Araki’s Lab Recent Publications


  • An environmental DNA survey on distribution of an endangered salmonid species, Parahucho perryi, in Hokkaido, Japan. H. Mizumoto, T. Mitsuzuka, H. ArakiFront. 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)
  • 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 00:1-6. (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)


  • 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)


  • 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. ArakiLimnology 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)


  • 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)


  • 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)


  • 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)


  • 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.


  • Wang, Si, Yao, Tian, Araki and Yang (2012) Genome-wide survey of Pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. PLoS One 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 const 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.


  • Araki (2009) A review essay of a genetic evaluation program on the natural reproductive success of hatchery-born fish using DNA-based parentage assignments. Fish Genetics and Breeding Science, 39 (1) 31-35. (in Japanese)
  • Araki, Ardren, Olsen, Cooper and Blouin (2008) Hatchery stocking for restoring wild populations: A genetic evaluation of the reproductive success of hatchery fish and their descendants. The Proceedings of the 5th World Fisheries Congress, Yokohama, Japan. (in English)


  • 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