97 Works

Data from: Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa

Kato Shuri, Teruyoshi Nagamitsu, Hiroyoshi Iwata, Yoshihiko Tsumura, Yuzuru Mukai, K Michiharu, K Saika & K Junko
Mating processes of local demes and spatial genetic structure of island populations at the self-incompatibility (S-) locus under negative frequency-dependent selection (NFDS) were evaluated in Prunus lannesiana var. speciosa in comparison with nuclear simple sequence repeat (SSR) loci that seemed to be evolutionarily neutral. Our observations of local mating patterns indicated that male-female pair fecundity was influenced by not only self-incompatibility, but also various factors such as kinship, pollen production and flowering synchrony. In spite...

Data from: The population demography of Betula maximowicziana, a cool temperate tree species in Japan, in relation to the last glacial period: Its admixture-like genetic structure is the result of simple population splitting not admixing

Yoshiaki T. Tsuda, Katsuhiro N. Nakao, Yuji I. Ide, Yoshihiko T. Tsumura, Y. Tsuda, Y. Tsumura & K. Nakao
Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag–simple sequence repeat (EST-SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three...

Data from: A novel growth model evaluating age-size effect on long-term trends in tree growth.

Michinari Matsushita, Katsuhiko Takata, Gaku Hitsuma, Tsutomu Yagihashi, Mahoko Noguchi, Mitsue Shibata & Takashi Masaki
1.One of the major problems in understanding growth trends in long-lived trees is the difficulty of separately quantifying the effects of tree size and age. Careful statistical control of the axiomatic age×size covariation is therefore required to identify long-term trends in tree growth and their drivers, and to predict forests’ responses to environmental changes reliably. 2.To address this issue, we present a novel tree growth model: a ‘two-dimensional lognormal growth model’. This is an extension...

Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)

James R. P. Worth, James R. Marthick, Maurizio Rossetto, Joel Cohen, Greg Bourke & Gregory J. Jordan
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall...

Field data and microsatellite genotypes of Cercidiphyllum japonicum

Atsushi Nakanishi
Field data and genotypes at five microsatellite loci of 281 Cercidiphyllum japonicum adults of a population distributed over a ca. 80 ha along a stream and 755 C. japonicum current-year seedlings sampled at approximate center of the populatoin. The population is located in Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan.

Role of individual dispersal in genetic resilience in fluctuating populations of the grey-sided vole Myodes rufocanus

Yasuyuki Ishibashi & Kenichi Takahashi
Population densities of the grey-sided vole Myodes rufocanus fluctuate greatly within and across years in Japan. Here, to investigate the role of individual dispersal in maintaining population genetic diversity, we examined how genetic diversity varied during fluctuations in density by analyzing eight microsatellite loci in voles sampled three times per year for 5 years, using two fixed trapping grids (approximately 0.5 ha each). At each trapping session, all captured voles at each trapping grid were...

Spruce trees absorb intact urea from soils on permafrost

Kazumichi Fujii
Biomass productivity of black spruce trees is strongly limited by soil nitrogen in shallow active layer on permafrost. Trees and mycorrhizal roots are known to absorb amino acids to bypass slow nitrogen mineralization in nitrogen-limited boreal forest soils. However, the amino acid uptake strategy of tree roots cannot fully explain their advantages in the competition for soil nitrogen with other plants and microbes. Here, we provide evidence that some spruce tree roots absorb intact urea....

International biological flora: Nervilia nipponica

Stephan Gale, Ayako Maeda, Ayana Miyashita, Daisuke Sugiura, Yuki Ogura-Tsujita, Akihiko Kinoshita, Shohei Fujimori, Michael Hutchings & Tomohisa Yukawa
This account presents information on all aspects of the biology of Nervilia nipponica Makino (mukago-saishin) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the International Biological Flora: distribution, habitat, communities, responses to biotic factors, responses to the environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, conservation and global heterogeneity. Nervilia nipponica is a small, stoloniferous, seasonally dormant herb...

Temporal variation in regeneration events affecting population structure in different size- and life-stages contributes to overall genetic diversity of natural Zelkova serrata population

Masakazu G. Iwaizumi, Makoto Takahashi & Keisuke Yano
To clarify the mechanisms underlying the maintenance of genetic diversity in long-lived forest tree populations, it is important to understand the influence of temporal variation in regeneration sites and its effect on population structure (i.e., nonrandom distribution of trees in spatial location and size) and the spatial genetic structure. Features of population structure in four different life stages (current-year seedlings, saplings, juveniles, and adults) were investigated in a natural population of Zelkova serrata. The genetic...

Additional file 11 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 11. Summary of assembly and characterization.

Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Abstract Background Japanese larch (Larix kaempferi) is an economically important deciduous conifer species that grows in cool-temperate forests and is endemic to Japan. Kuril larch (L. gmelinii var. japonica) is a variety of Dahurian larch that is naturally distributed in the Kuril Islands and Sakhalin. The hybrid larch (L. gmelinii var. japonica × L. kaempferi) exhibits heterosis, which manifests as rapid juvenile growth and high resistance to vole grazing. Since these superior characteristics have been...

Additional file 3 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 3. Description of Japanese larch used in this study.

Additional file 5 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 5. Number of open reading frames (ORFs) similar to NCBI sequeces and other species according to BLASTp E-value cutoff values. a) ORFs obtained from Japanese larch, b) ORFs obtained from ORF Kuril larch.

Additional file 4 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 4. Description of Kuril larch used in this study.

Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas

Thomas Jung, Ivan Milenković, Tamara Corcobado, Tomáš Májek, Josef Janoušek, Tomáš Kudláček, Michal Tomšovský, Zoltán Nagy, Álvaro Durán, Marthin Tarigan, Eugenio Sanfuentes Von Stowasser, Raghuwinder Singh, Monique Ferreira, Joan Webber, Bruno Scanu, Nguyen Minh Chi, Pham Quang Thu, Muhammad Junaid, Ade Rosmana, Baharuddin Baharuddin, Tutik Kuswinanti, Nasri Nasri, Koji Kageyama, Ayaka Hieno, Hayato Masuya … & Marília Horta Jung
During extensive surveys of Phytophthora diversity, 14 new species were detected in natural ecosystems in Chile, Louisiana, Sweden, Ukraine, Vietnam and Indonesia. Multigene phylogeny based on the nuclear LSU, rpl10, ITS, ßtub, enl, hsp90, tef-1α, ras-ypt1 and tigA and the mitochondrial cox1, nadh1 and rps10 gene sequences demonstrated that they belong to phylogenetic Clade 10 which is structured into three subclades. Subclades 10a and 10b comprise soil- and waterborne species with nonpapillate sporangia and variable...

Data from: Deep phylogeographic structure and parallel host range evolution in the leaf beetle Agelasa nigriceps

Tetsuo I. Kohyama, Kazuma Matsumoto & Haruo Katakura
To understand the mechanisms behind the diversification of herbivorous insects through insect-plant interactions, it is important to know how the insects change their diet breadth in response to environmental changes. In this study, we investigated the phylogeographic pattern of the leaf beetle Agelasa nigriceps to infer the evolutionary history of its host range. While this beetle commonly uses Actinidia arguta (Actinidiaceae) as a host plant, it has been recorded recently on Pterostyrax hispidus (Styracaceae), which...

Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia

Masato Ohtani, Toshiaki Kondo, Naoki Tani, Saneyoshi Ueno, Soon-Leong Lee, Kevin Kit Siong Ng, Norwati Muhammad, Reiner Finkeldey, Mohamad Na'iem, Sapto Indrioko, Koichi Kamiya, Ko Harada, Bibian Diway, Eyen Khoo, Kensuke Kawamura, Yoshihiko Tsumura & Leong S. Lee
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear...

Data from: Relationships between resprouting ability, species traits, and resource allocation patterns in woody species in a temperate forest

Rei Shibata, Hiroko Kurokawa, Mitsue Shibata, Hiroshi Tanaka, Shigeo Iida, Takashi Masaki & Tohru Nakashizuka
Many woody plants resprout to restore above-ground biomass after disturbances or to survive in stressful environments. Resprouting requires carbohydrate storage, but the general relationship between resource allocation patterns and resprouting ability remains unclear because it can be influenced by the disturbance regime to which species have adapted. We studied deciduous broadleaved trees that coexist in a Japanese cool-temperate forest to investigate the relationships among the biomass and total non-structural carbohydrate (TNC) allocation patterns of saplings,...

Data from: How many broadleaved trees are enough in conifer plantations? The economy of land sharing, land sparing, and quantitative targets

Yuichi Yamaura, Yasushi Shoji, Yasushi Mitsuda, Hajime Utsugi, Takahiro Tsuge, Koichi Kuriyama & Futoshi Nakamura
1. For biodiversity conservation to be an effective and significant social investment, non-marketed values of biodiversity conservation and its associated opportunity costs should be evaluated in monetary terms. 2. In this study, we measured the willingness to pay (WTP) for bird abundance using a choice experiment (CE) based on the random utility model. We performed a cost–benefit analysis to identify the optimal proportion of broad-leaved trees in conifer plantations on a volume basis to maximize...

Genetic consequences of plant edaphic specialisation to solfatara fields; phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae)

Koki Nagasawa, Hiroaki Setoguchi, Masayuki Maki, Hayato Goto, Keitaro Fukushima, Yuji Isagi, Yoshihisa Suyama, Yoshihiro Tsunamoto, Ayumi Matsuo, Kazuhiro Sawa & Shota Sakaguchi
Edaphic specialisation is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in similar habitats and its disjunct distribution, the species offers ideal settings to investigate the effects of adaptation to solfatara fields and historical biogeography on genetic consequences of plant...

Data from: Initial hydraulic failure followed by late-stage carbon starvation leads to drought-induced death in tree, Trema orientalis

Yuri Kono, Atsushi Ishida, Shin-Taro Saiki, Kenichi Yoshimura, Masako Dannoura, Kenichi Yazaki, Fuku Kimura, Jin Yoshimura & Shin-Ichi Aikawa
Drought-induced tree death has become a serious problem in global forest ecosystems. Two nonexclusive hypotheses, hydraulic failure and carbon starvation, have been proposed to explain tree die-offs. To clarify the mechanisms, we investigated the physiological processes of drought-induced tree death in saplings with contrasting Huber values (sapwood area/total leaf area). First, hydraulic failure and reduced respiration were found in the initial process of tree decline, and in the last stage carbon starvation leaded to tree...

Genetic diversity, structure, and demography of Pandanus boninensis(Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

Suzuki Setsuko, Kyoko Sugai, Ichiro Tamaki, Koji Takayama, Hidetoshi Kato & Hiroshi Yoshimaru
Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population diversity and structure across old and young islands, to assess potential differences in population demography with island age, and to collect any evidence of migration between old and young islands. We found that the genetic diversity of expressed...

Additional file 5 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 5. Number of open reading frames (ORFs) similar to NCBI sequeces and other species according to BLASTp E-value cutoff values. a) ORFs obtained from Japanese larch, b) ORFs obtained from ORF Kuril larch.

Additional file 6 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 6. Alignment of known MADS-box genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Additional file 8 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura & Makoto Takahashi
Additional file 8. Alignment of known FT/FT-like and MFT genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Registration Year

  • 2022
    40
  • 2021
    14
  • 2020
    8
  • 2019
    7
  • 2018
    7
  • 2017
    4
  • 2016
    3
  • 2015
    6
  • 2013
    4
  • 2012
    3

Resource Types

  • Dataset
    73
  • Text
    18
  • Collection
    4
  • Audiovisual
    2

Affiliations

  • Forestry and Forest Products Research Institute
    97
  • Kazusa DNA Research Institute
    24
  • Kyoto University
    11
  • Hokkaido University
    8
  • Nagoya University
    8
  • University of Tokyo
    8
  • Tohoku University
    6
  • University of Miyazaki
    5
  • University of Pretoria
    4
  • University of Florida
    4