genet6: 336-347 (2015).

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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 andAraki(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 Ecology5: 283-296.

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  • Bezault, Balaresque, Toguyeni, Fermon,Araki, Baroiler, Rognon (2011)
    Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa.
    BMC Genetics12: 102 (16 pages).

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  • Arakiand Schmid.(2010)
    Is hatchery stocking a help or harm? Genetics as a key for enhancement and natural reproduction.
    Aquaculture308: S2-S11.

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  • Blouin, Thuillier, Cooper, Amarasinghe,Arakiand Grunau. (2010)
    No evidence for large differences in genomic methylation between wild and hatchery steelhead trout (Oncorhynchus mykiss).
    Canadian Journal of Fisheries and Aquatic Sciences67, 217-224.

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  • Araki, Cooper and Blouin.
    Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild.
    Biology Letters5, 621-624. [Media coverage: Scientific American, SwissInfo]

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  • Araki, Berejikian, Ford and Blouin.
    Fitness of hatchery-reared salmonids in the wild.
    Evolutionary Applications1: 342-355.

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  • Araki, Cooper and Blouin.
    Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild.
    Science318:100-103. [Media coverage: BBC, The New York Times, AP, Nature News, Nikkei News, F1000]

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  • Araki, Waples and Blouin (2007)
    A potential bias in the temporal method for estimating Ne in admixed populations under natural selection.
    Molecular Ecology16: 2261-2271.

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  • 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 Ecology16: 953-966.

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  • 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 Biology21: 181-190. [Media coverage: AP, Oregonian, Asahi News, F1000]

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  • Arakiand Blouin.(2005)
    Unbiased estimation of relative reproductive success of different groups: evaluation and correction of bias caused by parentage assignment errors.
    Molecular Ecology14: 4097-4109.

POPULATION GENETICS & MOLECULAR EVOLUTION

  • Wang, Si, Yao, Tian,Arakiand Yang (2012)
    Genome-wide survey of Pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.
    PLoS One7:e51769 DOI: 10.1371/journal.pone.0051769

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  • Yue, Li, Wang,Araki, Tian and Yang (2010)
    Genome-wide investigation reveals high evolutionary rates in annual plants.
    BMC Plant Biology10: 242 (12 pages).

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  • Gu, Tan, Gou,Arakiand Tian.(2010)
    Avoidance of long mononucleotide repeats in codon pair usage.
    Genetics188: 1077-1084.

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  • Wang, Ho, Hung, Wang, Huang,Araki, Osada and Chiang (2010)
    Multi-locus analyzes of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.
    New Phytologist188: 488-500.

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  • Zhu, Wang, Tang,Arakiand Tian.(2009)
    Genome-wide association between insertions/deletions and the nucleotide diversity in bacteria.
    Molecular Biology and Evolution26: 2353-2361.

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  • Tian, Wang, Zhang,Araki, Yang, Kreitman, Nagylaki, Hudson, Bergelson and Chen. (2008)
    Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes.
    Nature455: 105-108. [Media coverage: F1000]

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

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  • Du, Gu, Tian,Araki, Yang and Tian (2008)
    Grouped nucleotide polymorphism: A major contributor to genetic variation in Arabidopsis.
    Gene426: 1-6.

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  • Araki, Innan, Kreitman and Bergelson (2007)
    Molecular evolution of pathogenicity-island genes in Pseudomonas viridiflava.
    Genetics177: 1031-1041.

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  • Ding,Araki, Wang, Zhang, Yang, Chen and Tian (2007)
    Highly asymmetric rice genomes.
    BMC Genomics8: 154.

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  • Orgil,Araki,Tangchaiburana, Berkey and Xiao (2007)
    Intraspecific genetic variations, fitness cost and benefit of RPW8, a disease resistance locus in Arabidopsis thaliana.
    Genetics176: 2317-2333.

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  • Yang, Jiang,Araki, Ding, Yang and Tian (2007)
    A molecular isolation mechanism associated with high intra-specific diversity in rice.
    Gene394: 87-95.

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  • Ding, Cheng, Jin,Araki, Yang and Tian (2007)
    Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis.
    Genetica129: 235-242.

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  • 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]

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  • Shen,Araki, Chen, Chen and Tian (2006)
    Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana.
    Genetics172: 1243-1250.

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  • Araki, Yoshizumi, Inomata and Yamazaki (2005)
    Genetic adaptation of the Amylase gene system inDrosophila melanogaster: Evidence for the selective advantage of the lowest AMY activity and of its epistatic genetic background.
    Journal of Heredity96: 388-395.

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  • 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.

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

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

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  • Araki, Inomata and Yamazaki (2001)
    Molecular evolution of duplicated amylase gene regions inDrosophila melanogaster: Evidence of positive selection in the coding regions and selective constraints in thecis-regulatory regions.
    Genetics157: 667-677.

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  • Arakiand Tachida. (1997)
    Bottleneck effect on evolutionary rate in the nearly neutral mutation model.
    Genetics147: 907-914.

BOOK SECTIONS

  • Yatsuyanagi,Minegishi,Mizumoto&Araki (2021)
    In "Environmental DNA - Understanding the True Form of Ecosystems" (Kyoritsu Shuppan)
    – Examples of species-specific environmental DNA methods

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  • 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”

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

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