180 Works

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: 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...

The effects of resource subsidy duration in a detritus-based stream ecosystem: a mesocosm experiment

Takuya Sato, Gaku Takimoto & Rui Ueda
1. Most resource subsidies are temporally variable, dynamically affecting the consumer populations, community structures, and ecosystem functions of recipient ecosystems. Temporally variable resource subsidies are characterized by the duration, magnitude, timing, and frequency of resource subsidy inputs. These different characteristics may have different mechanisms by which to affect recipient ecosystems. 2. Few studies have examined the duration of resource subsidy inputs on recipient ecosystems, although there exist previous studies focusing on magnitude, timing, and frequency....

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...

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...

Emergence of structures from parasitic species in a spatially distributed molecular system

Nathanael Aubert-Kato, Guillaume Gines, Yannick Rondelez & Teruo Fujii
This dataset contains microscopy images from a microfluidic setup implementing a localized autocatalytic molecular system based on the PEN DNA toolbox. Due to the enzymatic nature of the catalytic process, a variety of parasitic species eventually emerge and compete with the legitimate molecular process for fuel. The behaviors observed range from the creation of large stable structures to that of small diffusing particles. Those results, along with the modularity of the molecular system, show that...

Effects of body size divergence on male mating tactics in the ground beetle Carabus japonicus

Yutaka Okuzaki
Animal body size is involved in reproduction in various ways. Carabus japonicus exhibits considerable variation in adult body size across geographical locations depending on the larval environment. To investigate the effects of body size divergence on male mating traits, spermatophore deposition and weight, copulation duration, and post-copulatory mounting were observed using male-female pairs from C. japonicus populations with different body sizes. Then, variables with high predictive power on the mating traits were identified from individual...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

Biodiversity-productivity relationships are key to nature-based climate solutions

Akira Mori, Laura Dee, Andrew Gonzalez, Haruka Ohashi, Jane Cowles, Alexandra Wright, Michel Loreau, Yann Hautier, Tim Newbold, Peter Reich, Tetsuya Matsui, Wataru Takeuchi, Kei-Ichi Okada, Rupert Seidl & Forest Isbell
The global impacts of biodiversity loss and climate change are interlinked but the feedbacks between them are rarely assessed. Areas with greater tree diversity tend to be more productive, providing a greater carbon sink, and biodiversity loss could reduce these natural C sinks. Here, we quantify how tree and shrub species richness could affect biomass production at biome, national and regional scales. We find that greenhouse gas mitigation could help maintain tree diversity and thereby...

Data from: Modeling intraspecific adaptation of Abies sachalinensis to local altitude and responses to global warming, based on a 36-year reciprocal transplant experiment

Wataru Ishizuka & Susumu Goto
Intraspecific adaptation in Abies sachalinensis was examined using models based on long-term monitoring data gathered during a reciprocal transplant experiment with eight seed source populations and six transplantation sites along an altitudinal gradient. The consequence of local adaptation was evaluated by testing the home-site advantage for upslope and downslope transplants at five ages. The populations’ fitness-linked trait was set as their productivity (tree height ×survival rate) at each age. The effects of global warming were...

Data from: A metagenetic approach for revealing community structure of marine planktonic copepods

Junya Hirai, Mikiko Kuriyama, Tadafumi Ichikawa, Kiyotaka Hidaka & Atsushi Tsuda
Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering...

Data from: Rewiring of embryonic glucose metabolism via suppression of pfk-1/aldolase during mouse chorioallantoic branching

Hidenobu Miyazawa, Yoshifumi Yamaguchi, Yuki Sugiura, Kurara Honda, Koki Kondo, F. Matsuda, Takehiro Yamamoto & Makoto Suematsu
Adapting the energy metabolism state to changing bioenergetic demands is essential for mammalian development accompanying massive cell proliferation and cell differentiation. However, it remains unclear how developing embryos meet the changing bioenergetic demands during the chorioallantoic branching (CB) stage when the maternal-fetal exchange of gases and nutrients is promoted. In this study, using metabolome analysis with mass-labeled glucose, we found that developing embryos redirected glucose carbon flow into the pentose phosphate pathway (PPP) via suppression...

Data from: Taxon Influence Index: assessing taxon-induced incongruities in phylogenetic inference

Mahendra Mariadassou, Avner Bar-Hen & Hirohisa Kishino
Understanding the evolutionary history of species is at the core of molecular evolution and is done using several inference methods. The critical issue is to quantify the uncertainty of the inference. The posterior probabilities in Bayesian phylogenetic inference and the bootstrap values in frequentist approaches measure the variability of the estimates due to the sampling of sites from genes and the sampling of genes from genomes. However, they do not measure the uncertainty due to...

Data from: Postural control during quiet bipedal standing in rats

Tetsuro Funato, Yota Sato, Soichiro Fujiki, Yamato Sato, Shinya Aoi, Kazuo Tsuchiya & Dai Yanagihara
The control of bipedal posture in humans is subject to non-ideal conditions such as delayed sensation and heartbeat noise. However, the controller achieves a high level of functionality by utilizing body dynamics dexterously. In order to elucidate the neural mechanism responsible for postural control, the present study made use of an experimental setup involving rats because they have more accessible neural structures. The experimental design requires rats to stand bipedally in order to obtain a...

Data from: Tracking time evolution of collective attention clusters in twitter: time evolving nonnegative matrix factorisation

Shota Saito, Yoshito Hirata, Kazutoshi Sasahara & Hideyuki Suzuki
Micro-blogging services, such as Twitter, offer opportunities to analyse user behaviour. Discovering and distinguishing behavioural patterns in micro-blogging services is valuable. However, it is difficult and challenging to distinguish users, and to track the temporal development of collective attention within distinct user groups in Twitter. In this paper, we formulate this problem as tracking matrices decomposed by Nonnegative Matrix Factorisation for time-sequential matrix data, and propose a novel extension of Nonnegative Matrix Factorisation, which we...

Data from: Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberley M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu … & Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient...

Data from: A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda Van Leeuwen, Nydia Van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li … & Charles Boone
INTRODUCTION: Genetic interactions occur when mutations in two or more genes combine to generate an unexpected phenotype. An extreme negative or synthetic lethal genetic interaction occurs when two mutations, neither lethal individually, combine to cause cell death. Conversely, positive genetic interactions occur when two mutations produce a phenotype that is less severe than expected. Genetic interactions identify functional relationships between genes and can be harnessed for biological discovery and therapeutic target identification. They may also...

Data from: Vine tendrils use contact chemoreception to avoid conspecific leaves

Yuya Fukano
Movement and growth habit of climbing plants have attracted attention since the time of Charles Darwin; however, there are no reports on whether plants can choose suitable hosts or avoid unsuitable ones based on chemoreception. Here, I show that the tendrils of Cayratia japonica (Vitaceae) appear to avoid conspecific leaves using contact chemoreception for oxalates, which are highly concentrated in C. japonica leaves. The coiling experiments show that C. japonica has a flexible plastic response...

Data from: Duplication and diversification of trehalase confers evolutionary advantages on lepidopteran insects

Yanyan Zhou, Xiaotong Li, Susumu Katsuma, Yusong Xu, Liangen Shi, Toru Shimada & Huabing Wang
Gene duplication provides a major source of new genes for evolutionary novelty and ecological adaptation. However, the maintenance of duplicated genes and their relevance to adaptive evolution has long been debated. Insect trehalase (Treh) plays key roles in energy metabolism, growth, and stress recovery. Here, we show that the duplication of Treh in Lepidoptera (butterflies and moths) is linked with their adaptation to various environmental stresses. Generally, two Treh genes are present in insects: Treh1...

Data from: Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some...

Data from: Calcium dynamics regulating the timing of decision-making in C. elegans

Yuki Tanimoto, Akiko Yamazoe-Umemoto, Kosuke Fujita, Yuya Kawazoe, Yosuke Miyanishi, Shuhei J. Yamazaki, Xianfeng Fei, Karl Emanuel Busch, Keiko Gengyo-Ando, Junichi Nakai, Yuichi Iino, Yuishi Iwasaki, Koichi Hashimoto & Koutarou D. Kimura
Brains regulate behavioral responses with distinct timings. Here we investigate the cellular and molecular mechanisms underlying the timing of decision-making during olfactory navigation in Caenorhabditis elegans. We find that, based on subtle changes in odor concentrations, the animals appear to choose the appropriate migratory direction from multiple trials as a form of behavioral decision-making. Through optophysiological, mathematical and genetic analyses of neural activity under virtual odor gradients, we further find that odor concentration information is...

Data from: Dead or alive? Sexual conflict and lethal copulatory interactions in long-jawed Tetragnatha spiders

Yuki G. Baba, Akio Tanikawa, Mayura B. Takada & Kyoko Futami
Inter- and intra-sexual selection are important driving forces that lead to diversification of sexual characteristics. Tetragnatha spiders have elongated chelicerae and sexual dimorphism in chelicera length whose magnitude varies among species. Because they use their chelicerae during copulation and as weapons in male–male competition, this divergence reflects repeated inter- and intra-sexual selection. To infer the causes of chelicera length diversity, we examined the roles of the elongated chelicerae in copulatory behaviour of a Tetragnatha species...

Data from: Water-repellent plant surface structure induced by gall-forming insects for waste management

Keigo Uematsu, Mayako Kutsukake & Takema Fukatsu
Many animals and plants have evolved elaborate water-repellent microstructures on their surface, which often play important roles in their ecological adaptation. Here we report a unique type of water-repellent structure on plant surface, which develops as an insect-induced plant morphology in a social context. Some social aphids form galls on their host plant, in which they produce large amount of hydrophobic wax. Excreted honeydew is coated by the powdery wax to form “honeydew balls”, which...

Data from: Optimal lineage principle for age-structured populations

Yuichi Wakamoto, Alexander Y Grosberg & Edo Kussell
We present a formulation of branching and aging processes that allows distributions along lineages to be studied within populations, and provides a new interpretation of classical results in the theory of aging. We establish a variational principle for the stable age distribution along lineages. Using this optimal lineage principle, we show that the response of a population’s growth rate to age-specific changes in mortality and fecundity – a key quantity which was first calculated by...

Data from: Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

Hirohiko Takeshima, Kei'ichiro Iguchi, Yasuyuki Hashiguchi & Mutsumi Nishida
In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic...

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