32 Works

Data from: A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

Joel Nitta, Atsushi Ebihara & Alan Smith
Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176...

Infant cannibalism in wild white-faced capuchin monkeys

Mari Nishikawa, Nuria Ferrero, Saul Cheves, Ronald Lopez, Shoji Kawamura, Linda Fedigan, Amanda Melin & Katharine Jack
Cannibalism has been observed in a variety of animal taxa, however, it is relatively uncommon in primates. Thus we rely heavily on case reports of this behavior to advance our understanding of the contexts under which it occurs. Here we report the first observation of cannibalism in a group of wild white-faced capuchin monkeys (Cebus imitator). The subject was a dead infant, estimated to be 10 days old, and the probable victim of infanticide. Consumption...

Data from: Evaluation of the severity of major depression using a voice index for emotional arousal

Shuji Shinohara
We first developed an arousal level voice index (ALVI) to measure arousal levels using the Interactive Emotional Dyadic Motion Capture database. Then, we calculated ALVI from the voices of depressed patients from two hospitals H1 and H2 and compared them with the severity of depression as measured by the Hamilton Rating Scale for Depression (HAM-D). Depending on the HAM-D score, the datasets were classified into a no depression (HAM-D<8) and a depression group (HAM-D≥8) for...

Data from: Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific

Junya Hirai, Aiko Tachibana & Atsushi Tsuda
A clear insight into large-scale community structure of planktonic copepods is critical to understanding mechanisms controlling diversity and biogeography of marine taxa, owing to their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed...

Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea

Hu Dan, Yue-Hong Zhang, Yi-Fang Li, Yongjin Wang, Li Tan, Zhi-Qin Cao, Chao Xie, Guo Xie, Hai-Biao Gong, Wan-Yang Sun, Shu-Hua Ouyang, Wen-Jun Duan, Xiaoyun Lu, Ke Ding, Hiroshi Kurihara, Zhi-Min Zhang, Ikuro Abe & Rong-Rong He
Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. Due to its occasional side effects, reduction of caffeine in a natural way is of great importance and economic significance. Recent studies reveal that caffeine can be converted into non-stimulatory theacrine in the rare tea plant Camellia assamica var. kucha (Kucha), which involves oxidation at the C8 and methylation at the N9 positions of caffeine. However, the underlying molecular mechanism...

Intelligent classification of platelet aggregates by agonist type

Yuqi Zhou, Atsushi Yasumoto, Cheng Lei, Chun-Jung Huang, Hirofumi Kobayashi, Yunzhao Wu, Sheng Yan, Chia-Wei Sun, Yutaka Yatomi & Keisuke Goda
Platelets are anucleate cells in blood whose principal function is to stop bleeding by forming aggregates for hemostatic reactions. In addition to their participation in physiological hemostasis, platelet aggregates are also involved in pathological thrombosis and play an important role in inflammation, atherosclerosis, and cancer metastasis. The aggregation of platelets is elicited by various agonists, but these platelet aggregates have long been considered indistinguishable and impossible to classify. Here we present an intelligent method for...

Raw data used in A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factor

Jotaro Urabe, Takehiro Kazama, Masato Yamamichi, Kotaro Tokita, Xuwang Yin, Izumi Katano, Hideyuki Doi, Takehito YOSHIDA & Nelson Hairston
The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka-Volterra equations...

Modelled annual average percentage yield loss due to ozone damage for four global staple crops, 2010-2012 version 2

K. Sharps, G. Mills, D. Simpson, H. Pleijel, M. Frei, K. Burkey, L. Emberson, J. Uddling, M. Broberg, Z. Feng, K. Kobayashi & M. Agrawal
Modelled average percentage yield loss due to ground-level ozone pollution (per 1 degree by 1 degree grid cell) are presented for the crops maize (Zea mays), rice (Oryza sativa), soybean (Glycine max) and wheat (Triticum aestivum) for the period 2010-2012. Data are on a global scale, based on the distribution of production for each crop, according to the Food and Agriculture Organisation’s (FAO) Global Agro-Ecological Zones (GAEZ) crop production data for the year 2000. Modelled...

Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

Euki Yazaki, Keitaro Kume, Takashi Shiratori, Yana Eglit, Goro Tanifuji, Ryo Harada, Alastair Simpson, Ken-Ichiro Ishida, Tetsuo Hashimoto & Yuji Inagaki
We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and...

Yield Constraint Score (YCS) for the effect of five crop stresses on global production of four staple food crops

K. Sharps, G. Mills, D. Simpson, H. Pleijel, M. Frei, K. Burkey, L. Emberson, J. Uddling, M. Broberg, Z. Feng, K. Kobayashi & M. Agrawal
A Yield Constraint Score (YCS; scale of 1-5) was developed for the effect of five key crop stresses (ozone, pests and diseases, soil nutrients, heat stress and aridity) on the production of the crops maize (Zea mays), rice (Oryza sativa), soybean (Glycine max) and wheat (Triticum aestivum). Data are on a global scale at 1° by 1° resolution, based on the distribution of production for each crop, according to the Food and Agriculture Organisation’s (FAO)...

Capacity for freshwater acclimation and differences in the transcription of ion transporter genes underlying different migratory life histories of Takifugu fish

Masahiro Nakamura, Tao Jiang, Gangchun Xu, Jian Yang, Pao Xu, Soichi Watanabe, Toyoji Kaneko, Takashi Koyama, Kiyoshi Kikuchi, Katsumi Tsukamoto & Tsuguo Otake
The genus Takifugu is a group of approximately 20 species of puffer fishes living in a wide range of salinity environments around East Asian countries. This group presents a broad spectrum of evolutionary stages adapted to anadromy as a result of speciation that occurred a short time (2–5 million years) ago on an evolutionary timescale. This group thus can be considered as a model for studying the evolutionary mechanisms of anadromy. We firstly conducted a...

Data from: A new method of Bayesian causal inference in non-stationary environments

Shuji Shinohara, Pegio-Yukio Gunji, Tatsuji Takahashi, Kouta Suzuki, Ung-Il Chung, Yoshihiro Nakajima, Nobuhito Manome, Shunji Mitsuyoshi & Hiroshi Okamoto
Bayesian inference is the process of narrowing down the hypotheses (causes) to the one that best explains the observational data (effects). To accurately estimate a cause, a considerable amount of data is required to be observed for as long as possible. However, the object of inference is not always constant. In this case, a method such as exponential moving average (EMA) with a discounting rate is used to improve the ability to respond to a...

Data from: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies

John Chiang, Michael Herman, Kei Yoshimura & Inez Fung
This archive contain the isoGSM2 model output used in the publication Chiang, J. C. H., M. J. Herman, K. Yoshimura, and I. Y. Fung: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies. In press for Proceedings of the National Academy of Sciences, April 2020

Dataset for: Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs

Kenji Ohgane, Ryuta Shioi, Fumika Karaki, Hiromasa Yoshioka, Tomomi Noguchi-Yachide, Minoru Ishikawa, Kosuke Dodo, Mikiko Sodeoka & Yuichi Hashimoto
Niemann-Pick disease type C is a rare, fatal neurodegenerative disorder characterized by massive intracellular accumulation of cholesterol. In most cases, loss-of-function mutations in NPC1 gene that encodes for a lysosomal cholesterol transporter NPC1 are responsible for the disease, and more than half of the mutations are considered to interfere with biogenesis or folding of the protein. Previously we have identified a series of oxysterol derivatives and phenanthridine-6-one derivatives as pharmacological chaperones, small molecules that rescue...

Data from: Novel reverse radioisotope labelling experiment reveals carbon assimilation of marine calcifiers under ocean acidification conditions

Kozue Nishida, Yue Chin Chew, Yosuke Miyairi, Shoko Hirabayashi, Atsushi Suzuki, Masahiro Hayashi, Yuzo Yamamoto, Mizuho Sato, Yukihiro Nojiri & Yusuke Yokoyama
1. Ocean acidification by anthropogenic carbon dioxide emissions is projected to depress metabolic and physiological activity in marine calcifiers. To evaluate the sensitivity of marine organisms against ocean acidification, the assimilation of nutrients into carbonate shells and soft tissues must be examined. 2. We designed a novel experimental protocol, reverse radioisotope labelling, to trace partitioning of nutrients within a single bivalve species under ocean acidification conditions. Injecting CO2 gas, free from radiocarbon, can provide a...

Data from: Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

Yuji Inagaki, Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Tazuya Takahashi, Hideaki Miyashita, Ken-Ichiro Ishida, Mitsunori Iwataki, Euki Yazaki & Eriko Matsuo
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet...

Audio files for applying the Wizard of Oz method

Chang Li & Hideyoshi Yanagisawa
This data set consists of audio files used by the users to apply the Wizard of Oz method in the two reported experiments, in which the experimenter simulated an autonomous virtual assistant in the context of interactive task sections. The audio files serve the purpose of duplicating the reported experiments. The experimental protocol, including instructions, are presented in Support Information affilliated to the PLOS ONE manuscript.

Data from: An intermediate type of medusa from the early Cambrian Kuanchuanpu Formation, South China

Xing Wang, Jean Vannier, Xiaoguang Yang, Shin Kubota, Qiang Ou, Xiaoyong Yao, Kentaro Uesugi, Osamu Sasaki, Tsuyoshi Komiya & Jian Han
The tetraradial or pentaradial fossil embryos and related hatched individuals from the early Cambrian Kuanchuanpu Formation are of great interest for understanding the early evolution of medusozoans. The phylogenetic and evolutionary significance of their external and internal characters (e.g. manubrium, tentacles, septa and claustra) is still controversial. Here we describe a new pentamerous medusozoan, Hanagyroia orientalis gen. et sp. nov., characterized by five well-developed perradial oral lips around a remarkably large manubrium, a conspicuous equatorial...

Data from: Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe Meng, Yutaka Sato, Thomas Städler, Ueli Grossniklaus, Masahiro Kanaoka, Michael Lenhard, Magnus Nordborg & Kentaro Shimizu
The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures...

Data from: Older males are not only attractive to but also aggressive toward females in Gnatocerus cornutus

Kensuke Okada, Masako Katsuki, Katsuya Kiyose & Yasukazu Okada
In theory, a male should change the allocation of fighting and mating efforts in relation to his age. Thus, the consequences of sexual selection may be complicated by changes in the male resource allocation due to aging. However, previous studies have focused on changes in female mate choice and male-male competition with aging separately, and the impact of aging on the relationship between mate choice and male competition is unknown. Here, we examined how male...

Mere presence of co-eater automatically shifts foraging tactics toward “fast and easy” food in humans

Yukiko Ogura, Taku Masamoto & Tatsuya Kameda
Competition for food resources is widespread in nature. The foraging behavior of social animals should thus be adapted to potential food competition. We hypothesized that in the presence of co-foragers, animals would shift their tactics to forage more frequently for smaller food. Because smaller foods are more abundant in nature and allow faster consumption, such tactics should allow animals to consume food more securely against scrounging. We tested whether humans would exhibit such a shift....

Offspring sex-ratios are stable across the life-course in Drosophila simulans

C. Ruth Archer, Matthew Carey, Tomohito Noda, Stefan Store & David Hosken
Within populations, adult sex ratios influence population growth and extinction risk, mating behaviors and parental care. Additionally, sex ratio adjustment can have pronounced effects on individual fitness. Accordingly, it is important that we understand how often, and why, offspring sex ratios deviate from parity. In Drosophila melanogaster, females appear to improve their fitness by producing fewer sons when paired with older males. However, facultative sex ratio adjustment in D. melanogaster is controversial, and our understanding...

Contemporary adaptive divergence of plant competitive traits in urban and rural populations and its implication for weed management

Yuya Fukano, Wei Guo, Kei Uchida & Yuuya Tachiki
1. Competition among neighboring plants plays essential roles in growth, reproduction, population dynamics, and community assembly, but how competition drives local adaptation and the traits underlying the adaptation remain unclear. Here, we focused on populations of the aggressive weed Digitaria ciliaris from urban and rural habitats as low- and high-competition environments for light resources and examined how competitive interaction drove contemporary adaptive divergence of competitive traits. 2. To examine local adaptation to different competitive environments...

Data from: First measurements of field metabolic rate in wild juvenile fishes show strong thermal sensitivity but variations between sympatric ecotypes

Ming-Tsung Chung, Kris‐Emil Mose Jørgensen, Clive N. Trueman, Halvor Knutsen, Per Erik Jorde & Peter Grønkjær
The relationship between physiology and temperature has a large influence on population-level responses to climate change. In natural settings, direct thermal effects on metabolism may be exaggerated or offset by behavioural responses influencing individual energy balance. Drawing on a newly developed proxy, we provide the first estimates of the thermal performance curve of field metabolism in a wild fish. We investigate the thermal sensitivity of field metabolic rate in two sympatric, genetically distinct ecotypes of...

Modelled annual average production loss due to ozone damage for four global staple crops 2010-2012

K. Sharps, G Mills, D. Simpson, H. Pleijel, M. Frei, K. Burkey, L. Emberson, J. Uddling, M. Broberg, Z. Feng, K. Kobayashi & M. Agrawal
Modelled annual average production loss (thousand tonnes per 1 degree by 1 degree grid cell) due to ground-level ozone pollution is presented for the crops maize (Zea mays), rice (Oryza sativa), soybean (Glycine max) and wheat (Triticum aestivum), for the period 2010-2012. Data are on a global scale, based on the distribution of production for each crop, according to the Food and Agriculture Organisation’s (FAO) Global Agro-Ecological Zones (GAEZ) crop production data for the year...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Tokyo
  • Tohoku University
  • UK Centre for Ecology & Hydrology
  • University of Gothenburg
  • University of Bonn
  • Banaras Hindu University
  • National Museum of Nature and Science
  • Norwegian Meteorological Institute
  • Tokyo Metropolitan University
  • University of California, Berkeley