21 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...

Diversity of sex chromosomes in Sulawesian medaka fishes

Satoshi Ansai, Javier Montenegro, Kawilarang W. A. Masengi, Atsushi J. Nagano, Kazunori Yamahira & Jun Kitano
Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species...

Plant-plant communication and community of herbivores on tall goldenrod (dataset)

Kaori Shiojiri, Satomi Ishizaki & Yoshino Ando
1. The volatiles from damaged plants induce defense in neighboring plants. The phenomenon is called plant-plant communication, plant talk or plant eavesdropping. Plant-plant communication has been reported to be stronger between kin plants than genetically far plants in sagebrush. 2. Why do plants distinguish volatiles from kin or genetically far plants? We hypothesize that plants respond only to important conditions; the induced defense is not free of cost for the plant. To clarify the hypothesis,...

Data from: Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs

Yuichi Yamaura, Ayu Narita, Yoshinobu Kusumoto, Atsushi J. Nagano, Ayumi Tezuka, Toru Okamoto, Hikaru Takahara, Futoshi Nakamura, Yuji Isagi & David Lindenmayer
Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on...

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;...

Estimating household preferences for coastal flood risk mitigation policies under ambiguity

Si Ha, Toshio Fujimi, Xinyu Jiang, Nobuhito Mori, Rawshan Begum, Masahide Watanabe, Hirokazu Tatano & Eiichi Nakakita
Risk mitigation policies (like dike rising) are essential to address increasing coastal flood risks due to global warming. Furthermore, the optimal level of risk mitigation policy should be determined by public preferences for risk reduction. However, it is difficult to reveal public preferences for coastal flood risk reduction because projections of coastal flood risks inevitably involve uncertainty. This study aims to estimate household preference for coastal flood reduction under ambiguity and multiple projections of coastal...

Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Y. Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh & Wataru Iwasaki
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility...

Data from: A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

Kohei Koyama, Ken Yamamoto & Masayuki Ushio
Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees (Ulmus davidiana), the end products of a...

Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

Atsushi Maruyama, Kousuke Sugatani, Kazuki Watanabe, Hiroki Yamanaka & Akio Imamura
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan),...

Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha

Kiwako S. Araki, Atsushi J. Nagano, Ryohei Thomas Nakano, Tatsuya Kitazume, Katsushi Yamaguchi, Ikuko Hara-Nishimura, Shuji Shigenobu & Hiroshi Kudoh
The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, Cardamine leucantha. Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both...

Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish

Javier Montenegro, Shingo Fujimoto, Satoshi Ansai, Atsushi Nagano, Masahiro Sato, Yusuke Maeda, Rieko Fujitani, Kawilarang Masengi, Ryosuke Kimura, Jun Kitano & Kazunori Yamahira
Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called “pelvic-fin brooding,” wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved...

Data from: The evolution of between-species reproductive interference capability under different within-species mating regimes

Daisuke Kyogoku & Teiji Sota
Sexual selection sometimes favors male traits that benefit their bearers, but harm their mates. The harmful effects of male traits may also extend to females of other species via heterospecific mating interactions. This could affect the coexistence of closely related species during secondary contact. We examined the evolution of the interspecific interfering capability of a beetle (Callosobruchus chinensis) with a congener (C. maculatus) using C. chinensis males reared under conditions of monogamy and polygamy for...

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...

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....

Data from: Drastic shift in flowering phenology of F1 hybrids explains the population structure of Imperata cylindrica in Japan

Yasuyuki Nomura, Yoshiko Shimono, Nobuyuki Mizuno, Ikuya Miyoshi, Satoshi Iwakami, Kazuhiro Sato & Tohru Tominaga
Hybridization is a major source of phenotypic variation and a driving force for evolution. On the other hand, these novel traits can often disrupt adaptive relationships between the parental phenotypes and their environments. However, it remains unclear how new hybrid traits disrupt local adaptation. Here, we report how a new phenotype of hybrids between two ecotypes of Imperata cylindrica contributes to rapid reproductive isolation from their parents and affects hybrid fitness. We analyzed 350 accessions...

Data from: The release rate of environmental DNA from juvenile and adult fish

Atsushi Maruyama, Keisuke Nakamura, Hiroki Yamanaka, Michio Kondoh & Toshifumi Minamoto
The environmental DNA (eDNA) technique is expected to become a powerful, non-invasive tool for estimating the distribution and biomass of organisms. This technique was recently shown to be applicable to aquatic vertebrates by collecting extraorganismal DNA floating in the water or absorbed onto suspended particles. However, basic information on eDNA release rate is lacking, despite it being essential for practical applications. In this series of experiments with bluegill sunfish (Lepomis macrochirus), we examined the effect...

Data from: Optimal foraging by herbivores maintains polymorphism in defence in a natural plant population

Yasuhiro Sato, Koichi Ito & Hiroshi Kudoh
1. Many species of plants and animals exhibit polymorphism for defensive traits. Adaptive foraging by natural enemies has long been hypothesized to maintain such polymorphism, but this has not been clearly demonstrated in a natural prey or host population. 2. The purpose of this study was to address whether the brassica leaf beetle Phaedon brassicae promotes the maintenance of defence polymorphism in the trichome-producing (hairy) and trichomeless (glabrous) morphs of Arabidopsis halleri subsp. gemmifera. Here,...

Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Tsuji Satsuki, Hiroki Yamanaka, Hideyuki Doi & Satsuki Tsuji
The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b...

Data from: A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews … & Jun Kitano
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and...

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...

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...

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  • Ryukoku University
  • Kyoto University
  • Tohoku University
  • Sam Ratulangi University
  • Hokkaido University
  • National Institute of Genetics
  • University of the Ryukyus
  • Kobe University
  • Niigata University
  • University of Tokyo