Research Outcomes


The latest list of publications available at:


Araki’s pre-HU publications:


  • 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.


  • 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