63 Works

Data from: Low functional diversity promotes niche changes in natural island pollinator communities

Masayoshi K. Hiraiwa & Atushi Ushimaru
Functional diversity loss among pollinators has rapidly progressed across the globe and is expected to influence plant–pollinator interactions in natural communities. Although recent findings suggest that the disappearance of a certain pollinator functional group may cause niche expansions and/or shifts in other groups, no study has examined this prediction in natural communities with high plant and pollinator diversities. By comparing coastal pollination networks on continental and oceanic islands, we examined how community-level flower visit patterns...

Dataset for benchmark models (Final 2017-10-19)

Ji Yingfeng

Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling

Keiichi Fukaya, Hiroaki Murakami, Seokjin Yoon, Kenji Minami, Yutaka Osada, Satoshi Yamamoto, Reiji Masuda, Akihide Kasai, Kazushi Miyashita, Toshifumi Minamoto & Michio Kondoh
Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of...

Thermal state, slab metamorphism and interface seismicity in the Cascadia subduction zone based on 3-D modeling

Yingfeng JI, Shoichi Yoshioka & Yuval A. Banay
Giant earthquakes have repeatedly ruptured the Cascadia subduction zone, and similar earthquakes will likely also occur there in the near future. We employ a 3-D time-dependent thermomechanical model that incorporates an up-to-date description of the slab geometry to study the Cascadia subduction thrust. Results show a distinct band of 3-D slab dehydration that extends from Vancouver Island to the Seattle Basin and further southward to the Klamath Mountains in northern California, where episodic tremors cluster....

Data from: Historical changes in grassland area determined the demography of semi-natural grassland butterflies in Japan

Naoyuki Nakahama, Kei Uchida, Atushi Ushimaru & Yuji Isagi
Semi-natural grassland areas expanded worldwide several thousand years ago following an increase in anthropogenic activities. However, semi-natural grassland habitat areas have been declining in recent decades due to changes in landuse, which have caused a loss of grassland biodiversity. Reconstructing historical and recent demographic changes in semi-natural grassland species will help clarify the factors affecting their population decline. Here, we quantified past and recent demographic histories of Melitaea ambigua (Lepidoptera; Nymphalidae), an endangered grassland butterfly...

Earth and life evolve together from something ancestral — reply to Britz et al

Kazunori Yamahira, Shingo Fujimoto & Yasuoki Takami
Ricefishes of the family Adrianichthyidae are considered to have dispersed eastward “out-of-India” after the collision of the Indian subcontinent with Eurasia and subsequently diversified in Southeast-East Asia. In this study, we reconstructed ancestral areas of Adrianichthyidae with BioGeoBEARS, expanding the scope to include Cyprinodontiformes, the outgroup of Beloniformes to which Adrianichthyidae belongs. The results again supported the “out-of-India” dispersal scenario. The dataset contained all files necessary for the BioGeoBEARS analysis.

Additional file 3 of Olfactory marker protein contains a leucine-rich domain in the Ω-loop important for nuclear export

Noriyuki Nakashima, Akiko Nakashima, Kie Nakashima & Makoto Takano
Additional file 3: The Macrocodes to convert the MSA in a FASTA format into an Excel format.

Additional file 1 of Olfactory marker protein contains a leucine-rich domain in the Ω-loop important for nuclear export

Noriyuki Nakashima, Akiko Nakashima, Kie Nakashima & Makoto Takano
Additional file 1: The raw data presented in this study.

Dataset for the study of Enhancing the spectral range of plant and bacterial Light-Harvesting pigment-protein complexes with various synthetic chromophores incorporated into lipid vesicles

Ashley Hancock, David Swainsbury, Sophie Meredith, Kenichi Morigaki, Christopher Hunter & Peter Adams
The Light-Harvesting (LH) pigment-protein complexes found in photosynthetic organisms have the role of absorbing solar energy with high efficiency and transferring it to reaction centre complexes. LH complexes contain a suite of pigments that each absorb light at specific wavelengths, however, the natural combinations of pigments within any one protein complex do not cover the full range of solar radiation. Here, we provide an in-depth comparison of the relative effectiveness of five different organic “dye”...

Additional file 2 of Olfactory marker protein contains a leucine-rich domain in the Ω-loop important for nuclear export

Noriyuki Nakashima, Akiko Nakashima, Kie Nakashima & Makoto Takano
Additional file 2: The raw MSA of OMP in FASTA format downloaded from COBALT.

A critical role of the periplasm in copper homeostasis in Gram-negative bacteria

Jun-ichi Ishihara, Tomohiro Mekubo, Chikako Kusaka, Suguru Kondo, Ryotaro Oiko, Kensuke Igarashi, Hirofumi Aiba, Shu Ishikawa, Naotake Ogasawara, Taku Oshima & Hiroki Takahashi
Data from: Jun-ichi Ishihara, Tomohiro Mekubo, Chikako Kusaka, Suguru Kondo, Ryotaro Oiko, Kensuke Igarashi, Hirofumi Aiba, Shu Ishikawa, Naotake Ogasawara, Taku Oshima and Hiroki Takahashi. 2022.

Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

Sou Fukumoto, Atushi Ushimaru & Toshifumi Minamoto
1. To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics. 2. The identification of DNA fragments sampled from a body of water (environmental DNA) has become...

Data from: Colonization and persistence of urban ant populations as revealed by joint estimation of kinship and population genetic parameters

Junpei Yamamoto, Kei Uchida & Yasuoki Takami
The decrease in biodiversity due to increasing urbanization has been well documented, but the processes of colonization and maintenance of wildlife populations in urban areas remain poorly understood. We address this issue using 462 individuals from 10 urban populations of the ant Formica japonica in Kobe City, Japan. We sampled workers regardless of colony identity, genotyped them using 6 microsatellite loci, and estimated allele frequencies and genotypes of reproductive individuals, together with other population genetic...

Maternal gut microbiota in pregnancy dictates offspring metabolic phenotype

Ikuo Kimura, Junki Miyamoto, Ryuji Ohue-Kitano, Keita Watanabe, Takahiro Yamada, Masayoshi Onuki, Ryo Aoki, Yosuke Isobe, Daiji Kashihara, Daisuke Inoue, Akihiko Inaba, Yuta Takamura, Satsuki Taira, Shunsuke Kumaki, Masaki Watanabe, Masato Ito, Fumiyuki Nakagawa, Junichiro Irie, Hiroki Kakuta, Masakazu Shinohara, Ken Iwatsuki, Gozoh Tsujimoto, Hiroaki Ohno, Makoto Arita, Hiroshi Ito … & Koji Hase
Antibiotics and dietary habits can affect the gut microbial community, influencing disease susceptibility. Although the influence of microbiota on the postnatal environment has been well documented, much less is known regarding the impact of gut microbiota at the embryonic stage. Here, we show that maternal microbiota shapes the metabolic system of offspring. During pregnancy, short-chain fatty acids produced by the maternal microbiota dictate the differentiation of neural, intestinal, and pancreatic cells through embryonic GPR41 and...

Data from: Ecological implications of the correlation of avian footprints with wing characteristics: a mathematical approach

Ikuko Tanaka
The characteristics of avian wings that evolved for flying appear to show a distinct relationship to the shape of the pes and walking abilities as reflected in footprints. Wing area, wing span and body weight data of modern birds were collected and analysed in order to quantify the possible correlation, which was previously only inferred from empirical data. Discriminant analysis demonstrated that avian wings can be divided into three habitat groups, in a similar way...

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

Toshifumi Minamoto, Kana Hayami, Masayuki Sakata, Takashi Inagawa, Jiro Okitsu, Izumi Katano, Hideyuki Doi, Katsuki Nakai, Hidetaka Ichiyanagi, Ryo Gotoh, Masaki Miya, Hirotoshi Sato & Hiroki Yamanaka
Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly. To identify optimal sampling seasons and locations, we performed sampling monthly or at two-monthly intervals throughout the year in...

Data from: Successful escape of bombardier beetles from predator digestive systems

Shinji Sugiura & Takuya Sato
Some prey animals can escape from the digestive systems of predators after being swallowed. To clarify the ecological factors that determine the success of such an escape, we investigated how the bombardier beetle Pheropsophus jessoensis escapes from two toad species, Bufo japonicus and B. torrenticola, under laboratory conditions. Pheropsophus jessoensis ejects a hot chemical spray from the tip of the abdomen when it is attacked. Although all toads swallowed the bombardier beetles, 43% of the...

Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Tamara Spasojevic, Ilari E. Sääksjärvi, Masato Ito, Stanislav Korenko, Seraina Klopfstein, Gavin R. Broad & Martin Schwarz
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes,...

Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats

Tatsuya Tanaka, Rui Ueda & Takuya Sato
Supplementation of wild populations with captive-bred individuals is often ineffective for boosting long-term productivity of wild populations. On the other hand, it remains unknown whether supplementation can act to maintain life-history variation in natural habitats, which is also important for the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause rapid...

Dataset for the study of “Model Lipid Membranes Assembled from Natural Plant Thylakoids into 2D Microarray Patterns as a Platform to Assess the Organization and Photophysics of Light‐Harvesting Proteins”

Sophie Meredith, Takuro Yoneda, Ashley Hancock, Simon Connell, Stephen Evans, Kenichi Morigaki & Peter Adams
This dataset shows the raw data, analysed data and documentation related to figures and tables from the study "Model Lipid Membranes Assembled from Natural Plant Thylakoids into 2D Microarray Patterns as a Platform to Assess the Organization and Photophysics of Light‐Harvesting Proteins". This includes: absorbance and fluorescence spectra; images from Fluorescence Lifetime Imaging Microscopy (FLIM); images from Atomic Force Microscopy measurements; epifluorescence measurements; analysis of fluorescence data (FLIM); other graphical analyses; tabulated numerical data.

Data from: Non-random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi-natural grasslands

Kei Uchida, Masayoshi K. Hiraiwa & Marc W. Cadotte
1. Although biodiversity loss is a critically important topic, our understanding of how both land abandonment and land-use intensification in semi-natural grasslands alters the community diversity and assembly mechanisms is very limited. Large-scale economic drivers of land-use change might inadvertently result in the loss of vulnerable species and reduce ecosystem services provisioning. 2. In this study, we assessed non-random community change by examining patterns of low-abundance species loss, and community assembly in semi-natural grasslands due...

Venus Climate Orbiter Akatsuki LIR Longitude-Latitude Map Data

Shin-ya Murakami, Kazunori Ogohara, Masahiro Takagi, Hiroki Kashimura, Manabu Yamada, Toru Kouyama, Takeshi Horinouchi & Takeshi Imamura
This dataset contains longitude-latitude map data created from images acquired by the LIR instrument of the Venus Climate Orbiter (VCO, also known as PLANET-C and AKATSUKI) spacecraft. This dataset consists of NetCDF and FITS files. The longitude-latitude map data are included as Level 3 product in NetCDF. During process of creating longitude-latitude map data, pointing of spacecraft was corrected using limb-fitting technique. Detected limb points and information on fitted ellipse are provided as auxiliary data,...

Data set: Reproductive character displacement in genital morphology in Ohomopterus ground beetles

Taira Nishimura, Nobuaki Nagata, Karen Terada, Tian Xia, Kouhei Kubota, Teiji Sota & Yasuoki Takami
Genital morphology reveals rapid diversification among species, and species-specific divergence in genital morphology may result in reproductive isolation and promote speciation. Natural selection against maladaptive hybridization may cause species-specific genital divergence. In this context, divergence in mating traits is expected to be greater between sympatric populations than between allopatric populations in a pair of species, known as reproductive character displacement (RCD). However, there are few examples of RCD in the genital morphology of closely related...

Dataset for Xia et al.: Reproductive isolation via divergent genital morphology due to cascade reinforcement in Ohomopterus ground beetles

Yasuoki Takami
Secondary contact between incipient species and selection against maladaptive hybridization can drive reinforcement between populations in contact and result in reproductive character displacement (RCD). Resultant divergence in mating traits within a species may generate downstream reproductive isolation between populations with displaced and non-displaced traits, referred to as the cascade reinforcement hypothesis. We examined this hypothesis using three allopatric populations of the ground beetle Carabus maiyasanus with a genital lock-and-key system. This species shows RCD in...

Additional file 1 of Olfactory marker protein is unlikely to be cleaved by calpain 5

Noriyuki Nakashima, Kie Nakashima, Akiko Nakashima & Makoto Takano
Supplementary Material 1

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013

Resource Types

  • Dataset


  • Kobe University
  • Kyoto University
  • Kurume University
  • Hokkaido University
  • Chiba Institute of Technology
  • National Institute of Advanced Industrial Science and Technology
  • Tohoku University
  • University of the Ryukyus
  • Ryukoku University
  • University of Melbourne