The latest list of publications available at:
Araki’s pre-HU publications:
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.
- 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
- 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.
PROCEEDINGS & NON PEER-REVIEWED ARTICLES
- 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”