6 Works

A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set

Akio Onogi
It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. In this study, we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions...

Species divergence and repeated ancient hybridization in a Sulawesian lake system

Kazunori Yamahira, Ixchel Mandagi, Ryo Kakioka, Javier Montenegro, Hirozumi Kobayashi, Kawilarang Masengi, Nobuyuki Inomata, Atsushi Nagano, Atsushi Toyoda, Satoshi Ansai, Masatoshi Matsunami, Ryosuke Kimura, Jun Kitano & Junko Kusumi
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent, and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes;...

Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake

Ryo Kakioka, Nobu Sutra, Hirozumi Kobayashi, Satoshi Ansai, Kawilarang Masengi, Atsushi Nagano, Noboru Okuda, Rieko Tanaka, Masahiro Sato & Kazunori Yamahira
Sympatric speciation is considered to be difficult without the coupling between ecological traits that allow resource partitioning and reproductive traits that allow assortative mating. Such “magic traits” are known to be involved in most of the compelling examples of sympatric speciation. In this study, we report a possible case of sympatric speciation without magic traits. Three species of ricefish (genus Oryzias) are suggested to have diverged sympatrically within Lake Poso, an ancient lake in Sulawesi....

Phylogeographic and demographic modelling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana

Ryuuta Kyan, Takuma Kimura, Tadashi Yamashiro, Shinji Fujii, Shota Sakaguchi, Motomi Ito, Atsushi Nagano, Hiroshi Kudoh & Masayuki Maki
Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modelling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple...

Genomic prediction with non-additive effects in beef cattle: Stability of variance component and genetic effect estimates against population size

Akio Onogi
Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. Thus, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by...

Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

Watanabe Yoichi, Minami Takahashi, Atsushi J. Nagano, Koichi Uehara & Harue Abe
Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of Rhododendron tsusiophyllum, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of R. tsusiophyllum and three populations of R. tschonoskii as an outgroup. Phylogenetic relationships and...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Ryukoku University
  • Tohoku University
  • Sam Ratulangi University
  • Kyoto University
  • University of the Ryukyus
  • Kyushu University
  • Fukuoka Women's University
  • Chiba University
  • University of Human Environments
  • National Institute of Genetics